bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Cell-Free DNA Methylation Patterns Unique to the Human Left Ventricle as a Potential Indicator of Acute Cellular Rejection
Authors: Pattar Sabrina , Aleinati Mohammad , Iqbal Fatima , Madhu Aiswarya , Blais Samuel , Wang Xuemei , Dallaire Frederic , Wang Yinong , Isaac Debra , Fine Nowell , Greenway Steven C. 
Published: March 2021

AbstractIncreased levels of donor-derived cell-free DNA (dd-cfDNA) in recipient plasma have been associated with rejection after transplantation. DNA sequence differences have been used to distinguish between donor and recipient but epigenetic differences could also potentially identify dd-cfDNA. This pilot study aimed to identify ventricle-specific differentially methylated regions of DNA (DMRs) that could be detected in cfDNA. We identified 24 ventricle-specific DMRs and chose two for further study, one on chromosome 9 and one on chromosome 12. The specificity of both DMRs for the left ventricle was confirmed using genomic DNA from multiple human tissues. Serial matched samples of myocardium (n=33) and plasma (n=24) were collected from stable adult heart transplant recipients undergoing routine endomyocardial biopsy for rejection surveillance. Plasma DMR levels increased with biopsy-proven rejection grade for individual patients. Mean cellular apoptosis in biopsy samples increased significantly with rejection severity (2.4%, 4.4% and 10.0% for ACR 0R, 1R and 2R, respectively) but did not show a consistent relationship with DMR levels. We identified multiple DNA methylation patterns unique to the human ventricle and conclude that epigenetic differences in cfDNA populations represent a promising alternative strategy for the non-invasive detection of rejection.
Tiled-ClickSeq for targeted sequencing of complete coronavirus genomes with simultaneous capture of RNA recombination and minority variants
Authors: Jaworski Elizabeth , Langsjoen Rose M. , Mitchell Brooke , Judy Barbara , Newman Patrick , Plante Jessica A. , Plante Kenneth S. , Miller Aaron L. , Zhou Yiyang , Swetnam Daniele , Sotcheff Stephanea , Morris Victoria , Saada Nehad , Machado Rafael , McConnell Allan , Widen Steve , Thompson Jill , Dong Jianli , Ren Ping , Pyles Rick B. , Ksiazek Thomas , Menachery Vineet D. , Weaver Scott C. , Routh Andrew 
Published: March 2021

AbstractHigh-throughput genomics of SARS-CoV-2 is essential to characterize virus evolution and to identify adaptations that affect pathogenicity or transmission. While single-nucleotide variations (SNVs) are commonly considered as driving virus adaption, RNA recombination events that delete or insert nucleic acid sequences are also critical. Whole genome targeting sequencing of SARS-CoV-2 is typically achieved using pairs of primers to generate cDNA amplicons suitable for Next-Generation Sequencing (NGS). However, paired-primer approaches impose constraints on where primers can be designed, how many amplicons are synthesized and requires multiple PCR reactions with non-overlapping primer pools. This imparts sensitivity to underlying SNVs and fails to resolve RNA recombination junctions that are not flanked by primer pairs. To address these limitations, we have designed an approach called ‘Tiled-ClickSeq’, which uses hundreds of tiled-primers spaced evenly along the virus genome in a single reverse-transcription reaction. The other end of the cDNA amplicon is generated by azido-nucleotides that stochastically terminate cDNA synthesis, removing the need for a paired-primer. A sequencing adaptor containing a Unique Molecular Identifier (UMI) is appended to the cDNA fragment using click-chemistry and a PCR reaction generates a final NGS library. Tiled-ClickSeq provides complete genome coverage, including the 5’UTR, at high depth and specificity to the virus on both Illumina and Nanopore NGS platforms. Here, we analyze multiple SARS-CoV-2 isolates and clinical samples to simultaneously characterize minority variants, sub-genomic mRNAs (sgmRNAs), structural variants (SVs) and D-RNAs. Tiled-ClickSeq therefore provides a convenient and robust platform for SARS-CoV-2 genomics that captures the full range of RNA species in a single, simple assay.
Memory B cell repertoire for recognition of evolving SARS-CoV-2 spike
Authors: Tong Pei , Gautam Avneesh , Windsor Ian , Travers Meghan , Chen Yuezhou , Garcia Nicholas , Whiteman Noah B. , McKay Lindsay G.A. , Lelis Felipe J.N. , Habibi Shaghayegh , Cai Yongfei , Rennick Linda J. , Duprex W. Paul , McCarthy Kevin R. , Lavine Christy L. , Zuo Teng , Lin Junrui , Zuiani Adam , Feldman Jared , MacDonald Elizabeth A. , Hauser Blake M. , Griffths Anthony , Seaman Michael S. , Schmidt Aaron G. , Chen Bing , Neuberg Donna , Bajic Goran , Harrison Stephen C. , Wesemann Duane R. 
Published: March 2021

ABSTRACTMemory B cell reserves can generate protective antibodies against repeated SARS-CoV-2 infections, but with an unknown reach from original infection to antigenically drifted variants. We charted memory B cell receptor-encoded monoclonal antibodies (mAbs) from 19 COVID-19 convalescent subjects against SARS-CoV-2 spike (S) and found 7 major mAb competition groups against epitopes recurrently targeted across individuals. Inclusion of published and newly determined structures of mAb-S complexes identified corresponding epitopic regions. Group assignment correlated with cross-CoV-reactivity breadth, neutralization potency, and convergent antibody signatures. mAbs that competed for binding the original S isolate bound differentially to S variants, suggesting the protective importance of otherwise-redundant recognition. The results furnish a global atlas of the S-specific memory B cell repertoire and illustrate properties conferring robustness against emerging SARS-CoV-2 variants.
Variable autoinhibition among deafness-associated variants of Diaphanous 1 (DIAPH1)
Authors: Lakha Rabina , Montero Angela M. , Jabeen Tayyaba , Costeas Christina C. , Ma Jia , Vizcarra Christina L. 
Published: March 2021

AbstractOne of the earliest mapped human deafness genes,DIAPH1, encodes the formin DIAPH1. To date, at least three distinct mutations in the C-terminal domains and two additional mutations in the N-terminal region are associated with autosomal dominant hearing loss. The underlying molecular mechanisms are not known, and the role of formins in the inner ear is not well understood. In this study we use biochemical assays to test the hypotheses that autoinhibition and/or actin assembly activities are disrupted by DFNA1 mutations. Our results indicate that C-terminal mutant forms of DIAPH1 are functionalin vitroand promote actin filament assembly. Similarly, N-terminal mutants are well-folded and have quaternary structures and thermal stabilities similar to the WT protein. The strength of the autoinhibitory interactions varies widely among mutants, with thettaa, A265S and I530S mutations having an affinity similar to WT and the 1213x and Δagmutations completely abolishing autoinhibition. These data indicate that, in some cases, hearing loss may be linked to reduced inhibition of actin assembly.
A wing growth organizer in a hemimetabolous insect suggests wing origin
Authors: Ohde Takahiro , Mito Taro , Niimi Teruyuki 
Published: March 2021

ABSTRACTThe origin and evolution of insect wings remain enigmatic after a century-long discussion. Molecular dissection of wing development in hemimetabolous insects, in which the first functional wings evolved, is key to understand genetic changes required for wing evolution. We investigatedDrosophilawing marker genes in the cricket,Gryllus bimaculatus, and foundapterousandvestigialshow critical functions in nymphal tergal identity and margin formation, respectively. We further demonstrate that margin cells in the lateral-anterior tergal region constitute a growth organizer of wing blades. Transcriptome and RNAi analyses unveiled that Wnt, Fat-Dachsous, and Hippo pathways are involved in disproportional growth ofGrylluswings. Our data collectively support the idea that tergal margin cells of a wingless ancestor gave rise to the body wall extension required for evolution of the first powered flight.
Integrated Systems-Analysis of the Human and Murine Pancreatic Cancer Glycomes Reveal a Tumor Promoting Role for ST6GAL1
Authors: Kurz Emma , Chen Shuhui , Vucic Emily , Baptiste Gillian , Loomis Cynthia , Agarwal Praveen , Hajdu Cristina , Bar-Sagi Dafna , Mahal Lara K. 
Published: March 2021

ABSTRACTPancreatic ductal adenocarcinoma (PDA) is the 3rdleading cause of cancer-death in the U.S.. Glycans, such as CA-19-9, are biomarkers of PDA and are emerging as important modulators of cancer phenotypes. Herein, we utilized a systems-based approach integrating glycomic analysis of human PDA and the well-established KC mouse model, with transcriptomic data to identify and probe the functional significance of aberrant glycosylation in pancreatic cancer. We observed both common and distinct patterns of glycosylation in pancreatic cancer across species. Common alterations included increased levels of α-2,3- and α-2,6-sialic acids, bisecting GlcNAc and poly-LacNAc. However, core fucose, which was increased in human PDAC, was not seen in the mouse, indicating that not all human glycomic changes can be modeled in the KC mouse. In silico a nalysis of bulk and single cell sequencing data identified ST6GAL1, which underlies α-2,6-sialic acid, as overexpressed in human PDA, concordant with histological data. Enzymes levels correlated with the stage of clinical disease. To test whether ST6GAL1 promotes pancreatic cancer we created a novel mouse in which a pancreas-specific genetic deletion of this enzyme overlays the KC mouse model. Analysis of our new model showed delayed cancer formation and a significant reduction in fibrosis. Our results highlight the importance of a strategic systems-approach to identifying glycans whose functions can be modeled in mouse, a crucial step in the development of therapeutics targeting glycosylation in pancreatic cancer.SIGNIFICANCEPancreatic ductal adenocarcinoma (PDA) is the 3rdleading cause of cancer-death in the U.S.. Glycosylation is emerging as an important modulator of cancer phenotype. Herein we use a systems-approach integrating glycomics of human PDA and a well-established PDA mouse model with transcriptomic data to identify ST6GAL1, the enzyme underlying α-2,6-sialic acid, as a potential cancer promoter. A pancreatic specific ST6GAL1 knockout in the KC mouse showed delayed cancer formation and a reduction in fibrosis. Our results highlight the importance of a strategic systems-approach to identifying glycans whose functions can be modeled in mouse, a crucial step in the development of therapeutics targeting glycosylation in pancreatic cancer.
Different issue types have different signal intensity onb=0 images and its implication on intravoxel incoherent motion (IVIM) analysis: examples of liver MRI
Authors: Xiao Ben-Heng , Wáng Yì Xiáng J. 
Published: March 2021

AbstractIntravoxel incoherent motion (IVIM) theory in MRI was proposed to account for the effect of vessel/capillary perfusion on the aggregate diffusion weighted MR signal. The prevalent IVIM modeling is based on equation-1: SI(b)/SI(0)= (1 -PF) × exp(-b× Dslow) + PF × exp(-b× Dfast) [1] where SI(b)and SI(0)denote the signal intensity of images acquired with the b-factor value ofbandb=0 s/mm2, respectively. We recently reported that, for the liver and likely for other organs as well, IVIM modeling of the perfusion component is constrained by the diffusion component, with a reducedDslowmeasure leading to artificially higher PF andDfastmeasures. With higher b-value associated lower image signal of the targeted tissue, Euqation-1 is focused on describing the signal decay pattern along increasingly higherb-values by three IVIM parameters. Signal intensity at eachb-value (i.e., SI(b)) is normalised by the signal intensity ofb=0 image (i.e., SI(0)). We noted an apparent problem for Euqation-1. For example, if we want to compare the IVIM parameters of the normal liver parenchyma and a liver tumor, following Euqation-1 we will take the assumption that the SI(0)of the normal parenchyma and the tumor are the same and considered equally as 1 (or 100) for the biexponential decay modelling. However, this assumption is invalid for many scenarios. From our liver IVIM database of 27 healthy female subjects, we chose six of the youngest subjects (20-27 yrs) and six of the oldest subjects (58-71 yrs) and measured the signals of the liver and left erector spinae muscle onb=0 and 2 s/mm2images. The results show, while there was no apparent difference of left erector spinae muscle signal among the young and elderly groups, the elderly group’s liver SI(0)is approximately 20 % lower than that of young group. This difference skewed the ratios of various SI(b)/SI(0)and the followed IVIM parameter determination. The general trend is that lower liver SI(0)is associated with lowerDslowand higher PF andDfast. If IVIM bi-exponential decay fitting starts from a very low non-zero b images (such asb=2 s/mm2images), this problem persists. We performed an additional analysis of our IVIM database of five cirrhotic livers and the results show SI(b=2)of cirrhotic right liver is positively associatedDslow(Pearson r=0.687), and negatively associated with PF (Pearsonr=-0.733). Though the examples we used in this letter are on liver aging and liver fibrosis, the points discussed are expected to be generalisable to other pathologies and to other organs.
The level of synovial human VEGFA, IL-8 and MIP-1α correlate with truncation of lubricin glycans in osteoarthritis
Authors: Huang Shan , Thomsson Kristina A. , Jin Chunsheng , Ryberg Henrik , Das Nabangshu , Struglics André , Rolfson Ola , Björkman Lena I , Eisler Thomas , Schmidt Tannin A. , Jay Gregory D. , Krawetz Roman , Karlsson Niclas G. 
Published: March 2021

AbstractOsteoarthrithis (OA) is an endemic disease due to the increase of the world’s elderly population. Previously thought to be a consequence of an imbalance between cartilage degradation and biosynthesis, it is now recognized as a disease also involving inflammation, hence influencing the level of inflammatory cytokines, growth factors and chemokines. Lubricin is a mucin type molecule where its OA induced glycosylation truncation propels a deteriorating lubrication of the articular cartilage. The objective of this study was to explore the OA driven truncation ofO-linked glycosylation of synovial lubricin and its cross talk with systemic and local (synovial fluid, SF) inflammation. We compared the systemic level of cytokines/chemokine in OA patients’ and controls’ plasma with their local level in SF using a 44 plex screen. The level of 27 cytokines and chemokines was consistently measured in both plasma and SF. The data showed that the levels of cytokines and chemokines in OA plasma display limited correlation to their counterpart in SF. The level of synovial IL-8 and MIP-1α and VEGFA in OA patients, but not their plasma level, where the only cytokines that displayed a significant correlation to the observed lubricinO-linked glycosylation truncation. These cytokines were also shown to be upregulated exposing fibroblast like synoviocytes from healthy and OA patients to recombinant lubricin with truncated glycans mainly consisting of Tn-antigens, while lubricin with sialylated and non-sialylated T anigens did not have any effect. The data suggest that truncated glycans of lubricin, as found in OA, promotes the synovial cytokine production and exerebate the local synovial inflammation.
Loss of histone methyltransferase SETD1B in oogenesis results in the redistribution of genomic histone 3 lysine 4 trimethylation
Authors: Hanna Courtney W. , Huang Jiahao , Belton Christian , Reinhardt Susanne , Dahl Andreas , Andrews Simon , Stewart A. Francis , Kranz Andrea , Kelsey Gavin 
Published: March 2021

AbstractHistone 3 lysine 4 trimethylation (H3K4me3) is an epigenetic mark found at gene promoters and CpG islands. H3K4me3 is essential for mammalian development, yet mechanisms underlying its genomic targeting are poorly understood. H3K4me3 methyltransferases SETD1B and MLL2 are essential for oogenesis. We investigated changes in H3K4me3 inSetd1bconditional knockout (cKO) oocytes using ultra-low input ChIP-seq, with comparisons to DNA methylation and gene expression analyses. H3K4me3 was redistributed inSetd1bcKO oocytes showing losses at active gene promoters associated with downregulated gene expression. Remarkably, many regions also gained H3K4me3, in particular those that were DNA hypomethylated, transcriptionally inactive and CpG-rich, which are hallmarks of MLL2 targets. Consequently, loss of SETD1B disrupts the balance between MLL2 andde novoDNA methyltransferases in determining the epigenetic landscape during oogenesis. Our work reveals two distinct, complementary mechanisms of genomic targeting of H3K4me3 in oogenesis, with SETD1B linked to gene expression and MLL2 to CpG content.Graphical AbstractIn oogenesis, SETD1B and CXXC1 target H3K4me3 to actively transcribed gene promoters, while MLL2 targets transcriptionally inactive regions based on underlying CpG composition (upper panel). When SETD1B is ablated, H3K4me3 is lost at a subset of active promoters, resulting in downregulation of transcription (lower panel). Loss of SETD1B alters the activity of MLL2, permitting MLL2 to deposit H3K4me3 at CpG-rich regions, many of which should otherwise be DNA methylated. Thus, it is evident that MLL2 and de novo DNMTs compete for genomic occupancy late in oogenesis, and loss of SETD1B disrupts the balance of these mechanisms.
Reconstituting the genusMycobacterium
Authors: Meehan Conor J , Barco Roman A. , Loh Yong-Hwee E , Cogneau Sari , Rigouts Leen 
Published: March 2021

AbstractThe definition of a genus has wide ranging implications both in terms of binomial species names and also evolutionary relationships. In recent years, the definition of the genusMycobacteriumhas been debated due to the proposed split of this genus into five new genera (Mycolicibacterium, Mycolicibacter, Mycolicibacillus, Mycobacteroidesand an emendedMycobacterium). Since this group of species contains many important obligate and opportunistic pathogens, it is important that any renaming of species is does not cause confusion in clinical treatment as outlined by thenomen periculosumrule (56a) of the Prokaryotic Code.In this study, we evaluated the proposed and original genus boundaries for the mycobacteria, to determine if the split into five genera was warranted. By combining multiple approaches for defining genus boundaries (16S rRNA gene similarity, amino acid identity index, average nucleotide identity, alignment fraction and percentage of conserved proteins) we show that the original genusMycobacteriumis strongly supported over the proposed five-way split. Thus, we propose that the original genus label be reapplied to all species within this group, with the proposed five genera used as sub-genus complex names.
The feedback regulator Nord controls Dpp/BMP signaling via extracellular interaction with Dally in theDrosophilawing
Authors: Akiyama Takuya , Seidel Chris W. , Gibson Matthew C. 
Published: March 2021

AbstractTheDrosophilaBMP 2/4 homologue Decapentaplegic (Dpp) acts as a morphogen to regulate diverse developmental processes, including wing morphogenesis. Transcriptional feedback regulation of this pathway ensures tightly controlled signaling outputs to generate the precise pattern of the adult wing. Nevertheless, few direct Dpp target genes have been explored and our understanding of feedback regulation remains incomplete. Here, we employ transcriptional profiling followingdppconditional knockout to identifynord, a novel Dpp/BMP feedback regulator. Nord mutants generated by CRISPR/Cas9 mutagenesis produce a smaller wing and display low penetrance venation defects. At the molecular level,nordencodes a heparin-binding protein and we show that its overexpression is sufficient to antagonize Dpp/BMP signaling. Further, we demonstrate that Nord physically and genetically interacts with the Dpp/BMP co-receptor Dally. In sum we propose that Nord acts with Dally to fine tune Dpp/BMP signaling, with implications for both developmental and disease models.Impact statementFunctional analyses of theDrosophilahomologue of Neuron Derived Neurotrophic Factor reveal a new mode of extracellular heparan sulfate proteoglycan regulation required for proper morphogen action.
A New Type of Satellite associated with Cassava Mosaic Begomoviruses
Authors: Aimone Catherine D. , De León Leandro , Dallas Mary M. , Ndunguru Joseph , Ascencio-Ibáñez José T. , Hanley-Bowdoin Linda 
Published: March 2021

AbstractCassava mosaic disease (CMD), which is caused by single-stranded DNA begomoviruses, severely limits cassava production across Africa. A previous study showed that CMD symptom severity and viral DNA accumulation increase in cassava in the presence of a DNA sequence designated as SEGS-2 (sequenceenhancinggeminivirussymptoms). We report here that when SEGS-2 is co-inoculated withAfrican cassava mosaic virus(ACMV) ontoArabidopsis thaliana, viral symptoms increase. TransgenicArabidopsiswith an integrated copy of SEGS-2 inoculated with ACMV also display increased symptom severity and viral DNA levels. Moreover, SEGS-2 enablesCabbage leaf curl virus(CaLCuV) to infect a geminivirus resistant Arabidopsis accession. Although SEGS-2 is related to cassava genomic sequences, an earlier study showed that it occurs as episomes and is packaged into virions in CMD-infected cassava and viruliferous whiteflies. We identified SEGS-2 episomes in SEGS-2 transgenic Arabidopsis. The episomes occur as both double-stranded and single-stranded DNA, with the single-stranded form packaged into virions. In addition, SEGS-2 episomes replicate in tobacco protoplasts in the presence, but not the absence, of ACMV DNA-A. SEGS-2 episomes contain a SEGS-2 derived promoter and an open reading frame with the potential to encode a 75-amino acid protein. An ATG mutation at the beginning of the SEGS-2 coding region does not enhance ACMV infection in Arabidopsis. Together, the results established that SEGS-2 is a new type of begomovirus satellite that enhances viral disease through the action of a SEGS-2 encoded protein that may also be encoded in the cassava genome.IMPORTANCECassava is an important root crop in the developing world and a food and income crop for more than 300 million African farmers. Cassava is rising in global importance and trade as the demands for biofuels and commercial starch increase. More than half of the world’s cassava is produced in Africa, where it is primarily grown by smallholder farmers, many of whom are from the poorest villages. Although cassava can grow under high temperature, drought and poor soil conditions, its production is severely limited by viral diseases. Cassava mosaic disease (CMD) is one of the most important viral diseases of cassava and can cause up to 100% yield losses. We provide evidence that SEGS-2, which was originally isolated from cassava crops displaying severe and atypical CMD symptoms in Tanzanian fields, is a novel begomovirus satellite that can compromise the development of durable CMD resistance.