bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular basis of stepwise cyclic tetra-adenylate cleavage by the type III CRISPR ring nuclease Crn1/Sso2081
Authors: Du Liyang , Zhang Danping , Luo Zhipu , Lin Zhonghui 
Published: February 2023

AbstractThe cyclic oligoadenylates (cOAs) act as second messengers of the type III CRISPR immunity system through activating the auxiliary nucleases for indiscriminate RNA degradation. The cOA-degrading nucleases (ring nucleases) provide an ‘off-switch’ regulation of the signaling, thereby preventing cell dormancy or cell death. Here, we describe the crystal structures of the founding member of CRISPR-associated ring nuclease 1 (Crn1) Sso2081 from Saccharolobus solfataricus, alone, bound to phosphate ions or cA4 in both pre-cleavage and cleavage intermediate states. These structures together with biochemical characterizations establish the molecular basis of cA4 recognition and catalysis by Sso2081. The conformational changes in the C-terminal helical insert upon the binding of phosphate ions or cA4 reveal a gate-locking mechanism for ligand binding. The critical residues and motifs identified in this study provide a new insight to distinguish between cOA-degrading and -nondegrading CARF domain-containing proteins.
Mono-ADP-ribosylation by PARP10 and PARP14 in genome stability
Authors: Dhoonmoon Ashna , Nicolae Claudia M 
Published: February 2023

Abstract
ADP-ribosylation is a post-translational modification involved in a variety of processes including DNA damage repair, transcriptional regulation, and cellular proliferation. Depending on the number of ADP moieties transferred to target proteins, ADP-ribosylation can be classified either as mono-ADP-ribosylation (MARylation) or poly-ADP-ribosylation (PARylation). This post-translational modification is catalyzed by enzymes known as ADP-ribosyltransferases (ARTs), which include the poly (ADP-ribose)-polymerase (PARP) superfamily of proteins. Certain members of the PARP family including PARP1 and PARP2 have been extensively studied and assessed as therapeutic targets. However, the other members of the PARP family of protein are not as well studied but have gained attention in recent years given findings suggesting their roles in an increasing number of cellular processes. Among these other members are PARP10 and PARP14, which have gradually emerged as key players in maintenance of genomic stability and carcinogenesis. PARP10 and PARP14 catalyze the transfer of a single ADP moiety to target proteins. Here, we summarize the current knowledge on MARylation in DNA repair and cancer, focusing on PARP10 and PARP14. We highlight the roles of PARP10 and PARP14 in cancer progression and response to chemotherapeutics and briefly discuss currently known PARP10 and PARP14 inhibitors.
A computational map of the human-SARS-CoV-2 protein–RNA interactome predicted at single-nucleotide resolution
Authors: Horlacher Marc , Oleshko Svitlana , Hu Yue , Ghanbari Mahsa , Cantini Giulia , Schinke Patrick , Vergara Ernesto Elorduy , Bittner Florian , Mueller Nikola S , Ohler Uwe , Moyon Lambert , Marsico Annalisa 
Published: February 2023

AbstractRNA-binding proteins (RBPs) are critical host factors for viral infection, however, large scale experimental investigation of the binding landscape of human RBPs to viral RNAs is costly and further complicated due to sequence variation between viral strains. To fill this gap, we investigated the role of RBPs in the context of SARS-CoV-2 by constructing the first in silico map of human RBP-viral RNA interactions at nucleotide-resolution using two deep learning methods (pysster and DeepRiPe) trained on data from CLIP-seq experiments on more than 100 human RBPs. We evaluated conservation of RBP binding between six other human pathogenic coronaviruses and identified sites of conserved and differential binding in the UTRs of SARS-CoV-1, SARS-CoV-2 and MERS. We scored the impact of mutations from 11 variants of concern on protein–RNA interaction, identifying a set of gain- and loss-of-binding events, as well as predicted the regulatory impact of putative future mutations. Lastly, we linked RBPs to functional, OMICs and COVID-19 patient data from other studies, and identified MBNL1, FTO and FXR2 RBPs as potential clinical biomarkers. Our results contribute towards a deeper understanding of how viruses hijack host cellular pathways and open new avenues for therapeutic intervention.
FrangiPANe, a tool for creating a panreference using left behind reads
Authors: Christine Tranchant-Dubreuil , Clothilde Chenal , Mathieu Blaison , Laurence Albar , Valentin Klein , Cédric Mariac , Wing Rod A , Yves Vigouroux , Francois Sabot 
Published: February 2023

AbstractWe present here FrangiPANe, a pipeline developed to build panreference using short reads through a map-then-assemble strategy. Applying it to 248 African rice genomes using an improved CG14 reference genome, we identified an average of 8 Mb of new sequences and 5290 new contigs per individual. In total, 1.4 G of new sequences, consisting of 1 306 676 contigs, were assembled. We validated 97.7% of the contigs of the TOG5681 cultivar individual assembly from short reads on a newly long reads genome assembly of the same TOG5681 cultivar. FrangiPANe also allowed the anchoring of 31.5% of the new contigs within the CG14 reference genome, with a 92.5% accuracy at 2 kb span. We annotated in addition 3252 new genes absent from the reference. FrangiPANe was developed as a modular and interactive application to simplify the construction of a panreference using the map-then-assemble approach. It is available as a Docker image containing (i) a Jupyter notebook centralizing codes, documentation and interactive visualization of results, (ii) python scripts and (iii) all the software and libraries requested for each step of the analysis. We foreseen our approach will help leverage large-scale illumina dataset for pangenome studies in GWAS or detection of selection.
Petrogenesis of the Girnar Complex in the Deccan Traps Province, India
Authors: Halder Mahesh , Paul Debajyoti , Stracke Andreas 
Published: February 2023

AbstractThe c. 66 Ma Girnar Complex of the Deccan Traps consists of various mafic to silicic rocks and provides a unique setting for understanding the dynamics of magma chamber processes. The intrusive alkaline rocks in Girnar are diorites/monzodiorites and contain syenite/nepheline syenite veins. Several (alkaline) mafic dykes cut the alkaline rocks. These rocks are surrounded by intrusive tholeiitic gabbro and extrusive basaltic flows and a silicic (SiO2 &gt; 65 wt%) ring dyke at the outer margin of the complex. The tholeiitic gabbro and basaltic lavas have relatively flat light rare earth element (REE) patterns (La/SmN ~ 0.8 to 1.8) with positive Eu anomalies of 1.1–1.3. The tholeiitic basalts formed by 3–5% partial melting of an incompatible element depleted mid-ocean ridge basalts (MORB)-like source. Accumulating c. 20–30% of (olivine, orthopyroxene, clinopyroxene, and plagioclase) crystals from the tholeiitic melt generated the tholeiitic gabbro. The alkaline rocks display enriched light REE patterns (La/SmN ~ 5.0 to 7.8) consistent with (~9%) partial melting of a spinel lherzolite source, different from the MORB-like source for tholeiitic rocks. The subsequent 58–72% fractional crystallization of olivine, clinopyroxene, plagioclase, orthoclase, spinel, and apatite mineral assemblage formed the alkaline rocks. Reverse and oscillatory zoning in plagioclase (An30 to An50) phenocrysts of the silicic rocks suggest that convective movement of crystals in a magma chamber led to initial crystallization of high-An plagioclase in the hotter zone of the magma chamber, followed by addition of low-An plagioclase in cooler regions of the magma chamber. Pressure estimates from shattered (xenocryst or antecryst) clinopyroxene crystals in silicic rocks give a minimum value of 450 MPa. Ti-in-quartz geothermometry gives a crystallization temperature between 690°C and 1080°C. The distinct isotopic composition of the silicic rocks (87Sr/86Sri = 0.7204–0.7275, εNd(i) = −6.8 to −7.3, 206Pb/204Pbi = 18.74–19.02, 207Pb/204Pbi = 15.76–15.79, 208Pb/204Pbi = 39.63–40.03, εHf(i) = −6.0 to −7.3) further indicates that the silicic rocks assimilated 7 to 9% granitic basement rocks. Overall, therefore, the Girnar Complex started to form with the emplacement of mafic rocks (both alkaline and tholeiitic) in the central part along a reactivated fault lineament and silicic rocks along the concentric marginal fault. Petrography, mineral chemistry, and whole-rock geochemical and Sr-Nd-Pb-Hf isotope ratios of the Girnar Complex rocks indicate that despite the close spatial association of tholeiitic gabbro and basalt, alkaline rocks, and silicic rocks, these rocks originated from multiple sources and evolved in a complex magma drainage and storage network in a continental setting of the Deccan Large Igneous Province (LIP).
Reasoning by Analogy in Mathematical Practice
Authors: Cangiotti Nicolò , Nappo Francesco 
Published: February 2023

Abstract
In this paper, we offer a descriptive theory of analogical reasoning in mathematics, stating general conditions under which an analogy may provide genuine inductive support to a mathematical conjecture (over and above fulfilling the merely heuristic role of ‘suggesting’ a conjecture in the psychological sense). The proposed conditions generalize the criteria of Hesse in her influential work on analogical reasoning in the empirical sciences. By reference to several case studies, we argue that the account proposed in this paper does a better job in vindicating the use of analogical inference in mathematics than the prominent alternative defended by Bartha.
Soybean transporter AAT Rhg1 abundance increases along the nematode migration path and impacts vesiculation and ROS
Authors: Han Shaojie , Smith John M , Du Yulin , Bent Andrew F 
Published: February 2023

Abstract
Rhg1 (Resistance to Heterodera glycines 1) mediates soybean (Glycine max) resistance to soybean cyst nematode (SCN; H. glycines). Rhg1 is a 4-gene, ∼30-kb block that exhibits copy number variation, and the common PI 88788-type rhg1-b haplotype carries 9 to 10 tandem Rhg1 repeats. Glyma.18G022400 (Rhg1-GmAAT), 1 of 3 resistance-conferring genes at the complex Rhg1 locus, encodes the putative amino acid transporter AATRhg1 whose mode of action is largely unknown. We discovered that AATRhg1 protein abundance increases 7- to 15-fold throughout root cells along the migration path of SCN. These root cells develop an increased abundance of vesicles and large vesicle-like bodies (VLB) as well as multivesicular and paramural bodies. AATRhg1 protein is often present in these structures. AATRhg1 abundance remained low in syncytia (plant cells reprogrammed by SCN for feeding), unlike the Rhg1 α-SNAP protein, whose abundance has previously been shown to increase in syncytia. In Nicotiana benthamiana, if soybean AATRhg1 was present, oxidative stress promoted the formation of large VLB, many of which contained AATRhg1. AATRhg1 interacted with the soybean NADPH oxidase GmRBOHG, the ortholog of Arabidopsis thaliana RBOHD previously found to exhibit upregulated expression upon SCN infection. AATRhg1 stimulated reactive oxygen species (ROS) generation when AATRhg1 and GmRBOHG were co-expressed. These findings suggest that AATRhg1 contributes to SCN resistance along the migration path as SCN invades the plant and does so, at least in part, by increasing ROS production. In light of previous findings about α-SNAPRhg1, this study also shows that different Rhg1 resistance proteins function via at least 2 spatially and temporally separate modes of action.
Inverse square singularities and eigenparameter-dependent boundary conditions are two sides of the same coin
Authors: Guliyev Namig J 
Published: February 2023

Abstract
We show that inverse square singularities can be treated as boundary conditions containing rational Herglotz–Nevanlinna functions of the eigenvalue parameter with ‘a negative number of poles’. More precisely, we treat in a unified manner one-dimensional Schrödinger operators with either an inverse square singularity or a boundary condition containing a rational Herglotz–Nevanlinna function of the eigenvalue parameter at each endpoint and define Darboux-type transformations between such operators. These transformations allow one, in particular, to transfer almost any spectral result from boundary value problems with eigenparameter-dependent boundary conditions to those with inverse square singularities and vice versa.
Bioactive fibrous scaffolds with programmable release of polypeptides regulate inflammation and extracellular matrix remodeling
Authors: Xiang Zehong , Guan Xinghua , Ma Zhifang , Shi Qiang , Panteleev Mikhail , Ataullakhanov Fazly I 
Published: February 2023

AbstractInflammation manipulation and extracellular matrix (ECM) remodeling for healthy tissue regeneration are critical requirements for tissue engineering scaffolds. To this end, the bioactive polycaprolactone (PCL)-based scaffolds are fabricated to release aprotinin and thymosin β4 (Tβ4) in a programmable manner. The core part of the fiber is composed of hyaluronic acid and Tβ4, and the shell is PCL, which is further coated with heparin/gelatin/aprotinin to enhance biocompatibility. The in vitro assay demonstrates that the controlled release of aprotinin prevents initial excessive inflammation. The subsequent release of Tβ4 after 3 days induces the transition of macrophages from M1 into M2 polarization. The manipulation of inflammatory response further controls the expression of transforming growth factor-β and fibroblast activation, which oversee the quantity and quality of ECM remodeling. In addition, the gradual degradation of the scaffold allows cells to proliferate within the platform. In vivo implant evaluation convinces that PCL-based scaffolds possess the high capability to control the inflammatory response and restore the ECM to normal conditions. Hence, our work paves a new way to develop tissue engineering scaffolds for inflammation manipulation and ECM remodeling with peptide-mediated reactions.
Night-time smartphone use, sleep duration, sleep quality, and menstrual disturbances in young adult women: A population-based study with high-resolution tracking data
Authors: Severinsen Elin Rosenbek , Andersen Thea Otte , Dissing Agnete Skovlund , Jensen Andreas Kryger , Sejling Christoffer , Freiesleben Nina la Cour , Nielsen Henriette Svarre , Rod Naja Hulvej 
Published: February 2023

AbstractStudy ObjectivesTo explore the relationship among night-time smartphone use, sleep duration, sleep quality, and menstrual disturbances in young adult women.MethodsWomen aged 18–40 years were included in the SmartSleep Study in which they objectively tracked their smartphone use via the SmartSleep app between self-reported sleep onset and offset times (n = 764) and responded to a survey (n = 1068), which included background characteristics, sleep duration, sleep quality (Karolinska Sleep Questionnaire), and menstrual characteristics (International Federation of Gynecology and Obstetrics’ definitions).ResultsThe median tracking time was four nights (interquartile range: 2–8). Higher frequency (p = .05) and longer duration (p = .02) of night-time smartphone use were associated with long sleep duration (≥9 h), but not with poor sleep quality or short sleep duration (&lt;7 h). Short sleep duration was associated with menstrual disturbances (OR = 1.84, 95% confidence interval [CI] = 1.09 to 3.04) and irregular menstruation (OR = 2.17, 95% CI = 1.08 to 4.10), and poor sleep quality was associated with menstrual disturbances (OR = 1.43, 95% CI = 1.19 to 1.71), irregular menstruation (OR = 1.34, 95% CI = 1.04 to 1.72), prolonged bleedings (OR = 2.50, 95% CI = 1.44 to 4.43) and short-cycle duration (OR = 1.40, 95% CI = 1.06 to 1.84). Neither duration nor frequency of night-time smartphone use was associated with menstrual disturbances.ConclusionsNight-time smartphone use was associated with longer sleep duration, but not with menstrual disturbances in adult women. Short sleep duration and sleep quality were associated with menstrual disturbances. Further investigation of the effects of night-time smartphone use on sleep and female reproductive function in large prospective studies is needed.
Transcriptomic analysis reveals differentially expressed genes associated with pine wood nematode resistance in resistant Pinus thunbergii
Authors: Wang Xin-Yu , Wu Xiao-Qin , Wen Tong-Yue , Feng Ya-Qi , Zhang Yan 
Published: February 2023

Abstract
Pine wilt disease (caused by the nematode Bursaphelenchus xylophilus) is extremely harmful to pine forests in East Asia. As a low-resistance pine species, Pinus thunbergii is more vulnerable to pine wood nematode (PWN) than Pinus densiflora and Pinus massoniana. Field inoculation experiments were conducted on PWN-resistant and -susceptible P. thunbergii, and the difference in transcription profiles 24 h after inoculation was analyzed. We identified 2603 differentially expressed genes (DEGs) in PWN-susceptible P. thunbergii, while 2559 DEGs were identified in PWN-resistant P. thunbergii. Before inoculation, DEGs between PWN-resistant and PWN-susceptible P. thunbergii were enriched in the REDOX (Oxidation-Reduction) activity pathway (152 DEGs), followed by the oxidoreductase activity pathway (106 DEGs). After inoculation with PWN, however, the opposite was observed; DEGs were enriched in the oxidoreductase activity pathway (119 DEGs), followed by the REDOX activity pathway (84 DEGs). Before inoculation, according to the metabolic pathway analysis results, we found more genes upregulated in phenylpropanoid metabolic pathways and enriched in lignin synthesis pathways; cinnamoyl-CoA reductase-coding genes related to lignin synthesis were upregulated in PWN-resistant P. thunbergii and downregulated in PWN-susceptible P. thunbergii, and the lignin content was always higher in resistant than in susceptible P. thunbergii. These results reveal distinctive strategies of resistant and susceptible P. thunbergii in dealing with PWN infections.
Investigation of the role of TmMYB16/123 and their targets (TmMTP1/11) in the tolerance of Taxus media to cadmium
Authors: Feng Shangguo , Hou Kailin , Zhang Hongshan , Chen Cheng , Huang Jiefang , Wu Qicong , Zhang Zhenhao , Gao Yadi , Wu Xiaomei , Wang Huizhong , Shen Chenjia 
Published: February 2023

Abstract
The toxicity and stress caused by heavy metal contamination has become an important constraint to the growth and flourishing of trees. In particular, species belonging to the genus Taxus, which are the only natural source for the anti-tumor medicine paclitaxel, are known to be highly sensitive to environmental changes. To investigate the response of Taxus spp. to heavy metal stress, we analyzed the transcriptomic profiles of Taxus media trees exposed to cadmium (Cd2+). In total, six putative genes from the metal tolerance protein (MTP) family were identified in T. media, including two Cd2+ stress inducible TMP genes (TmMTP1, TmMTP11 and Taxus media). Secondary structure analyses predicted that TmMTP1 and TmMTP11, which are members of the Zn-CDF and Mn-CDF subfamily proteins, respectively, contained six and four classic transmembrane domains, respectively. The introduction of TmMTP1/11 into the ∆ycf1 yeast cadmium-sensitive mutant strain showed that TmMTP1/11 might regulate the accumulation of Cd2+ to yeast cells. To screen the upstream regulators, partial promoter sequences of the TmMTP1/11 genes were isolated using the chromosome walking method. Several myeloblastosis (MYB) recognition elements were identified in the promoters of these genes. Furthermore, two Cd2+-induced R2R3-MYB TFs, TmMYB16 and TmMYB123, were identified. Both in vitro and in vivo assays confirmed that TmMTB16/123 play a role in Cd2+ tolerance by activating and repressing the expression of TmMTP1/11 genes. The present study elucidated new regulatory mechanisms underlying the response to Cd stress and can contribute to the breeding of Taxus species with high environmental adaptability.
Overlapping Local and Systemic Defense Induced by an Oomycete Fatty Acid MAMP and Brown Seaweed Extract in Tomato
Authors: Lewis Domonique C. , Stevens Danielle M. , Little Holly , Coaker Gitta L. , Bostock Richard M. 
Published: February 2023

Eicosapolyenoic fatty acids are integral components of oomycete pathogens that can act as microbe-associated molecular patterns to induce disease resistance in plants. Defense-inducing eicosapolyenoic fatty acids include arachidonic acid (AA) and eicosapentaenoic acid and are strong elicitors in solanaceous plants, with bioactivity in other plant families. Similarly, extracts of a brown seaweed, Ascophyllum nodosum, used in sustainable agriculture as a biostimulant of plant growth, may also induce disease resistance. A. nodosum, similar to other macroalgae, is rich in eicosapolyenoic fatty acids, which comprise as much as 25% of total fatty acid composition. We investigated the response of roots and leaves from AA or a commercial A. nodosum extract (ANE) on root-treated tomatoes via RNA sequencing, phytohormone profiling, and disease assays. AA and ANE significantly altered transcriptional profiles relative to control plants, inducing numerous defense-related genes with both substantial overlap and differences in gene expression patterns. Root treatment with AA and, to a lesser extent, ANE also altered both salicylic acid and jasmonic acid levels while inducing local and systemic resistance to oomycete and bacterial pathogen challenge. Thus, our study highlights overlap in both local and systemic defense induced by AA and ANE, with potential for inducing broad-spectrum resistance against pathogens. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Milder Autumns May Increase Risk for Infection of Crops with Turnip Yellows Virus
Authors: Puthanveed Vinitha , Singh Khushwant , Poimenopoulou Efstratia , Pettersson Josefin , Siddique Abu Bakar , Kvarnheden Anders 
Published: February 2023

Climate change has increased the risk for infection of crops with insect-transmitted viruses. Mild autumns provide prolonged active periods to insects, which may spread viruses to winter crops. In autumn 2018, green peach aphids ( Myzus persicae) were found in suction traps in southern Sweden that presented infection risk for winter oilseed rape (OSR; Brassica napus) with turnip yellows virus (TuYV). A survey was carried out in spring 2019 with random leaf samples from 46 OSR fields in southern and central Sweden using DAS-ELISA, and TuYV was detected in all fields except one. In the counties of Skåne, Kalmar, and Östergötland, the average incidence of TuYV-infected plants was 75%, and the incidence reached 100% for nine fields. Sequence analyses of the coat protein gene revealed a close relationship between TuYV isolates from Sweden and other parts of the world. High-throughput sequencing for one of the OSR samples confirmed the presence of TuYV and revealed coinfection with TuYV-associated RNA. Molecular analyses of seven sugar beet ( Beta vulgaris) plants with yellowing, collected in 2019, revealed that two of them were infected by TuYV, together with two other poleroviruses: beet mild yellowing virus and beet chlorosis virus. The presence of TuYV in sugar beet suggests a spillover from other hosts. Poleroviruses are prone to recombination, and mixed infection with three poleroviruses in the same plant poses a risk for the emergence of new polerovirus genotypes. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .