bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clumpy coexistence in phytoplankton: The role of functional similarity in community assembly
Authors: Graco-Roza Caio , Segura Angel M , Kruk Carla , Domingos Patrícia , Soininen Janne , Marinho Marcelo Manzi 
Published: December 2019

AbstractEmergent neutrality (EN) suggests that species must be sufficiently similar or sufficiently different in their niches to avoid interspecific competition. Such a scenario results in a transient pattern with clumps and gaps of species abundance along the niche axis (e.g., represented by body size). From this perspective, clumps are groups of coexisting species with negligible fitness differences and stochastic abundance fluctuations. Plankton is an excellent model system for developing and testing ecological theories, especially those related to size structure and species coexistence. We tested EN predictions using the phytoplankton community along the course of a tropical river considering (i) body size structure, (ii) functional clustering of species in terms of morphology-based functional groups (MBFG), and (iii) the functional similarity among species concerning their functional traits. Two main clumps in the body size axis (clump I and II) were conspicuous through time and were detected in different stretches of the river. Clump I comprised medium-sized species from the MBFGs IV, V, and VI while clump II included large-bodied species from the MBFGs V and VI. Pairwise differences in species biovolume correlated with species functional similarity when the whole species pool was considered, but not among species within the same clump. Although clumps comprised multiple MBFGs, the dominant species within the clump belonged always to the same MBFG. Also, within-clump species biovolume increased with functional distinctiveness considering both seasons and stretches, except the lower course. These results suggest that species within clumps behave in a quasi-neutral state, but even minor shifts in trait composition may affect species biovolume. Our findings point that EN belongs to the plausible mechanisms explaining community assembly in river ecosystems.
Ulcerative colitis is characterized by amplified acute inflammation with delayed resolution
Authors: Wysoczanski Riccardo , Kendall Alexandra C , Motwani Madhur , Vega Roser , Rahman Farooq Z , McCartney Sara , Bloom Stuart L , Nicolaou Anna , Gilroy Derek W , Segal Anthony W , Marks Daniel J B 
Published: December 2019

AbstractThe cause of chronic inflammation in ulcerative colitis (UC) is incompletely understood. Here we tested the hypothesis that an excessive acute inflammatory response to bacteria contributes to the pathogenesis. Acute inflammatory responses were provoked in vivo in UC patients and healthy controls by intradermal inoculation with bacteria. Vascular responses were quantified by laser Doppler. Inflammatory exudates were recovered in superimposed suction blisters and cells measured by polychromatic flow cytometry, cytokines by multiplex array, and inflammatory lipids by mass spectrometry. Vascular responses in UC patients were heightened at 24h after bacterial injection (p=0·03), and remained abnormally high at 48h (p=0·0005) and this amplified response was seen in UC with Gram-positive as well as Gram-negative organisms (p=0·01). The cellular infiltrate over the injection site, composed largely of neutrophils at 4 hours a was greater in UC (p=0·002). At 48h, the increased numbers of cells in UC were composed of neutrophils (p=0·001) and CD4 lymphocytes (p=0·001). The exaggerated inflammation in UC was not a cytokine-driven phenomenon. Exaggerated onset was normalised in patients taking 5-aminosalicylates, accompanied by increased concentrations of hydroxy fatty acids 9-oxo-octadecadienoic acid (OxoODE; p=0·05) and 13-OxoODE (p=0·01) in resolving exudates. In vitro, these compounds suppressed macrophage inflammatory cytokine secretion through PPARγ (p<0·0001). Conversely, 5-aminosalicylates did not inhibit early inflammatory reactions in control participants. Acute inflammatory responses to bacteria in UC are both overly exuberant and slow to resolve. Neutrophils accumulate in excess and persist, in keeping with the pathological appearances of disease flares. These studies also provide new insight into the mechanism of 5-aminosalicylate (5ASA) drugs, which act as pro-resolution rather than indiscriminate anti-inflammatory agents by promoting formation of immunomodulatory hydroxy lipids. While production of these lipids is not defective as part of the underlying disease process, this identifies a novel mechanism of drug action harnessing pro-resolution pathways.SummaryWysoczanski and colleagues demonstrate that the inflammatory response to injected bacteria is exaggerated and prolonged in ulcerative colitis. This disordered inflammation appears to be associated with increased secretion of PGE2. 5-aminosalicylate drugs, which are used to treat this condition, normalize inflammation and PGE2 secretion, and appear to work through PPARγ
Quantification and Discovery of Acyl-ACPs by LC-MS/MS
Authors: Nam Jeong-Won , Jenkins Lauren M. , Li Jia , Evans Bradley S. , Jaworski Jan G. , Allen Doug K. 
Published: December 2019

ABSTRACTAcyl carrier proteins (ACPs) are the scaffolds for fatty acid biosynthesis in living systems, rendering them essential to a comprehensive understanding of lipid metabolism; however, accurate quantitative methods to assess individual acyl-ACPs do not exist. A robust method was developed to quantify acyl-ACPs at picogram levels. Acyl-ACP elongation intermediates (3-hydroxyacyl-ACPs and 2, 3-trans-enoyl-ACPs), and unexpected medium chain (C10:1, C14:1) and polyunsaturated long chain acyl-ACPs (C16:3) were also identified, indicating the sensitivity of the method and that descriptions of lipid metabolism and ACP function are incomplete. Such ACPs are likely important to medium chain lipid production for fuels and highlight poorly understood lipid remodeling events in the chloroplast. The approach is broadly applicable to Type II FAS systems found in plants, bacteria, and mitochondria of animal and fungal systems because it uses a strategy that capitalizes on a highly conserved Asp-Ser-Leu-Asp (DSLD) amino acid sequence in ACPs to which acyl groups are attached. This allows for sensitive quantification using LC-MS/MS withde novogenerated standards and an isotopic dilution strategy and will fill a gap in understanding, providing insights through quantitative exploration of fatty acid biosynthesis processes for optimal biofuels, renewable feed stocks, and medical studies in health and disease.
Phen2Gene: Rapid Phenotype-Driven Gene Prioritization for Rare Diseases
Authors: Zhao Mengge , Havrilla James M. , Fang Li , Chen Ying , Peng Jacqueline , Liu Cong , Wu Chao , Sarmady Mahdi , Botas Pablo , Isla Julián , Lyon Gholson , Weng Chunhua , Wang Kai 
Published: December 2019

AbstractHuman Phenotype Ontology (HPO) terms are increasingly used in diagnostic settings to aid in the characterization of patient phenotypes. The HPO annotation database is updated frequently and can provide detailed phenotype knowledge on various human diseases, and many HPO terms are now mapped to candidate causal genes with binary relationships. To further improve the genetic diagnosis of rare diseases, we incorporated these HPO annotations, gene-disease databases, and gene-gene databases in a probabilistic model to build a novel HPO-driven gene prioritization tool, Phen2Gene. Phen2Gene accesses a database built upon this information called the HPO2Gene Knowledgebase (H2GKB), which provides weighted and ranked gene lists for every HPO term. Phen2Gene is then able to access the H2GKB for patient-specific lists of HPO terms or PhenoPackets descriptions supported by GA4GH (http://phenopackets.org/), calculate a prioritized gene list based on a probabilistic model, and output gene-disease relationships with great accuracy. Phen2Gene outperforms existing gene prioritization tools in speed, and acts as a real-time phenotype driven gene prioritization tool to aid the clinical diagnosis of rare undiagnosed diseases. In addition to a command line tool released under the MIT license (https://github.com/WGLab/Phen2Gene), we also developed a web server and web service (https://phen2gene.wglab.org/) for running the tool via web interface or RESTful API queries. Finally, we have curated a large amount of benchmarking data for phenotype-to-gene tools involving 197 patients across 76 scientific articles and 85 patients’ de-identified HPO term data from CHOP.
Identification of GABAergic neurons innervating the zebrafish lateral habenula
Authors: Ramaswamy Mahathi , Cheng Ruey-Kuang , Jesuthasan Suresh 
Published: December 2019

AbstractHabenula neurons are constantly active. The level of activity affects mood and behaviour, with increased activity in the lateral habenula reflecting exposure to punishment and a switch to passive coping and depression. Here, we identify GABAergic neurons that could reduce activity in the lateral habenula of larval zebrafish. GAD65/67 immunohistochemistry and imaging of gad1b:DsRed transgenic fish suggest the presence of GABAergic terminals in the neuropil and between cell bodies in the lateral habenula. Retrograde tracing with the lipophilic dye DiD suggests that the former derives from the thalamus, while the latter originates from a group of cells in the posterior hypothalamus that are located between the posterior tuberal nucleus and hypothalamic lobes. Two-photon calcium imaging indicates that blue light causes excitation of thalamic GABAergic neurons and terminals in the neuropil, while a subpopulation of lateral habenula neurons show reduced intracellular calcium levels. Whole-cell electrophysiological recording indicates that blue-light reduces membrane potential of lateral habenula neurons. These observations suggest that GABAergic input from the thalamus may mediate inhibition in the zebrafish lateral habenula. Mechanisms governing release of GABA from the neurons in the posterior hypothalamus, which are likely to be in the tuberomammillary nucleus, remain to be defined.
Astrocytic regulation of synchronous bursting in cortical cultures: from local to global
Authors: Kumar Ravi , Huang Yu-Ting , Chen Chun-Chung , Tzeng Shun-Fen , Chan C. K. 
Published: December 2019

AbstractSynchronous bursting (SB) is ubiquitous in neuronal networks. It is known for a long time that SB is driven by glutamatergic neurotransmissions but its underlying mechanism is still unclear. Recent studies show that local glutamate recycle by astrocytes can affect neuronal activities nearby. Since SB is independent of network structure, it is conceivable that the local dynamics might also be the origin of SB in networks. We investigated the effects of local glutamate dynamics on SBs in both cultures developed on multi-electrode array (MEA) systems and a tripartite synapse simulation model. In our experiments, local glutamate recycle dynamics are studied by pharmacologically targeting the astrocytic glutamate transporters (GLT-1), while neuronal firing activities and synaptic glutamate level are simultaneously monitored with MEA and glutamate sensor (iGluSnFR) expressed on surface of astrocytes respectively. We found SBs to be synchronized with glutamate transients and the manipulation of local glutamate dynamics can indeed alter the global properties of the SBs. Detailed simulation of a network with astrocytic glutamate uptake and recycle mechanisms conforming with the experimental observations revealed that astrocytes function as a slow negative feedback for the neuronal activities in the network. With this model, SB can be understood as the alternation between the positive and negative feedback in the neurons and astrocytes in the network respectively. An understanding of this glutamate trafficking dynamics is of general application to explain disordered phenomena in neuronal systems, and therefore can provide new insights into the origin of fatal seizure-like behavior.SignificanceSynchronous bursting (SB) is a hallmark of neuronal circuits. Contrary to the common belief that the SB is governed mainly by neuron-neuron interactions, this study shows that SBs are orchestrated through a generic neuron-astrocyte tripartite interactions. These interactions, identified as glutamate uptake and recycle processes in astrocytes, control the excitability of neuronal networks and shape the overall SB patterns. Our simulation results suggest that astrocytes traffic more glutamate than neurons and actively regulating glutamate proceedings around synapses. A bipartite synapse is a good approximation of a tripartite synapse provided that astrocyte-dependent glutamate content is taken into account. Our findings provide key insights into the ubiquity of SB and the origin of fatal seizure-like behavior in brain arising from astrocytic malfunction.
SpecHap: a diploid phasing algorithm based on spectral graph theory
Authors: Yu Yonghan , Chen Lingxi , Miao Xinyao , Li Shuai Cheng 
Published: December 2019

ABSTRACTHaplotype phasing is essential to study diploid eukaryotic organisms. High-throughput sequencing, including next-generation sequencing and third-generation sequencing from different technologies, brings possibilities for haplotype assembly. Although there exist multiple haplotype phasing algorithms, only a few are portable across sequencing technologies with the premise of efficiency and accuracy. Herein, we proposed SpecHap, a novel haplotype assembly tool that leverages spectral graph theory, transforming haplotype phasing into an algebraic problem. On both in silico and whole-genome-sequencing datasets, SpecHap consumed less memory and required less CPU time, yet achieved comparable accuracy comparing to state-of-art methods across all the test instances of next-generation sequencing, linked-reads, high-throughput chromosome conformation capture sequencing, PacBio single-molecule real-time sequencing and Oxford Nanopore long-reads sequencing data. Furthermore, SpecHap successfully phased an individual Ambystoma mexicanumm, a species with gigantic diploid genomes, within 6 CPU hours and 945MB peak memory usage, while other tools failed to yield results either due to a memory overflow (40GB) or a time limit excess (5 days). Our results demonstrated that SpecHap is scalable, efficient and accurate for diploid phasing, supporting diverse sequencing platforms.
Activation of macrophages by lysophosphatidic acid through the lysophosphatidic acid receptor 1 as a novel mechanism in multiple sclerosis pathogenesis
Authors: Fransson Jennifer , Gómez Ana Isabel , Romero-Imbroda Jesús , Fernández Oscar , Leyva Laura , de Fonseca Fernando Rodriguez , Chun Jerold , Louapre Celine , Van-Evercooren Anne Baron , Zujovic Violetta , Estivill-Torrús Guillermo , García-Díaz Beatriz 
Published: December 2019

AbstractMultiple sclerosis (MS) is a neuro-inflammatory disease for which the pathogenesis remains largely unclear. Lysophosphatidic acid (LPA) is an endogenous phospholipid that is involved in multiple immune cell functions and is dysregulated in MS. Its receptor LPA1 is expressed in macrophages and regulates their activation, which is of interest due to the role of macrophage activation in MS in both destruction and repair.In this study, we studied the viable Malaga variant of LPA1-null mutation as well as pharmaceutical inhibition of LPA1 in mice with experimental autoimmune encephalomyelitis (EAE), a model of MS. LPA1 expression was also analyzed in both wild-type EAE mice and MS patient immune cells. The effect of LPA and LPA1 on macrophage activation was studied in human monocyte-derived macrophages.We show that lack of LPA1 activity induces a milder clinical course in EAE, and that Lpar1 expression in peripheral blood mononuclear cells (PBMCs) correlates with onset of relapses and severity in wild-type EAE mice. We see the same over-expression in PBMCs from MS patients during relapse compared to progressive forms of the disease, and in monocyte-derived macrophages after exposure to pro-inflammatory stimuli. In addition, LPA induced a pro-inflammatory-like response in macrophages through LPA1, providing a plausible way in which LPA and LPA1 dysregulation can lead to the inflammation seen in MS.These data show a new mechanism of LPA signaling in the pathogenesis of MS, prompting further research into its use as a therapeutic target biomarker.
Mutagenesis of two homologs ATP Binding cassette protein in tomato by CRISPR/Cas9 provide resistance against the plant parasite Phelipanche aegyptiaca
Authors: Bari Vinay Kumar , Nassar Jackline Abu , Meir Ayala , Aly Radi 
Published: December 2019

SUMMARYPlant parasitic weed Phelipanche aegyptiaca and Orobanche spp. are obligate plant parasites that cause heavy damage to agricultural crop plants. Germination of the parasite seeds require exposure to specific chemical known as strigolactone [SL]. The plant hormone SL is derived from plant carotenoids via cleavage by CCD7 and CCD8 enzymes and exuded by the host roots to the rhizosphere. Here, we provide evidence that CRISPR/Cas9 mediated targeted mutagenesis of two homologues ATP Binding cassette (ABC) protein in tomato (Solyc08g067610 and Solyc08g067620), significantly reduced the germination of the parasitic weed P.aegyptiaca. Constructs harboring specific single guide RNA were prepared and targeted against conserved region in the above tomato genes (Solyc08g067610 and Solyc08g067620). Selected T0-mutated tomato plants showed different type of deletions at both locuses. Furthermore, genotype analysis of T1 plants showed that the introduced mutations stably inherited to next generation with no identified off-targets. Mutated tomato lines, showed more branching, enhanced growth of axillary buds, reduced length of primary stems and significantly reduced development of the parasitic weed P. aegyptiaca as compared to wild type plants. Moreover, in ABCCas9 mutants the expression level of the genes (CCD8 and MAX1) related to SL biosynthesis were decreased, without alteration in the root extract orobanchol [SL] as compared to control plants. Development of genetic resistance based on genome editing of host key genes are novel approaches for enhancing host-parasite resistance. The current study offers insights into ABC protein homologs and mutagenesis of ABC protein that could be used in the development of efficient method to reduce parasitic weed germination.
In vitroinduced floral reversion in switchgrass (Panicum VirgatumL.)
Authors: Wang Yongfeng , Xie Kunliang , Sun Fengli , Zhang Chao , Liu Shudong , Xi Yajun 
Published: December 2019

AbstractSwitchgrass (Panicum VirgatumL.) is a warm-season perennial grass native to North America, it was used as forage and vegetative filter strips in early days, and have developed into a bioenergy crop in recent years. In this study, we found that the switchgrass cultivar ‘Alamo’ at elongation stage 4 have developed inflorescences about 1 cm in length, andin vitroincubation of the shoot apexes harboring inflorescences on Murashige and Skoog’s basal medium supplemented with 3 mg/L 6-benzylaminopurine generated multiple shoot clumps. Anatomical study showed that some of the regenerated shoots originated from axillary buds on the explants, some of them originated from adventurous buds and some of them originated from young florets. Further study of shoots originated from young florets found that the floral organs degenerated or developed into leaf-like organs, and the flower terminal transformed into a vegetative shoot apical meristem, that’s to say these shoots arise from flower reversion.In vitroinduction of floral reversion provided a novel protocol to manipulate flower development in switchgrass, which might contribute a fundamental for flower development study in switchgrass and other plants.
Disentangling spatial and environmental effects: flexible methods for community ecology and macroecology
Authors: Viana Duarte S. , Keil Petr , Jeliazkov Alienor 
Published: December 2019

AbstractCommunity ecologists and macroecologists have long sought to evaluate the importance of environmental conditions in determining species distributions, community composition, and diversity across sites. Different methods have been used to estimate species-environment relationships, but their differences to jointly fit and disentangle spatial autocorrelation and structure remain poorly studied. We compared how methods in four broad families of statistical models estimated the contribution of the environment and space to variation in species binary occurrence and abundance. These methods included distance-based regression, generalized linear models (GLM, and the special case of RDA), generalized additive models (GAM), and tree-based machine learning (ML): regression trees, boosted regression trees (BRT), and random forests. The spatial component of the model consisted of spatial distance (in distance-based regression), Moran’s Eigenvector Maps (MEM; in GLM and ML), smooth spatial splines (in GAM), or tree-based non-linear modelling of spatial coordinates (in ML). We simulated typical site-by-species data to assess the methods’ performance in (1) fitting environmental and spatial models, and (2) partitioning the variation explained by environmental and spatial predictors. We observed marked differences in performance mostly caused by imbalanced performance in estimating environmental and spatial effects. Such differences also manifested when analyzing eight different empirical datasets. GLM and BRT with MEMs were generally the most reliable methods for partitioning the variation explained by environmental and spatial effects across a wide range of simulated scenarios. The remaining methods tended to underfit simulated spatial structures, causing underestimation of spatial fractions of variation. Our results suggest that previously overlooked methods for performing variation partitioning, especially tree-based ML, offer flexible approaches to analyze site-by-species matrices. We provide general guidelines on the usefulness of different models under different ecological and sampling scenarios, for species distribution modelling, community ecology, and macroecology.
Characteristics of a novel NMR-based metabolomics platform for dogs
Authors: Ottka Claudia , Vapalahti Katariina , Puurunen Jenni , Vahtera Laura , Lohi Hannes 
Published: December 2019

AbstractMetabolomics has proven itself an invaluable research tool, providing comprehensive insight to systemic metabolism. However, the lack of scalable and quantitative methods with known reference intervals and documented reproducibility has prevented the use of metabolomics in the clinical setting. This study describes the development and validation of a quantitative nuclear magnetic resonance (NMR) -based metabolomics platform for canine serum and plasma samples. Altogether 8247 canine samples were analyzed using a Bruker’s 500 MHz NMR spectrometer. Using statistical approaches derived from international guidelines, we defined reference intervals for 123 biomarkers, studied method precision, analyte storage stability, the effect of prolonged contact to red blood cells, differences of blood collection tubes, interference of lipemia, hemolysis and bilirubinemia, method comparison, and demonstrated the method’s practical relevance in a hyperglycemic cohort. Owing to the advantages of quantitative results, high reproducibility, and scalability, this canine metabolomics platform holds great potential for numerous clinical and research applications to improve canine health and well-being.