bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenetic relationships in the southern African genusDrosanthemum(Ruschioideae, Aizoaceae)
Authors: Liede-Schumann Sigrid , Grimm Guido W. , Nürk Nicolai M. , Potts Alastair J. , Meve Ulrich , Hartmann Heidrun E.K. 
Published: November 2019

AbstractBackgroundDrosanthemum,the only genus of the tribe Drosanthemeae, is widespread over the Greater Cape Floristic Region in southern Africa. With 114 recognized species,Drosanthemumtogether with the highly succulent and species-rich tribe Ruschieae constitute the ‘core ruschioids’ in Aizoaceae. WithinDrosanthemum, nine subgenera have been described based on flower and fruit morphology. Their phylogenetic relationships, however, have not yet been investigated, hampering understanding of monophyletic entities and patterns of geographic distribution.MethodsUsing chloroplast and nuclear DNA sequence data, we performed network- and tree-based phylogenetic analyses of 73 species represented by multiple accessions ofDrosanthemum. A well-curated, geo-referenced occurrence data set comprising the phylogenetically studied and 867 further accessions was used to describe the distributional ranges of intrageneric lineages and the genus as a whole.ResultsPhylogenetic inference supports nine clades withinDrosanthemum, seven of them group in two major clades, while the remaining two show ambiguous affinities. The nine clades are generally congruent to previously described subgenera withinDrosanthemum, with exceptions such as (pseudo-) cryptic species. In-depth analyses of sequence patterns in each gene region revealed phylogenetic affinities not obvious in the phylogenetic tree. We observe a complex distribution pattern including widespread, species-rich clades expanding into arid habitats of the interior (subgeneraDrosanthemump.p., Vespertina, Xamera) that are molecular and morphologically diverse. In contrast, less species-rich, molecularly less divergent, and morphologically unique lineages are restricted to the central Cape region and more mesic conditions (Decidua,Necopina, Ossicula, Quastea, Quadrata, Speciosa). Our results suggest initial rapid radiation generating the main lineages, with some clades showing subsequent diversification.
A Multimodal and Integrated Approach to Interrogate Human Kidney Biopsies with Rigor and Reproducibility: The Kidney Precision Medicine Project
Authors: El-Achkar Tarek M. , Eadon Michael T. , Menon Rajasree , Lake Blue B. , Sigdel Tara K. , Alexandrov Theodore , Parikh Samir , Zhang Guanshi , Dobi Dejan , Dunn Kenneth W. , Otto Edgar A. , Anderton Christopher R. , Carson Jonas M. , Luo Jinghui , Park Chris , Hamidi Habib , Zhou Jian , Hoover Paul , Schroeder Andrew , Joanes Marianinha , Azeloglu Evren U. , Sealfon Rachel , Winfree Seth , Steck Becky , He Yongqun , D’Agati Vivette , Iyengar Ravi , Troyanskaya Olga G , Barisoni Laura , Gaut Joseph , Zhang Kun , Laszik Zoltan , Rovin Brad , Dagher Pierre C. , Sharma Kumar , Sarwal Minnie , Hodgin Jeffrey B. , Alpers Charles E. , Kretzler Matthias , Jain Sanjay ,   For the Kidney Precision Medicine Project
Published: November 2019

AbstractComprehensive and spatially mapped molecular atlases of organs at a cellular level are a critical resource to gain insights into pathogenic mechanisms and personalized therapies for diseases. The Kidney Precision Medicine Project (KPMP) is an endeavor to generate 3-dimensional (3D) molecular atlases of healthy and diseased kidney biopsies using multiple state-of-the-art OMICS and imaging technologies across several institutions. Obtaining rigorous and reproducible results from disparate methods and at different sites to interrogate biomolecules at a single cell level or in 3D space is a significant challenge that can be a futile exercise if not well controlled. We describe a “follow the tissue” pipeline for generating a reliable and authentic single cell/region 3D molecular atlas of human adult kidney. Our approach emphasizes quality assurance, quality control, validation and harmonization across different OMICS and imaging technologies from sample procurement, processing, storage, shipping to data generation, analysis and sharing. We established benchmarks for quality control, rigor, reproducibility and feasibility across multiple technologies through a pilot experiment using common source tissue that was processed and analyzed at different institutions and different technologies. A peer review system was established to critically review quality control measures and the reproducibility of data generated by each technology before being approved to interrogate clinical biopsy specimens. The process established economizes the use of valuable biopsy tissue for multi-OMICS and imaging analysis with stringent quality control to ensure rigor and reproducibility of results and serves as a model for precision medicine projects across laboratories, institutions and consortia.
Morphogenesis guided by 3D patterning of growth factors in biological matrices
Authors: Broguiere Nicolas , Lüchtefeld Ines , Traschel Lucca , Mazunin Dmitry , Bode Jeffrey , Lutolf Matthias P. , Zenobi-Wong Marcy 
Published: November 2019

AbstractThree-dimensional (3D) control over the placement of bioactive cues is fundamental to understand cell guidance and develop engineered tissues. Two-photon patterning (2PP) provides such placement at micro- to millimeter scale, but non-specific interactions between proteins and functionalized extracellular matrices (ECMs) restrict its use. Here we report a 2PP system based on non-fouling hydrophilic photocages and Sortase A-based enzymatic coupling offering unprecedented orthogonality and signal-to-noise ratio in both inert hydrogels and complex mammalian matrices. Improved photocaged peptide synthesis, and protein functionalization protocols with broad applicability are introduced. Importantly, the method enables 2PP in a single step and in the presence of fragile biomolecules and cells. As a corollary, we demonstrate the guidance of axons through 3D-patterned nerve growth factor (NGF) within brain-mimetic ECMs. Our approach allows for the interrogation of the role of complex signaling molecules in 3D matrices, thus helping to better understand biological guidance in tissue development and regeneration.
MoBPS - Modular Breeding Program Simulator
Authors: Pook T. , Schlather M. , Simianer H. 
Published: November 2019

ABSTRACTThe R-package MoBPS provides a computationally efficient and flexible framework to simulate complex breeding programs and compare their economic and genetic impact. Simulations are performed on the base of individuals and haplotypes are calculated on-the-fly by only saving founder haplotypes, points of recombination and mutations. MoBPS utilizes a highly efficient implementation with bit-wise storage of data and matrix multiplications from the associated R-package miraculix allowing to handle large scale populations. The modular structure of MoBPS allows to combine rather coarse simulations, as needed to generate founder populations, with a very detailed modeling of todays’ complex breeding programs, making use of all available biotechnologies. MoBPS provides pre-implemented functions for common breeding practices such as optimum genetic contributions and single-step GBLUP but also allows the user to replace certain steps with personalized and/or self-written solutions.
Systemic inflammation suppresses lymphoid tissue remodeling and B cell immunity during concomitant local infection
Authors: Alexandre Yannick O , Devi Sapna , Park Simone L , Mackay Laura K. , Heath William R. , Mueller Scott N. 
Published: November 2019

AbstractConcurrent infection with multiple pathogens occurs frequently in individuals and can result in exacerbated infections and altered immunity. However, the impact of such coinfections on immune responses remains poorly understood. Here we reveal that systemic infection results in an inflammation-induced suppression of local immunity. During localized infection or vaccination in barrier tissues including the skin or respiratory tract, concurrent systemic infection induced a type I interferon-dependent lymphopenia that impairs lymphocyte recruitment to the draining lymph node (dLN). This leads to suppressed lymphoid stromal cell expansion and dLN remodeling and impaired induction of B cell responses and antibody production. Our data suggest that contemporaneous systemic inflammation constrains the induction of regional immunity.
Effects of genetic variability of CYP2D6 on neural substrates of sustained attention during on-task activity
Authors: Viviani Roberto , Messina Irene , Bosch Julia E. , Dommes Lisa , Paul Anna , Schneider Katharina L. , Scholl Catharina , Stingl Julia C. 
Published: November 2019

AbstractThe polymorphic drug-metabolizing enzyme CYP2D6, which is responsible for the metabolism of most psychoactive compounds, is expressed not only in the liver, but also in the brain. The effects of its marked genetic polymorphism on the individual capacity to metabolize drugs are well known, but its role in metabolism of neural substrates affecting behavior personality or cognition, suggested by its CNS expression, is a long-standing unresolved issue. To verify earlier findings suggesting a potential effect on attentional processes, we collected functional imaging data while N=415 participants performed a simple task in which the reward for correct responses varied. CYP2D6 allelic variants predicting higher levels of enzymatic activity level were positively associated with cortical activity in occipito-parietal areas as well as in a right lateralized network known to be activated by spatial attentional tasks. Reward-related modulation of activity in cortical areas was more pronounced in poor metabolizers. In conjunction with effects on reaction times, our findings provide evidence for reduced cognitive efficiency in rapid metabolizers compared to poor metabolizers in on-task attentional processes manifested through differential recruitment of a specific neural substrate.
Regulation of electron transport is essential for photosystem I stability and plant growth
Authors: Storti Mattia , Segalla Anna , Mellon Marco , Alboresi Alessandro , Morosinotto Tomas 
Published: November 2019

AbstractLife depends on the ability of photosynthetic organisms to exploit sunlight to fix carbon dioxide into biomass. Photosynthesis is modulated by pathways such as cyclic and pseudocyclic electron flow (CEF and PCEF). CEF transfers electrons from photosystem I to the plastoquinone pool according to two mechanisms, one dependent on proton gradient regulators (PGR5/PGRL1) and the other on the type I NADH dehydrogenase (NDH) complex. PCEF uses electrons from photosystem I to reduce oxygen; in several groups of photosynthetic organisms but not in angiosperms, it is sustained by flavodiiron proteins (FLVs). PGR5/PGRL1, NDH and FLVs are all active in the moss Physcomitrella patens, and mutants depleted in these proteins show phenotypes under specific light regimes. Here, we demonstrated that CEF and PCEF exhibit strong functional overlap and that when one protein component is depleted, the others can compensate for most of the missing activity. When multiple mechanisms are simultaneously inactivated, however, plants show damage to photosystem I and strong growth reduction, demonstrating that mechanisms for the modulation of photosynthetic electron transport are indispensable.
Dopaminergic and opioidergic regulation of implicit hedonic facial reactions during anticipation and consumption of social and nonsocial rewards
Authors: Korb Sebastian , Götzendorfer Sebastian J. , Massaccesi Claudia , Sezen Patrick , Graf Irene , Willeit Matthäus , Eisenegger Christoph , Silani Giorgia 
Published: November 2019

AbstractThe observation of animal hedonic orofacial and behavioral reactions has played a fundamental role for the identification of a dopaminergic motivational, and an opioidergic hedonic component of reward. Translation to humans remains difficult, however, as human research has struggled to adopt a similar operationalization of reward. Here, we investigated the neurochemical basis of hedonic facial and behavioral reactions to different types of rewards in healthy adult volunteers, by pharmacologically reducing dopaminergic and opiodergic receptor-specific action. Subjective ratings, physical effort, and facial reactions to matched primary social (affective touch) and nonsocial (food) rewards were assessed. Both drugs resulted in reduced physical effort and increased negative facial reactions during reward anticipation, but only opioidergic manipulation caused reduced positive facial reactions during reward consumption. This suggest that facial reactions during anticipated and experienced pleasure rely on partly different neurochemical systems, providing novel evidence in support of existing theoretical models of reward.
A macro-ecological approach to predators’ functional response
Authors: Barbier Matthieu , Wojcik Laurie , Loreau Michel 
Published: November 2019

AbstractPredation often deviates from the law of mass action: many micro- and meso-scale experiments have shown that consumption saturates with resource abundance, and decreases due to interference between consumers. But does this observation hold at macro-ecological scales, spanning many species and orders of magnitude in biomass? If so, what are its consequences for large-scale ecological patterns and dynamics?We perform a meta-analysis of predator-prey pairs of mammals, birds and reptiles, and show that predation losses appear to increase, not as the product of predator and prey densities following the Lotka-Volterra (mass action) model, but rather as the square root of that product. This suggests a phenomenological power-law expression of the effective cross-ecosystem functional response. We discuss whether the same power-law may hold dynamically within an ecosystem, and assuming that it does, we explore its consequences in a simple food chain model. The empirical exponents fall close to the boundary between regimes of donor and consumer limitation. Exponents on this boundary are singular in multiple ways. First, they maximize predator abundance and some stability metrics. Second, they create proportionality relations between biomass and productivity, both within and between trophic levels. These intuitive relations do not hold in general in mass action models, yet they are widely observed empirically. These results provide evidence of mechanisms limiting predation across multiple ecological scales. Some of this evidence was previously associated with donor control, but we show that it supports a wider range of possibilities, including forms of consumer control. As limiting consumption counter-intuitively allows larger populations, it is worthwhile to reconsider whether the observed functional response arises from microscopic mechanisms, or could hint at selective pressure at the population level.This article has been peer-reviewed and recommended by Peer Community In Ecology (DOI: 10.24072/pci.ecology.100051)
Selective over-synthesis and rapid turnover of mitochondrial protein components of respiratory complexes
Authors: Bogenhagen Daniel F. 
Published: November 2019

AbstractMammalian mitochondria assemble four complexes of the respiratory chain (RCI, III, IV and V) by combining 13 polypeptides synthesized within mitochondria on mitochondrial ribosomes (mitoribosomes) with over 70 polypeptides encoded in nuclear DNA, translated on cytoplasmic ribosomes and imported into mitochondria. We report that pulse-chase SILAC can also serve as a valuable approach to study RC assembly as it reveals considerable differences in the rates and efficiency of assembly of different complexes. While assembly of RCV, ATPase, was rapid with little excess synthesis of subunits, RCI, NADH dehydrogenase, assembly was far less efficient with dramatic over-synthesis of numerous proteins, particularly in the matrix exposed N- and Q- Domains. Subunits that do not engage in assembly are generally degraded within three hours. Differential assembly kinetics were also observed for individual complexes immunoprecipitated with complex-specific antibodies. Immunoprecipitation with an antibody that recognizes the ND1 subunit of RCI co-precipitated a number of proteins implicated in FeS cluster assembly as well as newly-synthesized UQCRFS1, the Rieske FeS protein in RCIII, reflecting a degree of coordination of RCI and RCIII assembly.
Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows
Authors: Denisenko Elena , Guo Belinda B. , Jones Matthew , Hou Rui , de Kock Leanne , Lassmann Timo , Poppe Daniel , Clement Olivier , Simmons Rebecca K. , Lister Ryan , Forrest Alistair R. R. 
Published: November 2019

AbstractSingle-cell and single-nucleus RNA sequencing have been widely adopted in studies of heterogeneous tissues to estimate their cellular composition and obtain transcriptional profiles of individual cells. However, the current fragmentary understanding of artefacts introduced by sample preparation protocols impedes the selection of optimal workflows and compromises data interpretation. To bridge this gap, we compared performance of several workflows applied to adult mouse kidneys. Our study encompasses two tissue dissociation protocols, two cell preservation methods, bulk tissue RNA sequencing, single-cell and three single-nucleus RNA sequencing workflows for the 10x Genomics Chromium platform. These experiments enable a systematic comparison of recovered cell types and their transcriptional profiles across the workflows and highlight protocol-specific biases important for the experimental design and data interpretation.
Initiation and regulation of vascular tissue identity in theArabidopsisembryo
Authors: Smit Margot E. , Llavata-Peris Cristina I. , Roosjen Mark , van Beijnum Henriette , Novikova Daria , Levitsky Victor , Slane Daniel , Jürgens Gerd , Mironova Victoria , Brady Siobhan M. , Weijers Dolf 
Published: November 2019

AbstractDevelopment of plant vascular tissues involves tissue specification, growth, pattern formation and cell type differentiation. While later steps are understood in some detail, it is still largely unknown how the tissue is initially specified. We have used the early Arabidopsis embryo as a simple model to study this process. Using a large collection of marker genes, we find that vascular identity is established in the 16-cell embryo. After a transient precursor state however, there is no persistent uniform tissue identity. Auxin is intimately connected to vascular tissue development. We find that while AUXIN RESPONSE FACTOR5/MONOPTEROS/ (ARF5/MP)-dependent auxin response is required, it is not sufficient for tissue establishment. We therefore used a large-scale enhanced Yeast One Hybrid assay to identify potential regulators of vascular identity. Network and functional analysis of suggest that vascular identity is under robust, complex control. We found that one candidate regulator, the G-class bZIP transcription factor GBF2, modulates vascular gene expression, along with its homolog GBF1. Furthermore, GBFs bind to MP and modulate its activity. Our work uncovers components of a gene regulatory network that controls the initiation of vascular tissue identity, one of which involves the interaction of MP and GBF2 proteins.
CB2 distinguishes cells from background barcodes in 10x Genomics data
Authors: Ni Zijian , Chen Shuyang , Brown Jared , Kendziorski Christina 
Published: November 2019

SummaryAn important challenge in pre-processing data from the 10x Genomics Chromium platform is distinguishing barcodes associated with real cells from those binding background reads. Existing methods test barcodes individually, and consequently do not leverage the strong cell-to-cell correlation present in most datasets. To improve the power to identify real cells and rare subpopulations, we introduce CB2, a cluster-based approach for distinguishing real cells from background barcodes.
Downregulation of GPR183 on Infection Restricts the Early Infection and Intracellular Survival of Mycobacterium tuberculosis in Macrophage
Authors: Tang Jun , Shi Ya’nan , Zhan Lingjun , Qin Chuan 
Published: November 2019

AbstractGPR183/EBI2 is a key chemotactic receptor for the positioning of B cells in lymphoid organs, and also for the migration of T cells and other immune cells. Here, we demonstrate that the downregulation of GPR183 in macrophage induced during Mtb infection restrains the bacterial early infection and intracellular survival. Overexpression of GPR183 or stimulation with its natural ligand favors Mtb survival in macrophage, while treatment with its antagonist represses both Mtb early infection and intracellular survival. With mutational analysis, we find that substitution of Asp-73, Arg-83, Tyr-112, Tyr-256 abolished the promotive effect of GPR183 on Mtb early infection and survival in macrophage. In conclusion, we demonstrated that beside the known role of chemotaxis receptor, GPR183 also functions directly in the interaction between macrophage and Mtb in a cell-autonomous way.
GeneSwitches : Ordering gene-expression and functional events in single-cell experiments
Authors: Cao Elaine Y. , Ouyang John F. , Rackham Owen J.L. 
Published: November 2019

AbstractSummaryEmerging single-cell RNA-seq technologies has made it possible to capture and assess the gene expression of individual cells. Based on the similarity of gene expression profiles, many tools have been developed to generate an in silico ordering of cells in the form of pseudo-time trajectories. However, these tools do not provide a means to find the ordering of critical gene expression changes over pseudo-time. We present GeneSwitches, a tool that takes any single-cell pseudo-time trajectory and determines the precise order of gene-expression and functional-event changes over time. GeneSwitches uses a statistical framework based on logistic regression to identify the order in which genes are either switched on or off along pseudo-time. With this information, users can identify the order in which surface markers appear, investigate how functional ontologies are gained or lost over time, and compare the ordering of switching genes from two related pseudo-temporal processes.AvailabilityGeneSwitches is available at https://geneswitches.ddnetbio.comContactowen.rackham@duke-nus.edu.sgSupplementary Informationis available at http://www.ddnetbio.com/files/GeneSwitches_SI.pdf