bluuebunny/crossref_metadata_2025_split huggingface dataset:
The carrot monoterpene synthase gene cluster on chromosome 4 harbours genes encoding flavour-associated sabinene synthases
Authors: Reichardt Sven , Budahn Holger , Lamprecht Dominic , Riewe David , Ulrich Detlef , Dunemann Frank , Kopertekh Lilya 
Published: December 2020

AbstractIn plants, low molecular weight terpenes produced by terpene synthases (TPS) contribute to multiple ecologically and economically important traits. The present study investigates a carrot terpene synthase gene cluster on chromosome 4 associated with volatile monoterpene production. Two carrot mutants,yellowandcola, which are contrasting in the content of low molecular weight terpenes, were crossed to develop an F2mapping population. The mapping analysis revealed overlapping QTLs on chromosome 4 for sabinene, α-thujene, α-terpinene, γ-terpinene, terpinen-4-ol and 4-carene. The genomic region of this locus includes a cluster of five terpene synthase genes (DcTPS04,DcTPS26, DcTPS27, DcTPS54andDcTPS55).DcTPS04andDcTPS54displayed genotype- and tissue-specific variation in gene expression. Based on the QTL mapping results and the gene expression patterns,DcTPS04andDcTPS54were selected for functional characterization. In vitro enzyme assays showed thatDcTPS54 is a single-product enzyme catalysing the formation of sabinene, whereasDcTPS04 is a multiple-product terpene synthase producing α-terpineol as a major product and four additional products including sabinene, β-limonene, β-pinene and myrcene. Furthermore, we developed a functional molecular marker that could discriminate carrot genotypes with different sabinene content in a set of 85 accessions.
A chromosome-scale genome assembly of a diploid alfalfa, the progenitor of autotetraploid alfalfa
Authors: Li Ao , Liu Ai , Du Xin , Chen Jin-Yuan , Yin Mou , Hu Hong-Yin , Shrestha Nawal , Wu Sheng-Dan , Wang Hai-Qing , Dou Quan-Wen , Liu Zhi-Peng , Liu Jian-Quan , Yang Yong-Zhi , Ren Guang-Peng 
Published: December 2020

AbstractAlfalfa (Medicago sativa L.) is one of the most important and widely cultivated forage crops. It is commonly used as a vegetable and medicinal herb because of its excellent nutritional quality and significant economic value. Based on Illumina, Nanopore and Hi-C data, we assembled a chromosome-scale assembly of Medicago sativa spp. caerulea (voucher PI464715), the direct diploid progenitor of autotetraploid alfalfa. The assembled genome comprises 793.2 Mb of genomic sequence and 47,202 annotated protein-coding genes. The contig N50 length is 3.86 Mb. This genome is almost twofold larger and contains more annotated protein-coding genes than that of its close relative, Medicago truncatula (420 Mb and 44,623 genes). The more expanded gene families compared with those in M. truncatula and the expansion of repetitive elements rather than whole-genome duplication (i.e., the two species share the ancestral Papilionoideae whole-genome duplication event) may have contributed to the large genome size of M. sativa spp. caerulea. Comparative and evolutionary analyses revealed that M. sativa spp. caerulea diverged from M. truncatula ~5.2 million years ago, and the chromosomal fissions and fusions detected between the two genomes occurred during the divergence of the two species. In addition, we identified 489 resistance (R) genes and 82 and 85 candidate genes involved in the lignin and cellulose biosynthesis pathways, respectively. The near-complete and accurate diploid alfalfa reference genome obtained herein serves as an important complement to the recently assembled autotetraploid alfalfa genome and will provide valuable genomic resources for investigating the genomic architecture of autotetraploid alfalfa as well as for improving breeding strategies in alfalfa.
Multiomics analyses unveil the involvement of microRNAs in pear fruit senescence under high- or low-temperature conditions
Authors: Gu Chao , Xu Huan-Yu , Zhou Yu-Hang , Yao Jia-Long , Xie Zhi-Hua , Chen Yang-Yang , Zhang Shao-Ling 
Published: December 2020

AbstractSenescence leads to declines in fruit quality and shortening of shelf life. It is known that low temperatures (LTs) efficiently delay fruit senescence and that high temperatures (HTs) accelerate senescence. However, the molecular mechanism by which temperature affects senescence is unclear. Herein, through multiomics analyses of fruits subjected to postharvest HT, LT, and room temperature treatments, a total of 56 metabolic compounds and 700 mRNAs were identified to be associated with fruit senescence under HT or LT conditions. These compounds could be divided into antisenescent (I→III) and prosenescent (IV→VI) types. HT affected the expression of 202 mRNAs to enhance the biosynthesis of prosenescent compounds of types V and VI and to inhibit the accumulation of antisenescent compounds of types II and III. LT affected the expression of 530 mRNAs to promote the accumulation of antisenescent compounds of types I and II and to impede the biosynthesis of prosenescent compounds of types IV and V. Moreover, 16 microRNAs were isolated in response to HT or LT conditions and interacted with the mRNAs associated with fruit senescence under HT or LT conditions. Transient transformation of pear fruit showed that one of these microRNAs, Novel_188, can mediate fruit senescence by interacting with its target Pbr027651.1. Thus, both HT and LT conditions can affect fruit senescence by affecting microRNA–mRNA interactions, but the molecular networks are different in pear fruit.
Integrated transcriptome and proteome analysis provides insight into chilling-induced dormancy breaking in Chimonanthus praecox
Authors: Li Zhineng , Liu Ning , Zhang Wei , Wu Chunyu , Jiang Yingjie , Ma Jing , Li Mingyang , Sui Shunzhao 
Published: December 2020

AbstractChilling has a critical role in the growth and development of perennial plants. The chilling requirement (CR) for dormancy breaking largely depends on the species. However, global warming is expected to negatively affect chilling accumulation and dormancy release in a wide range of perennial plants. Here, we usedChimonanthus praecoxas a model to investigate the CR for dormancy breaking under natural and artificial conditions. We determined the minimum CR (570 chill units, CU) needed for chilling-induced dormancy breaking and analyzed the transcriptomes and proteomes of flowering and non-flowering flower buds (FBs, anther and ovary differentiation completed) with different CRs. The concentrations of ABA and GA3 in the FBs were also determined using HPLC. The results indicate that chilling induced an upregulation of ABA levels and significant downregulation ofSHORT VEGETATIVE PHASE(SVP) andFLOWERING LOCUS T(FT) homologs at the transcript level in FBs when the accumulated CR reached 570 CU (IB570) compared to FBs in November (FB.Nov, CK) and nF16 (non-flowering FBs after treatment at 16 °C for −300 CU), which suggested that dormancy breaking of FBs could be regulated by the ABA-mediated SVP-FT module. Overexpression inArabidopsiswas used to confirm the function of candidate genes, and early flowering was induced in35S::CpFT1transgenic lines. Our data provide insight into the minimum CR (570 CU) needed for chilling-induced dormancy breaking and its underlying regulatory mechanism inC. praecox, which provides a new tool for the artificial regulation of flowering time and a rich gene resource for controlling chilling-induced blooming.
Genome sequencing and phylogenetic analysis of allotetraploid Salix matsudana Koidz
Authors: Zhang Jian , Yuan Huwei , Li Yujuan , Chen Yanhong , Liu Guoyuan , Ye Meixia , Yu Chunmei , Lian Bolin , Zhong Fei , Jiang Yuna , Xu Jichen 
Published: December 2020

AbstractPolyploidy is a common phenomenon among willow species. In this study, genome sequencing was conducted for Salix matsudana Koidz (also named Chinese willow), an important greening and arbor tree species, and the genome of this species was compared with those of four other tree species in Salicaceae. The total genome sequence of S. matsudana was 655.72 Mb in size, with repeated sequences accounting for 45.97% of the total length. In total, 531.43 Mb of the genome sequence could be mapped onto 38 chromosomes using the published genetic map as a reference. The genome of S. matsudana could be divided into two groups, the A and B genomes, through homology analysis with the genome of Populus trichocarpa, and the A and B genomes contained 23,985 and 25,107 genes, respectively. 4DTv combined transposon analysis predicted that allotetraploidy in S. matsudana appeared ~4 million years ago. The results from this study will help reveal the evolutionary history of S. matsudana and lay a genetic basis for its breeding.
A macrophage-specific lncRNA regulates apoptosis and atherosclerosis by tethering HuR in the nucleus
Authors: Simion Viorel , Zhou Haoyang , Haemmig Stefan , Pierce Jacob B. , Mendes Shanelle , Tesmenitsky Yevgenia , Pérez-Cremades Daniel , Lee James F. , Chen Alex F. , Ronda Nicoletta , Papotti Bianca , Marto Jarrod A. , Feinberg Mark W. 
Published: December 2020

AbstractLong non-coding RNAs (lncRNAs) are emerging regulators of pathophysiological processes including atherosclerosis. Using RNA-seq profiling of the intima of lesions, here we identify a macrophage-specific lncRNA MAARS (Macrophage-Associated Atherosclerosis lncRNA Sequence). Aortic intima expression of MAARS increases by 270-fold with atherosclerotic progression and decreases with regression by 60%. MAARS knockdown reduces atherosclerotic lesion formation by 52% in LDLR−/− mice, largely independent of effects on lipid profile and inflammation, but rather by decreasing macrophage apoptosis and increasing efferocytosis in the vessel wall. MAARS interacts with HuR/ELAVL1, an RNA-binding protein and important regulator of apoptosis. Overexpression and knockdown studies verified MAARS as a critical regulator of macrophage apoptosis and efferocytosis in vitro, in an HuR-dependent manner. Mechanistically, MAARS knockdown alters HuR cytosolic shuttling, regulating HuR targets such as p53, p27, Caspase-9, and BCL2. These findings establish a mechanism by which a macrophage-specific lncRNA interacting with HuR regulates apoptosis, with implications for a broad range of vascular disease states.
Non-invasive focusing and imaging in scattering media with a fluorescence-based transmission matrix
Authors: Boniface Antoine , Dong Jonathan , Gigan Sylvain 
Published: December 2020

AbstractIn biological microscopy, light scattering represents the main limitation to image at depth. Recently, a set of wavefront shaping techniques has been developed in order to manipulate coherent light in strongly disordered materials. The Transmission Matrix approach has shown its capability to inverse the effect of scattering and efficiently focus light. In practice, the matrix is usually measured using an invasive detector or low-resolution acoustic guide stars. Here, we introduce a non-invasive and all-optical strategy based on linear fluorescence to reconstruct the transmission matrices, to and from a fluorescent object placed inside a scattering medium. It consists in demixing the incoherent patterns emitted by the object using low-rank factorizations and phase retrieval algorithms. We experimentally demonstrate the efficiency of this method through robust and selective focusing. Additionally, from the same measurements, it is possible to exploit memory effect correlations to image and reconstruct extended objects. This approach opens up a new route towards imaging in scattering media with linear or non-linear contrast mechanisms.
Reduced efficacy of HIV-1 integrase inhibitors in patients with drug resistance mutations in reverse transcriptase
Authors: Siedner Mark J. , Moorhouse Michelle A. , Simmons Bryony , de Oliveira Tulio , Lessells Richard , Giandhari Jennifer , Kemp Stephen A. , Chimukangara Benjamin , Akpomiemie Godspower , Serenata Celicia M. , Venter Willem D. F. , Hill Andrew , Gupta Ravindra K. 
Published: December 2020

AbstractLittle is known about the impact of pretreatment drug resistance (PDR) on the efficacy of second generation integrase inhibitors. We sequenced pretreatment plasma specimens from the ADVANCE trial (NCT03122262). Our primary outcome was 96-week virologic success, defined as a sustained viral load <1000 copies/mL from 12 weeks onwards, <200 copies/mL from 24 weeks onwards, and <50 copies/mL after 48 weeks. Here we report how this outcome was impacted by PDR, defined by the World Health Organization (WHO) mutation list. Of 1053 trial participants, 874 (83%) have successful sequencing, including 289 (33%) randomized to EFV-based therapy and 585 (67%) randomized to DTG-based therapy. Fourteen percent (122/874) have ≥1 WHO-defined mutation, of which 98% (120/122) are NNRTI mutations. Rates of virologic suppression are lower in the total cohort among those with PDR 65% (73/112) compared to those without PDR (85% [605/713], P < 0.001), and for those on EFV-based treatment (60% [12/20] vs 86% [214/248], P = 0.002) and for those on DTG-based treatment (61/92 [66%] vs 84% [391/465] P < 0.001, P for interaction by regimen 0.49). Results are similar in multivariable models adjusted for clinical characteristics and adherence. NNRTI resistance prior to treatment is associated with long-term failure of integrase inhibitor-containing first-line regimens, and portends high rates of first-line failure in sub Saharan Africa.
Quantitative modeling predicts mechanistic links between pre-treatment microbiome composition and metronidazole efficacy in bacterial vaginosis
Authors: Lee Christina Y. , Cheu Ryan K. , Lemke Melissa M. , Gustin Andrew T. , France Michael T. , Hampel Benjamin , Thurman Andrea R. , Doncel Gustavo F. , Ravel Jacques , Klatt Nichole R. , Arnold Kelly B. 
Published: December 2020

AbstractBacterial vaginosis is a condition associated with adverse reproductive outcomes and characterized by a shift from a Lactobacillus-dominant vaginal microbiota to a polymicrobial microbiota, consistently colonized by strains of Gardnerella vaginalis. Metronidazole is the first-line treatment; however, treatment failure and recurrence rates remain high. To understand complex interactions between Gardnerella vaginalis and Lactobacillus involved in efficacy, here we develop an ordinary differential equation model that predicts bacterial growth as a function of metronidazole uptake, sensitivity, and metabolism. The model shows that a critical factor in efficacy is Lactobacillus sequestration of metronidazole, and efficacy decreases when the relative abundance of Lactobacillus is higher pre-treatment. We validate results in Gardnerella and Lactobacillus co-cultures, and in two clinical cohorts, finding women with recurrence have significantly higher pre-treatment levels of Lactobacillus relative to bacterial vaginosis–associated bacteria. Overall results provide mechanistic insight into how personalized differences in microbial communities influence vaginal antibiotic efficacy.
Functionally impaired plasmacytoid dendritic cells and non-haematopoietic sources of type I interferon characterize human autoimmunity
Authors: Psarras Antonios , Alase Adewonuola , Antanaviciute Agne , Carr Ian M. , Md Yusof Md Yuzaiful , Wittmann Miriam , Emery Paul , Tsokos George C. , Vital Edward M. 
Published: December 2020

AbstractAutoimmune connective tissue diseases arise in a stepwise fashion from asymptomatic preclinical autoimmunity. Type I interferons have a crucial role in the progression to established autoimmune diseases. The cellular source and regulation in disease initiation of these cytokines is not clear, but plasmacytoid dendritic cells have been thought to contribute to excessive type I interferon production. Here, we show that in preclinical autoimmunity and established systemic lupus erythematosus, plasmacytoid dendritic cells are not effector cells, have lost capacity for Toll-like-receptor-mediated cytokine production and do not induce T cell activation, independent of disease activity and the blood interferon signature. In addition, plasmacytoid dendritic cells have a transcriptional signature indicative of cellular stress and senescence accompanied by increased telomere erosion. In preclinical autoimmunity, we show a marked enrichment of an interferon signature in the skin without infiltrating immune cells, but with interferon-κ production by keratinocytes. In conclusion, non-hematopoietic cellular sources, rather than plasmacytoid dendritic cells, are responsible for interferon production prior to clinical autoimmunity.
Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure
Authors: Zrimec Jan , Börlin Christoph S. , Buric Filip , Muhammad Azam Sheikh , Chen Rhongzen , Siewers Verena , Verendel Vilhelm , Nielsen Jens , Töpel Mats , Zelezniak Aleksej 
Published: December 2020

AbstractUnderstanding the genetic regulatory code governing gene expression is an important challenge in molecular biology. However, how individual coding and non-coding regions of the gene regulatory structure interact and contribute to mRNA expression levels remains unclear. Here we apply deep learning on over 20,000 mRNA datasets to examine the genetic regulatory code controlling mRNA abundance in 7 model organisms ranging from bacteria to Human. In all organisms, we can predict mRNA abundance directly from DNA sequence, with up to 82% of the variation of transcript levels encoded in the gene regulatory structure. By searching for DNA regulatory motifs across the gene regulatory structure, we discover that motif interactions could explain the whole dynamic range of mRNA levels. Co-evolution across coding and non-coding regions suggests that it is not single motifs or regions, but the entire gene regulatory structure and specific combination of regulatory elements that define gene expression levels.
Conformational maps of human 20S proteasomes reveal PA28- and immuno-dependent inter-ring crosstalks
Authors: Lesne Jean , Locard-Paulet Marie , Parra Julien , Zivković Dušan , Menneteau Thomas , Bousquet Marie-Pierre , Burlet-Schiltz Odile , Marcoux Julien 
Published: December 2020

AbstractHydrogen-Deuterium eXchange coupled to Mass Spectrometry (HDX-MS) is now common practice in structural biology. However, it is most of the time applied to rather small oligomeric complexes. Here, we report on the use of HDX-MS to investigate conformational differences between the human standard 20S (std20S) and immuno 20S (i20s) proteasomes alone or in complex with PA28αβ or PA28γ activators. Their solvent accessibility is analyzed through a dedicated bioinformatic pipeline including stringent statistical analysis and 3D visualization. These data confirm the existence of allosteric differences between the std20S and i20S at the surface of the α-ring triggered from inside the catalytic β-ring. Additionally, binding of the PA28 regulators to the 20S proteasomes modify solvent accessibility due to conformational changes of the β-rings. This work is not only a proof-of-concept that HDX-MS can be used to get structural insights on large multi-protein complexes in solution, it also demonstrates that the binding of the std20S or i20S subtype to any of its PA28 activator triggers allosteric changes that are specific to this 20S/PA28 pair.
Hippocampal adult-born granule cells drive network activity in a mouse model of chronic temporal lobe epilepsy
Authors: Sparks F. T. , Liao Z. , Li W. , Grosmark A. , Soltesz I. , Losonczy A. 
Published: December 2020

AbstractTemporal lobe epilepsy (TLE) is characterized by recurrent seizures driven by synchronous neuronal activity. The reorganization of the dentate gyrus (DG) in TLE may create pathological conduction pathways for synchronous discharges in the temporal lobe, though critical microcircuit-level detail is missing from this pathophysiological intuition. In particular, the relative contribution of adult-born (abGC) and mature (mGC) granule cells to epileptiform network events remains unknown. We assess dynamics of abGCs and mGCs during interictal epileptiform discharges (IEDs) in mice with TLE as well as sharp-wave ripples (SPW-Rs) in healthy mice, and find that abGCs and mGCs are desynchronized and differentially recruited by IEDs compared to SPW-Rs. We introduce a neural topic model to explain these observations, and find that epileptic DG networks organize into disjoint, cell-type specific pathological ensembles in which abGCs play an outsized role. Our results characterize identified GC subpopulation dynamics in TLE, and reveal a specific contribution of abGCs to IEDs.
The liverwort oil body is formed by redirection of the secretory pathway
Authors: Kanazawa Takehiko , Morinaka Hatsune , Ebine Kazuo , Shimada Takashi L. , Ishida Sakiko , Minamino Naoki , Yamaguchi Katsushi , Shigenobu Shuji , Kohchi Takayuki , Nakano Akihiko , Ueda Takashi 
Published: December 2020

AbstractEukaryotic cells acquired novel organelles during evolution through mechanisms that remain largely obscure. The existence of the unique oil body compartment is a synapomorphy of liverworts that represents lineage-specific acquisition of this organelle during evolution, although its origin, biogenesis, and physiological function are yet unknown. We find that two paralogous syntaxin-1 homologs in the liverwort Marchantia polymorpha are distinctly targeted to forming cell plates and the oil body, suggesting that these structures share some developmental similarity. Oil body formation is regulated by an ERF/AP2-type transcription factor and loss of the oil body increases M. polymorpha herbivory. These findings highlight a common strategy for the acquisition of organelles with distinct functions in plants, via periodical redirection of the secretory pathway depending on cellular phase transition.
Bioinformatic analysis of membrane and associated proteins in murine cardiomyocytes and human myocardium
Authors: Lee Shin-Haw , Hadipour-Lakmehsari Sina , Kim Da Hye , Di Paola Michelle , Kuzmanov Uros , Shah Saumya , Lee Joseph Jong-Hwan , Kislinger Thomas , Sharma Parveen , Oudit Gavin Y. , Gramolini Anthony O. 
Published: December 2020

AbstractIn the current study we examined several proteomic- and RNA-Seq-based datasets of cardiac-enriched, cell-surface and membrane-associated proteins in human fetal and mouse neonatal ventricular cardiomyocytes. By integrating available microarray and tissue expression profiles with MGI phenotypic analysis, we identified 173 membrane-associated proteins that are cardiac-enriched, conserved amongst eukaryotic species, and have not yet been linked to a ‘cardiac’ Phenotype-Ontology. To highlight the utility of this dataset, we selected several proteins to investigate more carefully, including FAM162A, MCT1, and COX20, to show cardiac enrichment, subcellular distribution and expression patterns in disease. We performed three-dimensional confocal imaging analysis to validate subcellular localization and expression in adult mouse ventricular cardiomyocytes. FAM162A, MCT1, and COX20 were expressed differentially at the transcriptomic and proteomic levels in multiple models of mouse and human heart diseases and may represent potential diagnostic and therapeutic targets for human dilated and ischemic cardiomyopathies. Altogether, we believe this comprehensive cardiomyocyte membrane proteome dataset will prove instrumental to future investigations aimed at characterizing heart disease markers and/or therapeutic targets for heart failure.