bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mediterranean oaks harbor more specific soil microbes at the dry end of a precipitation gradient
Authors: Rutten Gemma , Gómez-Aparicio Lorena , Frey Beat 
Published: May 2020

AbstractBackgroundRecent evidence suggests that soil microbial communities can regulate plant community dynamics. In addition, the drought tolerance of plants can be enhanced by soil microbes. So far, few studies have assessed the variation in the microbiome of specific plant species along environmental gradients. Yet understanding these dynamics is essential to improve predictions of plant-soil feedbacks and the consequences of ongoing climate changes. Here we characterized the soil microbiome of two co-occurring Mediterranean oaks along a precipitation gradient, using amplicon sequencing of phylogenetic marker genes for prokaryotes and fungi. Additionally, we identified tree-specific and locally-specific microbes potentially responsible for tree community dynamics.ResultsWe show that two co-occurring, evergreen Mediterranean oak species harbor distinct microbiomes along a precipitation gradient. The soil microbial diversity increased along the precipitation gradient, for prokaryotic α and β diversity and for fungal β diversity.Quercus ilexharbored richer fungal communities thanQuercus suber, and host-specific taxa more often belonged to fungi than to prokaryotes. Notably, the microbial communities at the dry end of the precipitation gradient harbored more locally-specific prokaryotic and fungal taxa than the microbial communities with a higher diversity, at the wet end of the gradient, suggesting higher specialization in drier areas.ConclusionsEven congeneric tree species, belonging to the same functional group, can harbor distinct and specific soil microbiomes. These microbiomes become more similar and consist of more specialized taxa under drier compared with wetter conditions. With this, our study offers a step towards a better understanding of the context-dependency of plant-soil feedbacks by going beyond α and β diversities and focusing on specialized taxa potentially driving community changes along environmental gradients. We hope that our study will stimulate future research assessing the importance of context-dependency of interactions between plants and soil communities in a changing world.
Recurrent evolution of two competing haplotypes in an insect DNA virus
Authors: Hill Tom , Unckless Robert L. 
Published: May 2020

AbstractHosts and viruses are constantly evolving in response to each other: as hosts attempt to suppress the virus, the virus attempts to evade and suppress the host’s immune system. This arms race results in the evolution of novel pathways in both the host and virus to gain the upper hand. Here we describe the coevolution betweenDrosophilaspecies and a common and virulent DNA virus. We identify two distinct viral types that differ 100-fold in viral titer in infected individuals, with similar effects across multiple species. Our analysis suggests that one of the viral types appears to have recurrently evolved at least 4 times in the past ∼30,000 years, including in another geographically distinct species, due to the high effective mutation rate which increases with titer. The higher titer viral type is associated with suppression of the host immune system and an increased transmission rate compared to the low viral titer type. Both types are maintained in all populations, likely due to an increased virulence in the high titer type creating a trade-off between effective transmission and virulence and resulting in nearly equal reproduction rates (R0) in both types. Together these results suggest that the reciprocal selective pressures caused by the co-evolution between host and virus has resulted in this recurrently evolving relationship.
Unique roles of ATAC and SAGA - KAT2A complexes in normal and malignant hematopoiesis
Authors: Arede Liliana , Foerner Elena , Wind Selinde , Kulkarni Rashmi , Domingues Ana Filipa , Kleinwaechter Svenja , Gupta Shikha , Scheer Elisabeth , Tora Laszlo , Pina Cristina 
Published: May 2020

ABSTRACTEpigenetic histone modifiers are key players in cell fate decisions. Significant research has focused on their enzymatic activity, but less is known about the contextual role of the complexes they integrate. We focus on KAT2A, a histone acetyltransferase we recently associated with leukemia stem cell maintenance, and which participates in ATAC and SAGA complexes. We show that ATAC is uniquely required for maintenance of normal and leukemia stem and progenitor cells, while SAGA more specifically contributes to cell identity. This dichotomy sets a paradigm for investigating epigenetic activities in their macromolecular context and informs epigenetic regulator targeting for translational purposes.
A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of novel growth-associated genes
Authors: Uengwetwanit Tanaporn , Pootakham Wirulda , Nookaew Intawat , Sonthirod Chutima , Angthong Pacharaporn , Sittikankaew Kanchana , Rungrassamee Wanilada , Arayamethakorn Sopacha , Wongsurawat Thidathip , Jenjaroenpun Piroon , Sangsrakru Duangjai , Leelatanawit Rungnapa , Khudet Jutatip , Koehorst Jasper J. , Schaap Peter J. , dos Santos Vitor Martins , Tangy Frédéric , Karoonuthaisiri Nitsara 
Published: May 2020

AbstractThe black tiger shrimp (Penaeus monodon) is one of the most prominent farmed crustacean species with an average annual global production of 0.5 million tons in the last decade. To ensure sustainable and profitable production through genetic selective breeding programs, several research groups have attempted to generate a reference genome using short-read sequencing technology. However, the currently available assemblies lack the contiguity and completeness required for accurate genome annotation due to the highly repetitive nature of the genome and technical difficulty in extracting high-quality, high-molecular weight DNA in this species. Here, we report the first chromosome-level whole-genome assembly ofP. monodon. The combination of long-read Pacific Biosciences (PacBio) and long-range Chicago and Hi-C technologies enabled a successful assembly of this first high-quality genome sequence. The final assembly covered 2.39 Gb (92.3% of the estimated genome size) and contained 44 pseudomolecules, corresponding to the haploid chromosome number. Repetitive elements occupied a substantial portion of the assembly (62.5%), highest of the figures reported among crustacean species. The availability of this high-quality genome assembly enabled the identification of novel genes associated with rapid growth in the black tiger shrimp through the comparison of hepatopancreas transcriptome of slow-growing and fast-growing shrimps. The results highlighted several gene groups involved in nutrient metabolism pathways and revealed 67 newly identified growth-associated genes. Our high-quality genome assembly provides an invaluable resource for accelerating the development of improved shrimp strain in breeding programs and future studies on gene regulations and comparative genomics.
Pituitary Tumor Transforming Gene 1orchestrates gene regulatory variation in mouse ventral midbrain during aging
Authors: Gui Yujuan , Thomas Mélanie H. , Garcia Pierre , Karout Mona , Halder Rashi , Michelucci Alessandro , Kollmus Heike , Zhou Cuiqi , Melmed Shlomo , Schughart Klaus , Balling Rudi , Mittelbronn Michel , Nadeau Joseph H. , Williams Robert W. , Sauter Thomas , Buttini Manuel , Sinkkonen Lasse 
Published: May 2020

AbstractBackgroundDopaminergic neurons in the midbrain are of particular interest due to their role in diseases such as Parkinson’s disease and schizophrenia. Genetic variation between individuals can affect the integrity and function of dopaminergic neurons but the DNA variants and molecular cascades modulating dopaminergic neurons and other cells types of ventral midbrain remain poorly defined. Three genetically diverse inbred mouse strains — C57BL/6J, A/J, and DBA/2J — differ significantly in their genomes (~7 million variants), motor and cognitive behavior, and susceptibility to neurotoxins.ResultsTo further dissect the underlying molecular networks responsible for these variable phenotypes, we generated RNA-seq and ChIP-seq data from ventral midbrains of the 3 mouse strains. We defined 1000–1200 transcripts that are differentially expressed among them. These widespread differences may be due to altered activity or expression of upstream transcription factors. Interestingly, transcription factors were significantly underrepresented among the differentially expressed genes, and only one TF,Pttg1, showed significant differences among all strains. The changes inPttg1expression were accompanied by consistent alterations in histone H3 lysine 4 trimethylation atPttg1transcription start site. The ventral midbrain transcriptome of three-month-old C57BL/6J congenicPttg1-/-mutants was only modestly altered, but shifted towards that of A/J and DBA/2J in nine-month-old mice. Principle component analysis identified the genes underlying the transcriptome shift and deconvolution of these bulk RNA-seq changes using midbrain single cell RNA-seq data suggested that the changes were occurring in several different cell types, including neurons, oligodendrocytes, and astrocytes.ConclusionTaken together, our results show thatPttg1contributes to gene regulatory variation between mouse strains and influences mouse midbrain transcriptome during aging.
scRNA-seq analysis of colon and esophageal tumors uncovers abundant microbial reads in myeloid cells undergoing proinflammatory transcriptional alterations
Authors: Robinson Welles , Stone Joshua K. , Schischlik Fiorella , Gasmi Billel , Kelly Michael C. , Seibert Charlie , Dadkhah Kimia , Gertz E. Michael , Lee Joo Sang , Zhu Kaiyuan , Ma Lichun , Wang Xin Wei , Sahinalp S. Cenk , Patro Rob , Leiserson Mark D.M. , Harris Curtis C. , Schäffer Alejandro A. , Ruppin Eytan 
Published: May 2020

AbstractThe study of the tumor microbiome has been garnering increased attention. We developed a computational pipeline (CSI-Microbes) for identifying microbial reads from single-cell RNA sequencing (scRNA-seq) data. Using a series of controlled experiments and analyses, we performed the first systematic evaluation of the efficacy of recovering microbial UMIs by multiple scRNA-seq technologies, which identified the newer 10x chemistries (3’ v3 and 5’) as the best suited approach. Based on these findings, we analyzed patient esophageal and colorectal carcinomas and found that reads from distinct genera tend to co-occur in the same host cells, testifying to possible intracellular polymicrobial interactions. Microbial reads are disproportionately abundant within myeloid cells that upregulate proinflammatory cytokines likeIL1ΒandCXCL8and downregulate antigen processing and presentation (APP) pathways. The latter, however, are markedly upregulated in infected tumor cells. These results testify that intracellular bacteria predominately reside within co-opted myeloid cells, which inflame the tumor microenvironment and may influence immunotherapy response.
Indoleamine 2,3-dioxygenase-1 expressing aggregate bone marrow dendritic cell populations are associated with systemic T-cell compartment changes in chronic myelomonocytic leukemia
Authors: Mangaonkar Abhishek A. , Reichard Kaaren K. , Binder Moritz , Coltro Giacomo , Lasho Terra L. , Carr Ryan M. , Chiu April , Negron Vivian , Hefazi Mehrdad , Anagnostou Theodora , Villasboas Jose C , Gonsalves Wilson , Gangat Naseema , Shah Mithun , Alkhateeb Hassan B , Al-Kali Aref , Elliott Michelle A , Begna Kebede H , Wolanskyj-Spinner Alexandra P , Litzow Mark R , Hogan William J , Ansell Stephen M , Pardanani Animesh , Tefferi Ayalew , Patnaik Mrinal M. 
Published: May 2020

AbstractSystemic immune tolerance is not well-characterized in chronic myelomonocytic leukemia (CMML). Due to the presence of clonal plasmacytoid dendritic cells (pDC) in CMML, and the established association of lymph node indoleamine 2,3-dioxygenase-1 (IDO1)-positive (+) DC populations (IDC) with systemic immune tolerance in other malignant contexts, we sought to determine the association of IDO1 expression and bone marrow (BM) DC populations with systemic T-cell compartment changes using primary CMML patient samples (BM, plasma, and peripheral blood mononuclear cells) via immunohistochemistry (IHC), liquid chromatography-mass spectrometry (LC-MS), and time-of-flight mass cytometry (CyTOF). Our results highlight that aggregate BM IDC (CD123 and/or CD11c positive) occur in 33% CMML patients at any disease time-point (IHC), correlate with accentuated tryptophan catabolism (LC-MS, increased kynurenine level, median 4.7 versus 3 microM, P=0.049*), systemic regulatory T-cell expansion (CyTOF, %parent cell type, 14.5 versus 4.9%, P=0.04*) and play a role in disease progression, as evidenced by a higher rate of transformation to acute myeloid leukemia (41 versus 13%, P=0.002**), when compared to CMML patients without BM IDC. Our data also highlight a perturbed immune system in CMML with specific systemic immune signatures, particularly type 1, IL-17 producing helper T, CD4 terminal effector and natural killer cell suppression.Key PointsAggregate IDO1+ dendritic cell populations occur in the CMML bone marrow microenvironment, and their presence correlates with disease progression.Systemic immune microenvironment signatures in CMML indicate an altered T- and natural killer (NK)-cell balance. Specifically, suppression of type 1 helper T (Th1), IL-17 producing helper T (Th17), CD4 terminal effector and NK cells.IDO1+ bone marrow dendritic cell populations in CMML are associated with a T-cell compartment shift towards a regulatory T cell phenotype.
SCA-1 micro-heterogeneity in the fate decision of dystrophic fibro/adipogenic progenitors
Authors: Giuliani Giulio , Vumbaca Simone , Fuoco Claudia , Gargioli Cesare , Giorda Ezio , Massacci Giorgia , Palma Alessandro , Reggio Alessio , Riccio Federica , Vinci Maria , Castagnoli Luisa , Cesareni Gianni 
Published: May 2020

AbstractThe term micro-heterogeneity refers to non-genetic cell to cell variability observed in a bell-shaped distribution of the expression of a trait within a population. The contribution of micro-heterogeneity to physiology and pathology remains largely uncharacterised. To address such an issue, we investigated the impact of heterogeneity in skeletal muscle fibro/adipogenic progenitors (FAPs) isolated from an animal model of Duchenne muscular dystrophy (DMD), themdxmouse. FAPs play an essential role in muscle homeostasis. However, in pathological conditions or ageing, they are the source of intramuscular infiltrations of fibrotic or adipose tissue. By applying a multiplex flow cytometry assay, we characterised and purified frommdxmuscles two FAP cell states expressing different levels of SCA-1. The two cell states are morphologically identical and repopulate each other after several growth cycles. However, they differ in theirin vitrobehaviour. Cells expressing higher levels of SCA-1 (SCA1-High-FAPs) differentiate more readily into adipocytes while, when exposed to a fibrogenic stimulation, increase the expression ofCOL1A1mRNA. In addition, SCA1-High-FAPs proliferate more extensivelyex vivoand display more proliferating cells in dystrophic muscles. Adipogenesis of FAP cell states is inhibitedin vitroby leukocytes from young dystrophic mice, while leukocytes isolated from aged dystrophic mice are less effective in limiting the adipogenesis of SCA1-High-FAPs suggesting a differential regulatory effect of the microenvironment on micro-heterogeneity. Our data suggest that FAP micro-heterogeneity is modulated in pathological conditions and that this heterogeneity in turn may impact on the behaviour of mesenchymal cells in genetic diseases.
The effect of vascular health factors on white matter microstructure mediates age-related differences in executive function performance
Authors: Hoagey David A. , Lazarus Linh T.T. , Rodrigue Karen M. , Kennedy Kristen M. 
Published: May 2020

AbstractEven within healthy aging, vascular risk factors can detrimentally influence cognition, with executive functions (EF) particularly vulnerable. Fronto-parietal white matter (WM) connectivity in part, supports EF and may be particularly sensitive to vascular risk. Here, we utilized structural equation modeling in 184 healthy adults (aged 20-94 years of age) to test the hypotheses that: 1) fronto-parietal WM microstructure mediates age effects on EF; 2) higher blood pressure (BP) and white matter hyperintensity (WMH) burden influences this association. All participants underwent comprehensive cognitive and neuropsychological testing including tests of processing speed, executive function (with a focus on tasks that require switching and inhibition) and completed an MRI scanning session that included FLAIR imaging for semi-automated quantification of white matter hyperintensity burden and diffusion-weighted imaging for tractography. Structural equation models were specified with age (as a continuous variable) and blood pressure predicting within-tract WMH burden and fractional anisotropy predicting executive function and processing speed. Results indicated that fronto-parietal white matter of the genu of the corpus collosum, superior longitudinal fasciculus, and the inferior frontal occipital fasciculus (but not cortico-spinal tract) mediated the association between age and EF. Additionally, increased systolic blood pressure and white matter hyperintensity burden within these white matter tracts contribute to worsening white matter health and are important factors underlying age-brain-behavior associations. These findings suggest that aging brings about increases in both BP and WMH burden, which may be involved in the degradation of white matter connectivity and in turn, negatively impact executive functions as we age.
Expandability differences in learning transfer between computerized and non-computerized games
Authors: Shigyo Maki , Tamura Kaori , Okamoto Tsuyoshi 
Published: May 2020

AbstractComputerized and non-computerized games are used in training designed to improve cognitive function. However, it is unclear which properties of the games influence the transfer of cognitive performance. This study aimed to examine the expandability of this transfer according to the properties of training tools. We introduced two training tools (virtual and standard Rubik’s Cubes) and examined bidirectional transfer between the two cube types and transfer to other cognitive tasks. The results showed that transfer from the virtual cube to the standard cube was greater relative to that observed from the standard cube to the virtual cube. Regarding transfer to other tasks, cognitive transfer did not differ significantly between the virtual and standard cubes, but the training exerted beneficial effects. These results suggest that transfer expandability differed between computerized and non-computerized games. The findings of the study could contribute to the provision of an effective cognitive training programme.
A bimodular PKS platform that expands the biological design space
Authors: Zargar Amin , Valencia Luis , Wang Jessica , Lal Ravi , Chang Samantha , Werts Miranda , Wong Andrew R. , Benites Veronica , Baidoo Edward , Katz Leonard , Keasling Jay D. 
Published: May 2020

AbstractTraditionally engineered to produce novel bioactive molecules, Type I modular polyketide synthases (PKSs) could be engineered as a new biosynthetic platform for the production ofde novofuels, commodity chemicals, and specialty chemicals. Previously, our investigations manipulated the first module of the lipomycin PKS to produce short chain ketones, 3-hydroxy acids, and saturated, branched carboxylic acids. Building upon this work, we have expanded to multi-modular systems by engineering the first two modules of lipomycin to generate unnatural polyketides as potential biofuels and specialty chemicals inStreptomyces albus. First, we produce 20.6 mg/L of the ethyl ketone, 4,6 dimethylheptanone through a reductive loop exchange in LipPKS1 and a ketoreductase knockouts in LipPKS2. We then show that an AT swap in LipPKS1 and a reductive loop exchange in LipPKS2 can produce the potential fragrance 3-isopropyl-6-methyltetrahydropyranone. Highlighting the challenge of maintaining product fidelity, in both bimodular systems we observed side products from premature hydrolysis in the engineered first module and stalled dehydration in reductive loop exchanges. Collectively, our work expands the biological design space and moves the field closer to the production of “designer” biomolecules.HighlightsEngineered lipomycin module 1 and module 2 to produce unnatural polyketides as valuable bio-based chemicalsA reductive loop swap and ketoreductase knockout used to produce 20 mg/mL of a novel ethyl ketone, a gasoline replacementAn acyltransferase swap and reductive loop swap successfully produced δ-lactone, a potential fragrant compoundIncomplete reduction and premature hydrolysis observed in engineered modulesGraphical abstract