bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of cfDNA and exovesicle-DNA for the molecular diagnosis of chronic Chagas disease
Authors: Lozano Noelia , Samblas Mercedes Gomez , Calabuig Eva , Giménez Martí María José , Gómez Ruiz Maria Dolores , Sahuquillo Arce José Miguel , Molina Moreno José Miguel , Trelis M. , Osuna Antonio 
Published: February 2023

AbstractChagas disease is, among others, considered a neglected tropical disease. Given the magnitude of the human movements that have occurred in recent years from Central and South America to other countries, Chagas should now be considered a disease of worldwide distribution, in which the transmission of the parasite is restricted to transplacental transmission or blood or organ donations from infected people.Parasite detection in chronically ill patients is restricted to serological tests that only determine previous contact and not the presence of the parasite, especially in those patients undergoing treatment evaluation or in newborns.In this study, we evaluate the use of nucleic acids from both circulating serum exovesicles and cell-free DNA (cfDNA) from 448 serum samples from immunologically diagnosed chronic chagasic patients, which were re-evaluated by nested PCR on the amplicons resulting from amplification with kDNA-specific primers 121F-122R. Of the total number of samples selected, 50 were used to isolate and purify exovesicles from circulating serum and cell-free DNA (cfDNA).When the nucleic acids thus purified were assayed as a template and amplified with primers 121F-122R and SAT, a percentage positivity of 100% was obtained for all positive samples assayed with the kDNA-specific primers and 96% when SAT primers were used. However, isolation of cfDNA forT. cruziand amplification with SAT primers also showed 100% positivity. Hence, both samples can be used in those cases where it is necessary to demonstrate the active presence of the parasite.
Unraveling the immune signature of herpes zoster: Insights into pathophysiology and the HLA risk profile
Authors: Vandoren Romi , Boeren Marlies , Schippers Jolien , Bartholomeus Esther , Michels Nele , Aerts Olivier , Leysen Julie , Bervoets An , Lambert Julien , Leuridan Elke , Wens Johan , Peeters Karin , Emonds Marie-Paule , Jansens Hilde , Suls Arvid , Van Tendeloo Viggo , Ponsaerts Peter , Delputte Peter , Ogunjimi Benson , Meysman Pieter , Laukens Kris 
Published: February 2023

ABSTRACTThe varicella-zoster virus (VZV) infects over 95% of the population and establishes latency afterwards. Reactivation of VZV causes herpes zoster (HZ), commonly known as shingles, which presents as a painful rash in mostly the elderly and people with a weakened immune system. However, HZ might occur in otherwise healthy individuals too. In this study, we have studied the immune signature of HZ to better understand HZ’s pathophysiology. We provide a general overview of the antiviral state and the activation of innate and adaptive immune responses during HZ. Differential gene expression and gene ontology analyses revealed upregulation of several genes and host immune pathways during herpes zoster, especially related to type I IFN response but also related to adaptive immune responses. Intriguingly, no differences in gene expression were noted during convalescence between HZ patients and controls. Furthermore, we conducted the largest HLA association study on HZ to date using the UK Biobank and identified seven protective and four risk HLA alleles associated with the development of herpes zoster. These findings reveal key genes and pathways involved in the host immune response to symptomatic VZV reactivation and provide new molecular insights into the development of HZ.
APPLICATION OF THE ACMG/AMP FRAMEWORK TO CAPTURE EVIDENCE RELEVANT TO PREDICTED AND OBSERVED IMPACT ON SPLICING: RECOMMENDATIONS FROM THE CLINGEN SVI SPLICING SUBGROUP
Authors: Walker Logan C. , de la Hoya Miguel , Wiggins George A.R. , Lindy Amanda , Vincent Lisa M. , Parsons Michael T , Canson Daffodil M , Bis-Brewer Dana , Cass Ashley , Tchourbanov Alexander , Zimmermann Heather , Byrne Alicia B , Pesaran Tina , Karam Rachid , Harrison Steven , Spurdle Amanda B 
Published: February 2023

ABSTRACTThe American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) framework for classifying variants uses six evidence categories related to the splicing potential of variants: PVS1 (null variant in a gene where loss-of-function is the mechanism of disease), PS3 (functional assays show damaging effect on splicing), PP3 (computational evidence supports a splicing effect), BS3 (functional assays show no damaging effect on splicing), BP4 (computational evidence suggests no splicing impact), and BP7 (silent change with no predicted impact on splicing). However, the lack of guidance on how to apply such codes has contributed to variation in the specifications developed by different Clinical Genome Resource (ClinGen) Variant Curation Expert Panels. The ClinGen Sequence Variant Interpretation (SVI) Splicing Subgroup was established to refine recommendations for applying ACMG/AMP codes relating to splicing data and computational predictions. Our study utilised empirically derived splicing evidence to: 1) determine the evidence weighting of splicing-related data and appropriate criteria code selection for general use, 2) outline a process for integrating splicing-related considerations when developing a gene-specific PVS1 decision tree, and 3) exemplify methodology to calibrate bioinformatic splice prediction tools. We propose repurposing of the PVS1_Strength code to capture splicing assay data that provide experimental evidence for variants resulting in RNA transcript(s) with loss of function. Conversely BP7 may be used to capture RNA results demonstrating no impact on splicing for both intronic and synonymous variants, and for missense variants if protein functional impact has been excluded. Furthermore, we propose that the PS3 and BS3 codes are applied only for well-established assays that measure functional impact that is not directly captured by RNA splicing assays. We recommend the application of PS1 based on similarity of predicted RNA splicing effects for a variant under assessment in comparison to a known Pathogenic variant. The recommendations and approaches for consideration and evaluation of RNA assay evidence described aim to help standardise variant pathogenicity classification processes and result in greater consistency when interpreting splicing-based evidence.
Optineurin provides a mitophagy contact site for TBK1 activation
Authors: Yamano Koji , Sawada Momoha , Kikuchi Reika , Nagataki Kafu , Kojima Waka , Sugihara Atsushi , Fujino Tomoshige , Tanaka Keiji , Hayashi Gosuke , Murakami Hiroshi , Matsuda Noriyuki 
Published: February 2023

AbstractTank-binding kinase 1 (TBK1) is a Ser/Thr kinase involved in many intracellular processes including innate immunity, cell cycle, and apoptosis. TBK1 is also important for phosphorylating autophagy adaptors critical in selective autophagic removal of damaged mitochondria (mitophagy). However, the mechanism by which TBK1 is activated by PINK1/Parkin-mediated mitophagy remains largely unknown. Here, we show that the autophagy adaptor OPTN provides a unique platform for TBK1 activation. The OPTN-ubiquitin and OPTN-autophagy machinery interaction axes facilitate assembly of the OPTN-TBK1 complex at a contact site between damaged mitochondria and the autophagosome formation site. This assembly point serves as a positive feedback loop for TBK1 activation by accelerating hetero-autophosphorylation of the protein. Furthermore, expression of monobodies engineered in this study against OPTN impaired assembly of OPTN at the contact sites as well as the subsequent activation of TBK1 and mitochondrial degradation. Taken together the findings reveal that a positive reciprocal relationship between OPTN and TBK1 initiates autophagosome biogenesis on damaged mitochondria.
Spatial transcriptomic atlas of shoot organogenesis in tomato callus
Authors: Song Xiehai , Guo Pengru , Wang Meiling , Chen Lichuan , Zhang Jinhui , Xu Mengyuan , Liu Naixu , Liu Min , Fang Liang , Xu Xun , Gu Ying , Xia Keke , Li Bosheng 
Published: February 2023

AbstractCallus is a reprogrammed transitional cell mass during plant regeneration. Pluripotent callus cells develop into fertile shoots throughde novoshoot organogenesis. This study represents a pioneering effort in exploring the spatial transcriptome of tomato callus during shoot regeneration, using technologies including BGI Stereo-seq, BMKMANU S1000, and 10x Visium. The results indicate that the callus comprises highly heterogeneous cells, classified into various cell types based on spatial gene expression and histological observation, including epidermis, shoot primordium, vascular tissue, inner callus, and outgrowth shoots. The developmental trajectories from shoot primordium to outgrowth shoot are traced, and vascular tissue development is characterized. The single-cell resolution spatial approach reveals the origin of shoot primordia from the sub-epidermis. The spatial full length RNA sequencing shows high incompletely spliced (IS) ratios in the shoot primordium cells. These findings enhance our knowledge of plant organogenesis and highlight the significance of spatial biology in plant research.
A chromosome-level genome assembly of a model conifer plant, the Japanese cedar,Cryptomeria japonicaD. Don
Authors: Fujino Takeshi , Katsushi Yamaguchi , Yokoyama Toshiyuki T , Hamanaka Toshiya , Harazono Yoritaka , Kamada Hiroaki , Kobayashi Wataru , Ujino-Ihara Tokuko , Uchiyama Kentaro , Matsumoto Asako , Izuno Ayako , Tsumura Yoshihiko , Toyoda Atsushi , Shigenobu Shuji , Moriguchi Yoshinari , Ueno Saneyoshi , Kasahara Masahiro 
Published: February 2023

AbstractJapanese cedar (Cryptomeria japonicaD. Don) is the most important Japanese forest tree, occupying about 44% of artificial forests in Japan, and planted in East Asia, Azores Archipelago, and some islands in the Indian Ocean. Although the huge genome of the species (ca. 11 Gb) with abundant repeat elements might have been an obstacle for genetic analysis, the species is easily propagated by cutting, flowered by plant hormones like gibberellic acid, transformed by agrobacterium, and edited by CRISPR/Cas9. These characteristics ofC. japonicaare preferable to make the species a model conifer for which reference genome sequences are necessary. In this study, we report the first chromosome-level assembly forC. japonica(2n = 22) using a third generation selfed progeny with an estimated homozygosity of 0.96. Young leaf tissue was used to extract high-molecular-weight DNA (>50 kb) for HiFi PacBio long read sequencing and to construct Hi-C/Omni-C library for Illumina short read sequencing. Using the 29× and 26× genome coverage of HiFi and Illumina reads, respectively, de novo assembly resulted in 2,650 contigs (9.1 Gb in total) with N50 contig size of 12.0 Mb. The Hi-C analysis mapped 97% of the nucleotides on the 11 chromosomes. The assembly was verified by comparing with a consensus linkage map of 7,785 markers. The BUSCO analysis confirmed ~91% of conserved genes. Annotations of genes, repeat elements and synteny with other Cupressaceae and Pinaceae species were performed, providing fundamental resources for genomic research of conifers.
Community diversity affects functionality and species sorting during propagation of a natural microbial community
Authors: Leale Alanna , Auxier Ben , Smid Eddy J. , Schoustra Sijmen 
Published: February 2023

ABSTRACTThe influence of community diversity on community function has long been a central question in ecology. Particularly, the dynamics over time of this relationship as a function of levels of diversity remains unclear. Natural populations may vary in levels of species diversity, for instance after they experience disturbances that remove significant amounts of their genetic and species variation, including rare but functionally unique guilds. We investigated the influence of diversity on associated community function by propagating natural microbial communities from a traditionally fermented milk beverage diluted to various levels. Specifically, we assessed the influence of less abundant microbial types such as yeast and rarer bacterial types on community functionality and species sorting trajectories over approximately 100 generations. We observed repeatable changes in bacterial community compositions, metabolic profiles, and acidity related to starting diversity levels. The influence of a single ecological guild, yeast in our study, played a dramatic role on function, but interestingly not on long-term species sorting trajectories of the remaining bacterial community. Our results together evidence ecological selection on the microbial communities in our system and suggest an unexpected niche division between yeast and bacterial communities.
A conformational-dependent interdomain redox relay at the core of Protein Disulfide Isomerase activity
Authors: Melo Eduardo P. , El-Guendouz Soukaina , Correia Cátia , Teodoro Fernando , Lopes Carlos 
Published: February 2023

AbstractProtein disulfide isomerases (PDIs) are a family of molecular chaperones resident in the endoplasmic reticulum (ER) emerging as important factors in disease. In addition to an holdase function, some members catalyse disulfide bond formation and isomerization, a crucial step for native folding and prevention of aggregation of misfolded proteins. PDIs are characterized by a modular arrangement of thioredoxin-like domains, with the canonical, first identified PDIA1, organized as four thioredoxin-like domains forming a horseshoe with two active sites at the extremities. Using two fluorescent redox sensors, roGFP2 and HyPer, as client substrates either unfolded or native, and thein vitroreconstitution of the full pathways of oxidative protein in the ER, we clarified important aspects underlying the catalytic cycle of PDIA1. The N-terminalaactive site is the main oxidant of thiols and can transfer electrons to the C-terminala’active site relying on the redox-dependent conformational flexibility of PDIA1 that allows the formation of an interdomain disulfide bond. Thea’active site act then as a crossing point to redirect electrons to the ER downstream oxidases or back to client proteins. The two active sites of PDIA1 work cooperatively as an interdomain redox relay that explains PDIA1 oxidative activity to form native disulfides and PDIA1 reductase activity to resolve scrambled disulfides. Moreover, this mechanism reveals a new rational for shutting down oxidative protein folding under ER redox imbalance or when the levels of unfolded proteins and folding intermediates exceed the folding capacity of the system.
Morphological trait evolution inSolanum(Solanaceae): evolutionary lability of key taxonomic characters
Authors: Hilgenhof Rebecca , Gagnon Edeline , Knapp Sandra , Aubriot Xavier , Tepe Eric J. , Bohs Lynn , Giacomin Leandro L. , Gouvêa Yuri F. , Martine Christopher T. , Orejuela Andrés , Orozco Clara Inés , Peralta Iris E. , Särkinen Tiina 
Published: February 2023

AbstractSolanumL. is one of the world’s largest and economically most important plant genera, including 1,245 currently accepted species and several major and minor crops (e.g., tomato, potato, brinjal eggplant, scarlet eggplant, Gboma eggplant, lulo, and pepino). Here we provide an overview of the evolution of 25 key morphological traits for the major and minor clades of this giant genus based on stochastic mapping using a well-sampled recently published phylogeny ofSolanum. The most evolutionarily labile traits (showing >150 transitions across the genus) relate to plant structure (growth form and sympodial unit structure), herbivore defence (glandular trichomes), pollination (corolla shape and colour), and dispersal (fruit colour). Ten further traits show evolutionary lability with 50-100 transitions across the genus (e.g., specialised underground organs, trichome structure, leaf type, inflorescence position and branching, stamen heteromorphism). Our results reveal a number of highly convergent traits inSolanum, including tubers, rhizomes, simple leaves, yellow corollas, heteromorphic anthers, dioecy, and dry fruits, and some unexpected pathways of trait evolution that could be explored in future studies. We show that informally named clades ofSolanumcan be morphologically defined by trait combinations providing a tool for identification and enabling predictive phylogenetic placement of unsampled species.
Understanding Activity-Stability Tradeoffs in Biocatalysts by Enzyme Proximity Sequencing
Authors: Vanella Rosario , Küng Christoph , Schoepfer Alexandre A. , Doffini Vanni , Ren Jin , Nash Michael A. 
Published: February 2023

AbstractUnderstanding the complex relationships between enzyme sequence, folding stability and catalytic activity is crucial for applications in industry and biomedicine. However, current enzyme assay technologies are limited by an inability to simultaneously resolve both stability and activity phenotypes and to couple these to gene sequences at large scale. Here we developed Enzyme Proximity Sequencing (EP-Seq), a deep mutational scanning method that leverages peroxidase-mediated radical labeling with single cell fidelity to dissect the effects of thousands of mutations on stability and catalytic activity of oxidoreductase enzymes in a single experiment. We used EP-Seq to analyze how 6,399 missense mutations influence folding stability and catalytic activity in a D-amino acid oxidase (DAOx) fromR.gracilis. The resulting datasets demonstrate activity-based constraints that limit folding stability during natural evolution, and identify hotspots distant from the active site as candidates for mutations that improve catalytic activity without sacrificing stability. EP-Seq can be extended to other enzyme classes and provides valuable insights into biophysical principles governing enzyme structure and function.
U1 AMO (antisense morpholino oligo) disrupts U1 snRNP structure to promote intronic premature cleavage and polyadenylation (PCPA)
Authors: Feng Qiumin , Lin Zejin , Deng Yanhui , Ran Yi , Xiang Andy Peng , Ye Congting , Yao Chengguo 
Published: February 2023

AbstractFunctional depletion of U1 snRNP with a 25 nt U1 AMO (antisense morpholino oligonucleotides) may lead to intronic premature cleavage and polyadenylation (PCPA) of thousands of genes, a phenomenon known as U1 snRNP telescripting; however, the underlying mechanism remains elusive. In this study, we demonstrated that U1 AMO could disrupt U1 snRNP structure both in vitro and in vivo, thereby affecting U1 snRNP/RNAP polymerase II (RNAPII) interaction. We further showed that U1 AMO treatment might promote RNAPII disassociation with pre-mRNA in an RNA pull-down assay. By performing ChIP-seq for phosphorylation of Ser2 (Ser2P) and Ser5 (Ser5P) of the C-terminal domain (CTD) of RNA polymerase II (RNAPII), we showed that transcription elongation was disturbed upon U1 AMO treatment, with a particular high Ser2P signal at intronic cryptic polyadenylation sites (PASs). In addition, we showed that core 3’ processing factors CPSF/CstF are involved in the processing of intronic cryptic PAS. Their recruitment accumulated toward cryptic PASs upon U1 AMO treatment, as indicated by ChIP-seq and iCLIP-seq analysis. Furthermore, we showed that most of these PCPAed transcripts could be exported to cytoplasm and have the potential to be translated. Conclusively, our data provide more insight into U1 snRNP telescripting, and suggest a common theme that modulation of transcription elongation may be an important mode for the regulation of mRNA polyadenylation.
HIV-1 Gag colocalizes with euchromatin histone marks at the nuclear periphery
Authors: Chang Jordan , Parent Leslie J. 
Published: February 2023

AbstractThe retroviral Gag protein of human immunodeficiency virus type 1 (HIV-1) plays a central role in the selection of unspliced viral genomic RNA for packaging into new virions. Previously, we demonstrated that full-length HIV-1 Gag undergoes nuclear trafficking where it associates with unspliced viral RNA (vRNA) at transcription sites. To further explore the kinetics of HIV-1 Gag nuclear localization, we used biochemical and imaging techniques to examine the timing of HIV-1 entry into the nucleus. We also aimed to determine more precisely Gag’s subnuclear distribution to test the hypothesis that Gag would be associated with euchromatin, the transcriptionally active region of the nucleus. We observed that HIV-1 Gag localized to the nucleus shortly after its synthesis in the cytoplasm, suggesting that nuclear trafficking was not strictly concentration-dependent. Furthermore, we found that HIV-1 Gag preferentially localized to the transcriptionally active euchromatin fraction compared to the heterochromatin-rich region in a latently-infected CD4+ T cell line (J-Lat 10.6) treated with latency-reversal agents. Interestingly, HIV-1 Gag was more closely associated with transcriptionally-active histone markers near the nuclear periphery, where the HIV-1 provirus was previously shown to integrate. Although the precise function of Gag’s association with histones in transcriptionally-active chromatin remains uncertain, together with previous reports, this finding is consistent with a potential role for euchromatin-associated Gag molecules to select newly transcribed unspliced vRNA during the initial stage of virion assembly.ImportanceThe traditional view of retroviral assembly posits that HIV-1 Gag selection of unspliced vRNA begins in the cytoplasm. However, our previous studies demonstrated that HIV-1 Gag enters the nucleus and binds to unspliced HIV-1 RNA at transcription sites, suggesting that genomic RNA selection may occur in the nucleus. In the present study, we observed nuclear entry of HIV-1 Gag and co-localization with unspliced viral RNA within 8 hours post-expression. In CD4+ T cells (J-Lat 10.6) treated with latency reversal agents, as well as a HeLa cell line stably expressing an inducible Rev-dependent provirus, we found that HIV-1 Gag preferentially localized with histone marks associated with enhancer and promoter regions of transcriptionally active euchromatin near the nuclear periphery, which favors HIV-1 proviral integration sites. These observations support the hypothesis that HIV-1 Gag hijacks euchromatin-associated histones to localize to active transcription sites, promoting capture of newly synthesized genomic RNA for packaging.