bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA nanostructure-templated antibody complexes provide insights into the geometric requirements of human complement cascade activation
Authors: Abendstein Leoni , Noteborn Willem E. M. , Veenman Luc S. , Dijkstra Douwe J. , van de Bovenkamp Fleur S. , Trouw Leendert A. , Sharp Thomas H. 
Published: October 2023

AbstractThe classical complement pathway is activated by antigen-bound IgG antibodies. Monomeric IgG must oligomerize to activate complement via the hexameric C1q complex, and hexamerizing mutants of IgG appear as promising therapeutic candidates. However, structural data have shown that it is not necessary to bind all six C1q arms to initiate complement, revealing a symmetry mismatch between C1 and the hexameric IgG complex, which has not been adequately explained. Here we use DNA nanotechnology to produce specific nanostructures to template antigens, and thereby control IgG valency. These DNA nano-templated IgG complexes can activate complement on cell-mimetic lipid membranes, which enabled us to determine the effect of IgG valency on complement activation without the requirement to mutate antibodies. We investigated this using biophysical assays together with 3D cryo-electron tomography. Our data revealed that the cleavage of complement component C4 by the C1 complex is proportional to the number of antigens. Increased IgG valency also translated to better terminal pathway activation and membrane attack complex formation. Together, these data provide insights into how nanopatterning antigen-antibody complexes influence the activation of the C1 complex and suggest routes to modulate complement activation by antibody engineering. Furthermore, to our knowledge this is the first time DNA nanotechnology has been used to study the activation of the complement system.
Assigning credit where it’s due: An information content score to capture the clinical value of Multiplexed Assays of Variant Effect
Authors: Ranola John Michael O , Horton Carrie , Pesaran Tina , Fayer Shawn , Starita Lea M. , Shirts Brian H 
Published: October 2023

AbstractBackgroundA variant can be pathogenic or benign with relation to a human disease. Current classification categories from benign to pathogenic reflect a probabilistic summary of current understanding. A primary metric of clinical utility for multiplexed assays of variant effect (MAVE) is the number of variants that can be reclassified from uncertain significance (VUS). However, we hypothesized that this measure of utility underrepresents the information gained from MAVEs and that an information theory approach which includes data that does not reclassify variants will better reflect true information gain. We used this information theory approach to evaluate the information gain, in bits, for MAVEs ofBRCA1, PTEN, andTP53. Here, one bit represents the amount of information required to completely classify a single variant starting from no information.ResultsBRCA1MAVEs produced a total of 831.2 bits of information, 6.58% of the total missense information inBRCA1and a 22-fold increase over the information that only contributed to VUS reclassification.PTENMAVEs produced 2059.6 bits of information which represents 32.8% of the total missense information inPTENand an 85-fold increase over the information that contributed to VUS reclassification.TP53MAVEs produced 277.8 bits of information which represents 6.22% of the total missense information inTP53and a 3.5-fold increase over the information that contributed to VUS reclassification.ConclusionsAn information content approach will more accurately portray information gained through MAVE mapping efforts than counting the number of variants reclassified. This information content approach may also help define the impact of modifying information definitions used to classify many variants, such as guideline rule changes.
A simplified disease resistance assay using YFP-expressingPotato Virus XinN. benthamianareveals a cell death-independent immune function of RBA1
Authors: Hasegawa Keiichi , Timmers Ton , Chai Jijie , Maekawa Takaki 
Published: October 2023

SummaryR (resistance) proteins, such as intracellular NLRs (nucleotide-binding leucine-rich repeat receptors), are integral components of the plant innate immune system (van Wersch et al., 2020). Host responses following R protein activation include the generation of reactive oxygen species, sustained increases in cytosolic Ca2+, transcriptional reprogramming and, typically, rapid host cell death at sites of pathogen infection, which together ultimately lead to pathogen growth restriction (Wang et al., 2023). To assess the activity of R proteins, agroinfiltration-mediated transient gene expression assays have been widely used inNicotianaspecies (e.g.,N. benthamiana). In these transient assays, host cell death is often chosen as an indicator of R protein activity from the host responses mentioned above, in part because of the ease of experimentation. However, the extent to which host cell death is a proxy for disease resistance signaling has long been debated, as host cell death and pathogen growth restriction can be uncoupled in several cases (Bendahmane et al., 1999; Coll et al., 2010; Heidrich et al., 2011, Maekawa et al., 2023). To assess the disease resistance activity of R proteins, bacterial growth assays have been employed in combination with transientRgene expression inN. benthamiana(Sun et al., 2021). Bacterial growth assays, however, require multiple experimental procedures, including agroinfiltration, pathogen infection and bacterial counts, which hinders high-throughput studies ofRgene-mediated disease resistance. Here, we report a simple plate reader-based assay to assessRgene-mediated disease resistance activity against PVX (Potato virus X) that expresses YFP (PVX-YFP). Unlike bacterial pathogens, PVX proliferation inN. benthamianais not restricted by the intrinsic activity of the EDS1 signaling pathway as previously shown by virus-inducedNbEDS1gene silencing (Peart et al., 2002) and as we consistently show in this study using aNbeds1gene knockout mutant. This feature would increase the sensitivity of the assay, allowing it to capture a weak-to-moderate disease resistance activity of R proteins, as the contribution of basal immunity to PVX via theNbEDS1 pathway is negligible. Using this assay, we show that a non-cell death-inducing mutant of the R protein of RBA1 (Response to HopBA1), which lacks 2′,3′-cAMP/cGMP synthetase activity but retains NADase activity, confers PVX resistance in an EDS1 signaling pathway-dependent manner.
High-throughput and in-depth analysis of plasma proteome by UV-assisted protein digestion, 5-plex labeling and MS-based high abundance protein removal method
Authors: Wang Zhiting , Qu Boxin , Zhang Weijie , Liang Zhen , Wang Liming , Liu Jianhui , Yuan Huiming , Zhang Lihua , Zhang Yukui 
Published: October 2023

AbstractHuman plasma contains various proteins, some of which reflect individuals’ physiological health state or predict diseases. Therefore, plasma analysis can provide a wealth of information on novel biomarkers for clinical diagnosis and prognosis. The use of mass spectrometry (MS) for high-throughput and in-depth quantitative proteomic analysis of plasma allows for highly specific and quantitative readout, but is challenging because of the high dynamic range of protein abundances. Here, we introduce a robust, high-throughput, and in-depth workflow for plasma proteome analysis based on UV-assisted rapid protein digestion, 5-plex dimethyl labeling, and MS-based high abundance protein removal. UV-assisted protein digestion could quantify the same protein numbers as traditional enzymatic hydrolysis and achieve a low miss-cleavage rate in only 20 minutes. And the MS-based high abundance protein removed 5-plex DIA method, which does not require extra protein depletion procedures, enables quantitative analysis of more than 600 proteins using an equivalent MS analysis time of 30 minutes per sample. The average relative error was 6.9%. We believe the method is beneficial for analyzing large numbers of trace-level clinical samples and broaden a vision for the discovery of low abundance protein markers.
Genome sequencing and molecular networking analysis of the wild fungusAnthostomella pineareveal its ability to produce a diverse range of secondary metabolites
Authors: Iacovelli R. , He T. , Allen J. L. , Hackl T. , Haslinger K. 
Published: October 2023

AbstractBackgroundFilamentous fungi are prolific producers of bioactive molecules and enzymes with important applications in industry. Yet, the vast majority of fungal species remain undiscovered or uncharacterized. Here we focus our attention to a wild fungal isolate that we identified asAnthostomella pinea. The fungus belongs to a complex polyphyletic genus in the family ofXylariaceae, which is known to comprise endophytic and pathogenic fungi that produce a plethora of interesting secondary metabolites. Despite that,Anthostomellais largely understudied and only two species have been fully sequenced and characterized at a genomic level.ResultsIn this work, we used long-read sequencing to obtain the complete 53.7 Mb genome sequence including the full mitochondrial DNA. We performed extensive structural and functional annotation of coding sequences, including genes encoding enzymes with potential applications in biotechnology. Among others, we found that the genome ofA. pineaencodes 91 biosynthetic gene clusters, more than 600 CAZymes, and 164 P450s. Furthermore, untargeted metabolomics and molecular networking analysis of the cultivation extracts revealed a rich secondary metabolism, and in particular an abundance of sesquiterpenoids and sesquiterpene lactones. We also identified the polyketide antibiotic xanthoepocin, to which we attribute the anti–Gram-positive effect of the extracts that we observed in antibacterial plate assays.ConclusionsTaken together, our results provide a first glimpse into the potential ofAnthstomella pineato provide new bioactive molecules and biocatalysts and will facilitate future research into these valuable metabolites.
Determination of Optimal Nutrient Levels in Baru Seedlings (Dipterix alata Vog.) Using the Mathematical Chance Method
Authors: Kusano Daniel , Larson Leia , Camacho Marcos Antonio 
Published: October 2023

AbstractThis work aimed to determine the optimal ranges by the Mathematical Chance (ChM) method in baru seedlings. To determine optimal ranges by ChM, the nutritional information from an experiment conducted in a protected environment from October 13, 2011, to February 11, 2012, in Selvíria-MS and for seedling production, used a nursery with 50% light reduction polypropylene mesh and 15 x 21.5 cm plastic bags, which have a capacity of 1.8 L, which were filled with different substrate combinations. The ranges found for macronutrients with the ChM method were, in g kg-1, from 19.06 to 28.14; 1.52 to 3.38; 17.9 to 24.0; 1.76 to 3.54; 0.74 to 1.50; 1.26 to 2.26 for N, P, K, Ca, Mg and S, respectively. The ranges found for micronutrients with the ChM method were, in mg kg 1, from 21.79 to 33.59; 1.0 to 21.40; 75 to 104.4; 14.0 to 82.8; 18.0 to 24.4 for B, Cu, Fe, Mn, and Zn, respectively.
Early root architectural traits and their relationship with yield inIpomoea batatasL
Authors: Duque L.O. , Hoffman G. , Pecota K. , Yencho G. C. 
Published: October 2023

AbstractRoot system architecture in storage root crops are an important component of plant growth and yield performance that has received little attention by researchers because of the inherent difficulties posed byin-situroot observation. Sweetpotato (Ipomoea batatasL.) is an important climate-resilient storage root crop of worldwide importance for both tropical and temperate regions, and identifying genotypes with advantageous root phenotypes and improved root architecture to facilitate breeding for improved storage root yield and quality characteristics in both high and low input scenarios would be beneficial. We evaluated 38 diverse sweetpotato genotypes for early root architectural traits and correlated a subset of these with storage root yield. Early root architectural traits were scanned and digitized using the RhizoVision Explorer software system. Significant genotypic variation was detected for all early root traits including root mass, total root length, root volume, root area and root length by diameter classes. Based on the values of total root length, we separated the 38 genotypes into three root sizes (small, medium, and large). Principal component analysis identified four clusters, primarily defined by shoot mass, root volume, root area, root mass, total root length and root length by diameter class. Average total and marketable yield and number of storage roots, was assessed on a subset of eight genotypes in the field. Several early root traits were positively correlated with total yield, marketable yield, and number of storage roots. These results suggest that root traits, particularly total root length and root mass could improve yield potential and should be incorporated into sweetpotato ideotypes. To help increase sweetpotato performance in challenging environments, breeding efforts may benefit through the incorporation of early root phenotyping using the idea of integrated root phenotypes.
Terpenoid balance inAspergillus nidulansunveiled by heterologous squalene synthase expression
Authors: Park Sung Chul , Steffan Breanne N. , Lim Fang Yun , Gupta Raveena , Butun Fatma Ayaloglu , Chen Hongyu , Ye Rosa , Decker Timothy , Wu Chengcang C. , Kelleher Neil L. , Bok Jin Woo , Keller Nancy P. 
Published: October 2023

AbstractFilamentous fungi produce numerous uncharacterized natural products (NPs) that are often challenging to characterize due to cryptic expression in laboratory conditions. Previously, we have successfully isolated novel NPs by expressing fungal artificial chromosomes (FACs) from a variety of fungal species intoAspergillus nidulans. Here, we demonstrate a new twist to FAC utility wherein heterologous expression of aPseudogymnoascus destructansFAC inA. nidulansaltered endogenous terpene biosynthetic pathways. In contrast to wildtype, the FAC transformant produced increased levels of squalene and aspernidine type compounds, including three new nidulenes (1–2, 5), and lost nearly all ability to synthesize the majorA. nidulanscharacteristic terpene, austinol. Deletion of a squalene synthase gene in the FAC restored wildtype chemical profiles. The altered squalene to farnesyl pyrophosphate ratio leading to synthesis of nidulenes and aspernidines at the expense of farnesyl pyrophosphate derived austinols provides unexpected insight into routes of terpene synthesis in fungi.TeaserReshaping terpenes: Heterologous FAC expression reroutes terpene pathways.
Respiration and growth ofParacoccus denitrificansR-1 with nitrous oxide as an electron acceptor
Authors: Zhou Jiaxian , Deng Wenfang , Wu Jiapeng , Xiang Hua , Lin Jih-Gaw , Hong Yiguo 
Published: October 2023

ABSTRACTIn the nitrogen biogeochemical cycle, the reduction of nitrous oxide (N2O) to N2by N2O reductase, which is encoded bynosgene cluster, is the only biological pathway for N2O consumption. However, the capability and mechanisms of microbial N2O reduction are poorly understood. In this study, we investigated the ability to obtain energy for growth ofParacoccus denitrificansR-1 by coupling the oxidation of various electron donors to N2O reduction. This strain has strong N2O reduction capability, and the average N2O reduction rate was 5.10±0.11×10-9μmol·h-1·cell-1under anaerobic condition at 30℃ using acetate as the electron donor in a defined medium. This reduction was accompanied by the stoichiometric consumption of acetate over time when N2O served as the sole electron acceptor and the reduction can yield energy to support microbial growth, suggesting that microbial N2O reduction is an electron transport process. Cu2+, silver nanoparticles, O2, and acidic conditions can strongly inhibit the reduction, whereas NO3-or NH4+can promote it. Genomic analysis showed that the gene cluster encoding N2O reductase ofP. denitrificansR-1 was composed ofnosR,nosZ,nosD,nosF,nosY, andnosL, andnosZ, which was identified as clade I. The respiratory inhibitors test indicated that the pathway of electron transport for N2O reduction was different from that of the traditional electron transport chain for aerobic respiration. These findings suggest that modular N2O reduction byP. denitrificansR-1 is linked to the electron transport chain and energy conservation, and that dissimilatory N2O reduction is a form of microbial anaerobic respiration.IMPOETANCEIn the nitrogen biogeochemical cycle, the reduction of N2O to N2by N2O reductase, which is encoded bynos genes, is the only biological pathway for N2O consumption. However, the capacity and mechanisms of microbial N2O reduction are poorly understood. We investigated the ability to obtain energy for growth of Paracoccus denitrificans R-1 by coupling the oxidation of various electron donors to N2O reduction. Our study showed that the nosZ type I bacterium, P. denitrificans R-1, can respire N2O as the sole electron donor. Thus, the modular N2O reduction process of clade I denitrifiers not only can consume N2O produced by themselves but can also consume the external N2O generated from non-denitrification biological or abiotic pathways under suitable conditions, which is critical for controlling the release of N2O from ecosystems into the atmosphere.
Multiplexed CRISPR/Cas9 mutagenesis of rice PSBS1 non-coding sequences for transgene-free overexpression
Authors: Patel-Tupper Dhruv , Kelikian Armen , Leipertz Anna , Maryn Nina , Tjahjadi Michelle , Karavolias Nicholas G. , Cho Myeong-Je , Niyogi Krishna K. 
Published: October 2023

AbstractUnderstanding CRISPR/Cas9’s capacity to generate native overexpression (OX) alleles would accelerate agronomic gains achievable by gene editing. To generate OX alleles with increased RNA and protein abundance, we leveraged multiplexed CRISPR/Cas9 mutagenesis of non-coding DNA sequences located upstream of the ricePSBS1gene. We isolated 120 transgene-free, gene-edited alleles with varying NPQ capacityin vivo—ranging from complete knockout to overexpression, using a high-throughput phenotyping and transgene screening pipeline. Overexpression ofOsPSBS1increased protein abundance 2-3-fold, matching fold changes obtained by transgenesis. Increased PsbS protein abundance enhanced non-photochemical quenching capacity and improved water-use efficiency. Across our resolved genetic variation, we identify the role of 5’UTR indels and inversions in driving knockout/knockdown and overexpression phenotypes, respectively. Complex structural variants, such as the 252kb duplication/inversion generated in this study, evidence the potential of CRISPR/Cas9 to facilitate significant genomic changes with negligible off-target transcriptomic perturbations. Our results may inform future gene-editing strategies for hypermorphic alleles and have opened the door to the pursuit of gene-edited, non-transgenic rice plants with accelerated relaxation of photoprotection.
Modeling alternative translation initiation sites in plants reveals evolutionarily conservedcis-regulatory codes in eukaryotes
Authors: Wu Ting-Ying , Li Ya-Ru , Chang Kai-Jyun , Urano Daisuke , Liu Ming-Jung 
Published: October 2023

AbstractmRNA translation relies on identifying translation initiation sites (TISs) in mRNAs. Alternative TISs are prevalent across plant transcriptomes, but the mechanisms for their recognition are unclear. Using ribosome profiling and machine learning, we developed models for predicting alternative TISs inArabidopsis thalianaand tomato (Solanum lycopersicum). Distinct feature sets were predictive of AUG and non-AUG TISs in 5′ untranslated regions and coding sequences, including a novel CU-rich sequence that promoted plant TIS activity, a translational enhancer found across dicots and monocots and also in humans and viruses. Our results elucidate the mechanistic and evolutionary basis of TIS recognition, wherebycis-regulatory RNA signatures affect start site selection. The TIS prediction model provides global estimates of TISs to discover neglected protein-coding genes across plant genomes. The prevalence ofcis-regulatory signatures across eukaryotes and viruses suggests their broad, critical roles in reprogramming the translational landscape in the plant–virus arms race.TeaserNew insights into how plant ribosomes distinguish AUG and non-AUG triplets for protein synthesis via a conserved eukaryoticcis-regulatory strategy.
Shrinking the capital costs and beta risk impediments through ESG: study of an emerging market
Authors: Gupta Santushti , Aggarwal Divya 
Published: October 2023

PurposeThis study aims to empirically examine environment, social, and governance (ESG) as an effective strategy to reduce major impediments for a corporation in the form of costs of capital (COC) and systematic risk, especially for emerging markets such as India.Design/methodology/approachA sample of 114 Indian firms from eight prominent industries based on Thomson Reuters classification (TRBC) are used in the study. A panel regression with industry-fixed effects is carried out to account for industry heterogeneity. For robustness, the authors also carry out a matched sample analysis.FindingsThe authors observe a negative and significant relationship between ESG performance with COC and systematic risk, respectively. For the pillar-wise analysis, the authors observe that only governance performance is negatively and significantly related to COC whereas the environmental and social performances are negative and insignificant. For ESG pillar level analysis for beta, the authors observe that all pillars are negative and significant, thus making a case for how firms can fine-tune their ESG strategies according to each pillar.Research limitations/implicationsAs the ESG concept is still in a very nascent stage, data availability is a definite challenge in India.Practical implicationsAs ESG is increasingly becoming relevant for multiple stakeholders, this study aims to provide evidence that can potentially guide the regulators, practitioners, and academicians to address the contemporary needs of these stakeholders, while also doing good for the firm in the traditional sense.Social implicationsThe transition to a sustainable economy is a challenge for emerging economies, especially for a country like India where stakeholders are not only varied but also huge in number. With this study's contribution towards an incremental understanding of ESG, Indian regulators and policymakers can bring forward mandates as to ESG compliances that are rewarding for the firms and give them enough impetus towards complying with ESG norms.Originality/valueThe extant literature on ESG majorly discusses the relationship between ESG performance and financial performance. This study addresses the lacuna of the relationship of ESG with COC and beta in the Indian context.