bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of the ARTIC version 3 and version 4 SARS-CoV-2 primers and their impact on the detection of the G142D amino acid substitution in the spike protein
Authors: Davis James J. , Long S. Wesley , Christensen Paul A. , Olsen Randall J. , Olson Robert , Shukla Maulik , Subedi Sishir , Stevens Rick , Musser James M. 
Published: September 2021

ABSTRACTThe ARTIC Network provides a common resource of PCR primer sequences and recommendations for amplifying SARS-CoV-2 genomes. The initial tiling strategy was developed with the reference genome Wuhan-01, and subsequent iterations have addressed areas of low amplification and sequence drop out. Recently, a new version (V4) was released, based on new variant genome sequences, in response to the realization that some V3 primers were located in regions with key mutations. Herein, we compare the performance of the ARTIC V3 and V4 primer sets with a matched set of 663 SARS-CoV-2 clinical samples sequenced with an Illumina NovaSeq 6000 instrument. We observe general improvements in sequencing depth and quality, and improved resolution of the SNP causing the D950N variation in the spike protein. Importantly, we also find nearly universal presence of spike protein substitution G142D in Delta-lineage samples. Due to the prior release and widespread use of the ARTIC V3 primers during the initial surge of the Delta variant, it is likely that the G142D amino acid substitution is substantially underrepresented among early Delta variant genomes deposited in public repositories. In addition to the improved performance of the ARTIC V4 primer set, this study also illustrates the importance of the primer scheme in downstream analyses.ImportanceARTIC Network primers are commonly used by laboratories worldwide to amplify and sequence SARS-CoV-2 present in clinical samples. As new variants have evolved and spread, it was found that the V3 primer set poorly amplified several key mutations. In this report, we compare the results of sequencing a matched set of samples with the V3 and V4 primer sets. We find that adoption of the ARTIC V4 primer set is critical for accurate sequencing of the SARS-CoV-2 spike region. The absence of metadata describing the primer scheme used will negatively impact the downstream use of publicly available SARS-Cov-2 sequencing reads and assembled genomes.
Heterologous expression of the human ZIP4 zinc transporter in Saccharomyces cerevisiae
Authors: Liu Yuting , Bafaro Elizabeth M. , Dempski Robert E. 
Published: September 2021

ABSTRACTThe human (h) transporter, hZIP4 is the primary zinc importer in the intestine and is also expressed in a variety of organs such as the pancreas and brain. Dysfunction of hZIP4 can result in the zinc deficiency disease acrodermatitis enteropathica (AE), which disrupts digestive and immune system homeostasis. Structure-function studies of hZIP4 have been greatly hindered by the absence of a robust heterologous expression system. Here, we report the heterologous expression of hZIP4 in Saccharomyces cerevisiae. Both a wild type and a mutant S. cerevisiae strain, in which the endogenous zinc transporters are deleted, were used to test the expression and localization of an hZIP4-GFP fusion protein. A full-length hZIP4-GFP and a truncated membrane domain only (mhZIP4-GFP) protein were successfully produced and targeted to the plasma membrane in yeast.
Cardenolide Increase in Foxglove During Stresses Corresponds to Cholesterol and Phytosterol Biosynthesis
Authors: Raghavan Indu , Ravi Baradwaj G. , Carroll Emily , Wang Zhen Q. 
Published: September 2021

AbstractCardenolides are a group of steroidal metabolites found in Digitalis lanata with potent cardioactive effects on animals. In plants, cardenolides are involved in various stress responses. However, the molecular mechanism of cardenolide increase during stresses is mostly unknown. Here we show that cardenolides were increased upon methyl jasmonate (MJ), sorbitol, potassium (KCl) chloride, and salicylic acid analog (BTH: 2,1,3-benzothiadiazole) treatments. However, the expression of three known genes for cardenolide biosynthesis did not correlate well with these increases. Specifically, the expression of progesterone-5β-reductases (P5βR and P5βR2) did not correlate with cardenolide increase. The expression of 3β-hydroxysteroid dehydrogenase (3βHSD) correlated with cardenolide levels only during the BTH treatment. Mining the D. lanata transcriptome identified genes involved in cholesterol and phytosterol biosynthesis: SSR1 (sterol sidechain reductase), SMO1, and SMO3 (sterol methyl oxidase). Surprisingly, the expression of all three genes correlated well with the cardenolide increase after BTH treatment. Phylogenetic analysis showed that SSR1 is likely involved in both cholesterol and phytosterol biosynthesis. In addition, SMO1 is likely specific to phytosterol biosynthesis, and SMO3 is specific to cholesterol biosynthesis. These results suggest that both cholesterol and phytosterol are involved in cardenolide biosynthesis. In summary, this work shows that cardenolides are important for stress responses in D. lanata and revealed a novel relationship between phytosterol and cardenolide biosynthesis.
Intergenerational hormesis is regulated by heritable 18S rRNA methylation
Authors: Liberman Noa , Gerashchenko Maxim V. , Boulias Konstantinos , MacWhinnie Fiona G , Ying Albert Kejun , Taylor Anya Flood , Al Haddad Joseph , Shibuya Hiroki , Roach Lara , Dong Anna , Gladyshev Vadim N. , Greer Eric Lieberman 
Published: September 2021

SummaryHeritable non-genetic information can regulate a variety of complex phenotypes. However, what specific non-genetic cues are transmitted from parents to their descendants are poorly understood. Here, we perform metabolic methyl-labelling experiments to track the heritable transmission of methylation from ancestors to their descendants in the nematode Caenorhabditis elegans. We find that methylation is transmitted to descendants in proteins, RNA, DNA and lipids. We further find that in response to parental starvation, fed naïve progeny display reduced fertility, increased heat stress resistance, and extended longevity. This intergenerational hormesis is accompanied by a heritable increase in N6’-dimethyl adenosine (m6,2A) on the 18S ribosomal RNA at adenosines 1735 and 1736. We identified the conserved DIMT-1 as the m6,2A methyltransferase in C. elegans and find that dimt-1 is required for the intergenerational hormesis phenotypes. This study provides the first labeling and tracking of heritable non-genetic material across generations and demonstrates the importance of rRNA methylation for regulating the heritable response to starvation.
Omics profiling identifies MAPK/ERK pathway as a gatekeeper of nephron progenitor metabolism
Authors: Kwon Hyuk Nam , Kurtzeborn Kristen , Jin Xing , Loh Abigail , Escande-Beillard Nathalie , Reversade Bruno , Park Sunghyouk , Kuure Satu 
Published: September 2021

ABSTRACTNephron endowment is defined by fetal kidney growth and critically dictates renal health in adults. Despite the advances in understanding the molecular regulation of nephron progenitors, the causes for low congenital nephron count and contribution of basic metabolism to nephron progenitor biology remain poorly understood. Here we characterized the metabolic consequences of MAPK/ERK-deficiency in nephron progenitors, whose maintenance and propagation in developing kidney critically depends on ERK activation. Our LC/MS-based metabolomics profiling identified 42 reduced metabolites, of which 26 were further supported by in vivo transcriptional characterization of MAPK/ERK-deficient nephron progenitors. This revealed a severe shortage of energy and nucleotide biosynthesis precursors, blockage in glycolysis and diminished pyruvate and proline metabolism. Utilization of in vitro kidney cultures demonstrated a dosage-specific function for glycolytic pyruvate as an energy source that controls the shape of the ureteric bud tip kwon to serve as a niche for nephron progenitor regulation. Analysis of the proline biosynthesis effects in developing kidney in vivo revealed premature loss of nephron progenitor maintenance in the absence of Pycr1/2 functions. Our results suggest that MAPK/ERK-dependent nephron progenitor metabolism functionally contributes to progenitor preservation by controlling pyruvate availability and proline metabolism in developing kidneys.
Gene expression phylogenies and ancestral transcriptome reconstruction resolves major transitions in the origins of pregnancy
Authors: Mika Katie , Whittington Camilla M. , McAllan Bronwyn M. , Lynch Vincent J. 
Published: September 2021

AbstractStructural and physiological changes in the female reproductive system underlie the origins of pregnancy in multiple vertebrate lineages. In mammals, for example, the glandular portion of the lower reproductive tract has transformed into a structure specialized for supporting fetal development. These specializations range from relatively simple maternal provisioning in egg-laying monotremes to an elaborate suite of traits that support intimate maternal-fetal interactions in Eutherians. Among these traits are the maternal decidua and fetal component of the placenta, but there is considerable uncertainty about how these structures evolved. We identified the origins of pregnancy utilizing ancestral transcriptome reconstruction to infer functional evolution of the maternal-fetal interface. Remarkably, we found that maternal gene expression profiles are correlated with degree of placental invasion. These results indicate that an epitheliochorial-like placenta evolved early in the mammalian stem-lineage and that the ancestor of Eutherians had a hemochorial placenta, and suggest maternal control of placental invasiveness. Collectively, these data resolve major transitions in the evolution of pregnancy and indicate that ancestral transcriptome reconstruction can be used to study the function of ancestral cell, tissue, and organ systems.
mSOD1-NSG mice: a new in vivo model to test human T cells in ALS
Authors: Graber David J , Sentman Marie-Louise , Cook W. James , Sentman Charles L 
Published: September 2021

AbstractAmyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease with unclear etiology and few treatment options. Engineering of human cells for therapy has great potential to provide a means to create long-lived therapeutics that can respond to local signals within tissues. One challenge for development of human cell therapeutics is to have disease models that do not reject transplanted human cells. G93A mutant superoxide dismutase-1 (mSOD1) transgenic mouse model is a robust disease model for ALS, with development of local inflammation, activation of microglia and astrocytes, motor neuron death, and development of paralysis. To create a mouse model for ALS that permits the transplantation of human T cells without immune-mediate rejection, we bred the G93A transgene onto the NOD-SCID-IL-2Rγ-deficient (NSG) mouse model to create mSOD1-NSG mice. We report that mSOD1-NSG mice develop a progressive ALS-like disease with microgliosis, astrogliosis, and paralysis development with an average onset at 11 weeks and end-stage at 14 weeks. Transplanted human T regulatory cells survive in these mice for at least 60 days. This mSOD1-NSG mouse model for ALS can be used to test human T cell-based therapeutics, and it may be helpful to test any human cell-based therapy for ALS.Significance StatementG93A SOD1 transgenic NSG mice develop a progressive ALS-like disease and are an in vivo model for testing human T cell-based therapies for ALS.
The cytokine receptor DR3 identifies and activates thymic NKT17 cells
Authors: Luo Shunqun , Liman Nurcin , Crossman Assiatu , Park Jung-Hyun 
Published: September 2021

AbstractInvariant natural killer T (iNKT) cells are thymus-generated T cells with innate-like characteristics and effector function. Several functionally distinct iNKT subsets have been identified, but NKT17 is the only iNKT subset that produces the proinflammatory cytokine IL-17. NKT17 cells are generated in the thymus and then exported into the periphery to populate lymphoid organs and barrier tissues, such as the lung, to provide critical support in host defense. However, the molecular mechanisms that drive the thymic development and subset-specific activation of NKT17 cells remain mostly unknown. Here, we identify the cytokine receptor DR3, a member of the TNF receptor superfamily, being selectively expressed on NKT17 cells but absent on all other thymic iNKT subsets. We further demonstrate that DR3 ligation leads to the in vivo activation of thymic NKT17 cells and provides in vitro costimulatory effects upon α-GalCer-stimulation. Thus, our study reports the identification of a specific surface marker for thymic NKT17 cells that selectively triggers their activation both in vivo and in vitro. These findings provide new insights for deciphering the role and function of IL-17-producing NKT17 cells and for understanding the development and activation mechanisms of iNKT cells in general.
The short flagella 1 (SHF1) gene in Chlamydomonas encodes a Crescerin TOG-domain protein required for late stages of flagellar growth
Authors: Perlaza Karina , Mirvis Mariya , Ishikawa Hiroaki , Marshall Wallace 
Published: September 2021

ABSTRACTLength control of flagella represents a simple and tractable system to investigate the dynamics of organelle size. Models for flagellar length control in the model organism, Chlamydomonas reinhardtii have focused on the length-dependence of the intraflagellar transport (IFT) system which manages the delivery and removal of axonemal subunits at the tip of the flagella. One of these cargoes, tubulin, is the major axonemal subunit, and its frequency of arrival at the tip plays a central role in size control models. However, the mechanisms determining tubulin dynamics at the tip are still poorly understood. We discovered a loss-of-function mutation that leads to shortened flagella, and found that this was an allele of a previously described gene, SHF1, whose molecular identity had not previously been determined. We found that SHF1 encodes a Chlamydomonas ortholog of Crescerin, previously identified as a cilia-specific TOG-domain array protein that can bind tubulin via its TOG domains and increase tubulin polymerization rates. In this mutant, flagellar regeneration occurs with the same initial kinetics as wild-type cells, but plateaus at a shorter length. Using a computational model in which the flagellar microtubules are represented by a differential equation for flagellar length combined with a stochastic model for cytoplasmic microtubule dynamics, we found that our experimental results are best described by a model in which Crescerin/SHF1 binds tubulin dimers in the cytoplasm and transports them into the flagellum. We suggest that this TOG-domain protein is necessary to efficiently and preemptively increase intra-flagella tubulin levels to offset decreasing IFT cargo at the tip as flagellar assembly progresses.
Construction of multicellular yeast networks using the communication toolkit with variable specificity and attenuation
Authors: Krink Nicolas , Loechner Anne C. , Anders Alexander , Kahnt Jörg , Rensing Stefan , Hochberg Georg , Sourjik Victor 
Published: September 2021

AbstractThe key next step in synthetic biology is to extend cellular network engineering to the multicellular level by utilizing cell-cell communication for information processing. To facilitate the implementation of multicellular networks in the most commonly used eukaryotic chassis, Saccharomyces cerevisiae, we developed the yeast communication toolkit (YCTK). This toolkit is based on the fungal mating pathway and contains five pheromone-inducible promoters (response parts), eleven pheromones (α-factors; sender parts), eleven pheromone receptors (Ste2; receiver parts), as well as five Bar1 proteases (suppressor parts). All YCTK parts were thoroughly characterized and are compatible with the commonly used yeast Golden Gate cloning standard. We demonstrated the application of the YCTK by implementing several different logic gate-like population networks. Furthermore, we used this toolkit to investigate the pheromone-receptor promiscuity patterns among different yeast species. This toolkit extends currently available resources for construction of complex multicellular eukaryotic networks with varying degrees of promiscuity and attenuation.
Evolutionary dynamics ofBegomovirusescausing Papaya leaf curl disease in India
Authors: Srivasatava Aarshi , Pandey Vineeta , Sahu Anurag Kumar , Yadav Dinesh , Gaur R.K. 
Published: September 2021

AbstractThe genusbegomovirusrepresents a group of multipartite viruses that significantly damages many agricultural crops, including papaya and drastically influence the overall production. Understanding the genetic variations, mutations and recombination of thebegomoviruspopulation infecting papaya has several important implications in alleviating substantial losses, mainly in developing countries, including India. In an attempt for a bioinformatics driven study of diversity and variability of papaya leaf curl disease in India, a total of thirty-two (32) DNA-A and sixteen (16) betasatellite sequences were retrieved from GenBank. An uneven distribution of evolutionary divergence has been observed across the branch length, which triggered the estimated recombinational event. Interestingly, a maximum of thebegomoviruseswere found to be intra-species recombinants. Further genetic variability, selection pressure, and substitution rate acting on the population were estimated and found to be high enough to support the evolution of geminiviruses. Genetic divergence composition in allbegomovirusdatasets revealed predominance of nucleotide diversity driven by mutation. The analysis indicates that even though a significant fraction of the genetic variations might be due to recombination but, it was constantly lower than the mutation rate. Thus, the diversification of thebegomoviruspopulation is principally impelled by mutational dynamics.
Phosphorus uptake and toxicity is delimited by mycorrhizal symbiosis in P-sensitive Eucalyptus marginata but not in P-tolerant Acacia celastrifolia
Authors: Tibbett Mark , Daws Matthew I. , Ryan Megan H. 
Published: September 2021

AbstractMany plant species from regions with ancient, highly-weathered nutrient-depleted soils have specialised adaptations for acquiring P and are sensitive to excess P-supply. Mycorrhizal associations may regulate P-uptake at high external P-concentrations, potentially reducing P-toxicity. We predicted that excess P-application will negatively impact species from the nutrient-depleted jarrah forest of Western Australia and that mycorrhizal inoculation will reduce P-toxicity by regulating P-uptake. For seedlings of the N2-fixing legume Acacia celastrifolia and the tree species Eucalyptus marginata, we measured growth at P-concentrations of 0 to 90 mg kg−1 soil and in relation to inoculation with the arbuscular mycorrhizal fungus (AMF) Rhizophagus irregularis. Non-inoculated A. celastrifolia maintained leaf P-concentrations at <2 mg g−1 dry mass (DM) across the range of external P-concentrations. However, for non-inoculated E. marginata, as external P-concentrations increased leaf P also increased, reaching >9 mg g−1 DM at 30 mg P kg−1 soil. A. celastrifolia DM increased with increasing external P-concentrations, while E. marginata DM was maximal at 15 mg P kg−1 soil, declining at higher external P concentrations. Neither DM nor leaf P of A. celastrifolia were affected by inoculation with AMF. For E. marginata, even at 90 mg P kg−1 soil, inoculation with AMF resulted in leaf P remaining <1 mg g−1 DM, and DM being maintained. These data strengthen the evidence base that AMF may not only facilitate P-uptake at low external P-concentrations, but are also important for moderating P-uptake at elevated external P-concentrations and maintaining plant P concentrations within a relatively narrow concentration range.
Drivers of sustainable healthcare supply chain performance: multi-criteria decision-making approach under grey environment
Authors: Hossain Md Kamal , Thakur Vikas 
Published: September 2021

PurposeThis paper aims to explore the drivers of sustainable healthcare supply chain (SHCSC) performance measurement through extensive literature review and experts' opinions. The drivers are then scrutinized and their priority vector is calculated to provide quality and cost-effective healthcare supply chain (HCSC) services.Design/methodology/approachThe drivers of the SHCSC performance measurement are validated using the grey-Delphi technique. After validating the drivers, they are prioritized using the grey-analytic hierarchy process (G-AHP), a multi-criteria decision-making tool.FindingsThe findings of the study highlight the prioritized drivers based on the preferences given by the experts. The findings of the study highlight the most prioritized drivers of healthcare (HC) by-product management system, coordinating and facilitating green suppliers in the HCSC and green packaging of pharmaceutical as well as other essential items.Practical implicationsThe HCSC managers should coordinate with all the stakeholders across the supply chain and involve them in the decision-making process to make products and services greener and become complicit in complying with the sustainable policy guidelines. The study highlights the strategic policy and managerial implications for implementing sustainability in the HCSC.Originality/valueThe validation and prioritization of the drivers of SHCSC in developing nations' contexts is the key contribution of the study. Grey-AHP enables a practical approach towards enhancing the sustainability of the HCSC and opening the doors for generalizing the study for future research works.
Product eco-design practice in green supply chain management: a China-global examination of research
Authors: Li Jingjing , Sarkis Joseph 
Published: September 2021

PurposeThis paper comprehensively and systematically reviews and critiques the product eco-design practice in green supply chain management studies. It seeks to explore drivers, barriers and initiatives of eco-design practice with a specific emphasis on China in comparison to non-China countries.Design/methodology/approachThis paper adopts a systematic literature review approach. It also uses a conceptual thematic landscape of the global eco-design practice along supply chains to critically evaluate published studies. The Web of Science™ Core Collection database is used as the source.FindingsResults show that although common factors exist, China exhibits a higher number of barriers, leading to an overall lag in eco-design adoption. China’s advantage lies in pressing market demand, actively engaged human resources and a cooperative culture. Alternatively, non-China countries demonstrate their relative superiority in eco-design tools, knowledge and innovation. Findings also indicate stakeholders simultaneously act as the three roles of eco-design practice in all countries, so do environmental regulations in China.Originality/valueA thematic framework is introduced that can be used to further investigate and identify research opportunities. This study aids practitioners take stock of current eco-design management issues. It also includes pertinent recommendations on international eco-design performance improvement. It especially provides significant insights into successful eco-design implementation to green supply chains in China.