bluuebunny/crossref_metadata_2025_split huggingface dataset:
Serial coupling of chromatographic columns having orthogonal selectivity to improve the coverage of oxidised lipidome for mass spectrometry analysis
Authors: Thakker Alpesh , Pitt Andrew , Spickett Corinne 
Published: August 2019

1AbstractPhospholipid oxidation (OxPL) generates a wide variety of products with potentially novel biological activities that may be associated with disease pathogenesis. To understand their role in disease requires precise information about their abundance in biological samples. Liquid chromatography-mass spectrometry (LCMS) is a sensitive technique that can provide detailed information about the oxidative lipidome, but challenges remain. Furthermore, variation in charge of the polar head groups and the extreme diversity of oxidised species make analysis of several classes of OxPLs within one analytical run challenging.The work in this study aims to develop improved methods for detection of OxPLs by improvement of chromatographic separation through the serial coupling of polystyrene-divinylbenzene based monolithic, and mixed-mode hydrophilic interaction (HILIC) with use of semi-targeted mass spectrometry approaches. The results suggests that by serially coupling two columns, HILIC and monolith, provided the better coverage of OxPL species in a single analytical run. We tested in-vitro generated oxidized species for phosphatidylcholine (PC) and phosphatidylethanolamine (PE) class and the combination of orthogonal chromatographic separation allowed separation of oxdised species from both the classes, which otherwise coeluted.
A new variance ratio metric to detect the timescale of compensatory dynamics
Authors: Zhao Lei , Wang Shaopeng , Hallett Lauren M. , Rypel Andrew , Sheppard Lawrence W. , Castorani Max C.N. , Shoemaker Lauren G. , Cottingham Kathryn L. , Suding Katharine , Reuman Daniel C. 
Published: August 2019

AbstractUnderstanding the mechanisms governing ecological stability – why a property such as primary productivity is stable in some communities and variable in others – has long been a focus of ecology. Compensatory dynamics, in which anti-synchronous fluctuations between populations buffer against fluctuations at the community level, is a key theoretical mechanism of stability. Classically, compensatory dynamics have been quantified using a “variance ratio” approach that compares the ratio between community variance and aggregate population variance, such that a lower ratio indicates compensation and a higher ratio indicates synchrony among species fluctuations. However, population dynamics may be influenced by different drivers that operate on different timescales, and evidence from aquatic systems indicates that communities can be compensatory on some timescales and synchronous on others. The variance ratio and related metrics cannot reflect this timescale-specificity, yet have remained popular, especially in terrestrial systems. Here, we develop a timescale-specific variance ratio approach that formally decomposes the classical variance ratio according to the timescales of distinct contributions. The approach is implemented in a new R package, called tsvr, that accompanies this paper. We apply our approach to a long-term, multi-site grassland community dataset. Our approach demonstrates that the degree of compensation versus synchrony in community dynamics can vary by timescale. Across sites, population variability was typically greater over longer compared to shorter timescales. At some sites, minimal timescale-specificity in compensatory dynamics translated this pattern of population variability into a similar pattern of greater community variability on longer compared to shorter timescales. But at other sites, differentially stronger compensatory dynamics at longer compared to shorter timescales produced lower-than-expected community variability on longer timescales. Within every site there were plots that exhibited shifts in the strength of compensation between timescales. Our results highlight that compensatory versus synchronous dynamics are intrinsically timescale-dependent concepts, and our timescale-specific variance ratio provides a metric to quantify timescale-specificity and relate it back to the classic variance ratio.
Neutrophils Suppress Mucosal-Associated Invariant T Cells
Authors: Schneider M , Hannaway RF , Lamichhane R , de la Harpe SM , Tyndall JDA , Vernall AJ , Kettle A , Ussher JE 
Published: August 2019

AbstractMucosal-associated invariant T (MAIT) cells are innate-like T lymphocytes that are abundant in mucosal tissues and the liver where they can respond rapidly to a broad range of riboflavin producing bacterial and fungal pathogens. Neutrophils, which are recruited early to sites of infection, play a non-redundant role in pathogen clearance and are crucial for controlling infection. The interaction of these two cell types is poorly studied. Here, we investigated both the effect of neutrophils on MAIT cell activation and the effect of activated MAIT cells on neutrophils. We show that neutrophils suppress the activation of MAIT cells by a cell-contact and H2O2dependent mechanism. Moreover, highly activated MAIT cells were able to produce high levels of TNFα that induced neutrophil death. We therefore provide evidence for a negative regulatory feedback mechanism in which neutrophils prevent over-activation of MAIT cells and, in turn, MAIT cells limit neutrophil survival.
Population Structure, Stratification and Introgression of Human Structural Variation
Authors: Almarri Mohamed A. , Bergström Anders , Prado-Martinez Javier , Yang Fengtang , Fu Beiyuan , Dunham Alistair S. , Chen Yuan , Hurles Matthew E. , Tyler-Smith Chris , Xue Yali 
Published: August 2019

AbstractStructural variants contribute substantially to genetic diversity and are important evolutionarily and medically, yet are still understudied. Here, we present a comprehensive analysis of deletions, duplications, insertions, inversions and non-reference unique insertions in the Human Genome Diversity Project (HGDP-CEPH) panel, a high-coverage dataset of 911 samples from 54 diverse worldwide populations. We identify in total 126,018 structural variants (25,588 <100 bp in size), of which 78% are novel. Some reach high frequency and are private to continental groups or even individual populations, including a deletion in the maltase-glucoamylase gene MGAM involved in starch digestion, in the South American Karitiana and a deletion in the Central African Mbuti in SIGLEC5, potentially leading to immune hyperactivity. We discover a dynamic range of copy number expansions and find cases of regionally-restricted runaway duplications, for example, 18 copies near the olfactory receptor OR7D2 in East Asia and in the clinically-relevant HCAR2 in Central Asia. We identify highly-stratified putatively introgressed variants from Neanderthals or Denisovans, some of which, like a deletion within AQR in Papuans, are almost fixed in individual populations. Finally, by de novo assembly of 25 genomes using linked-read sequencing we discover 1631 breakpoint-resolved unique insertions, in aggregate accounting for 1.9 Mb of sequence absent from the GRCh38 reference. These insertions show population structure and some reside in functional regions, illustrating the limitation of a single human reference and the need for high-quality genomes from diverse populations to fully discover and understand human genetic variation.
Residue retention promotes soil carbon accumulation in minimum tillage systems: Implications for conservation tillage
Authors: Li Yuan , Li Zhou , Chang Scott X. , Cui Song , Jagadamma Sindhu , Zhang Qingping , Cai Yanjiang 
Published: August 2019

AbstractCrop residue retention and minimum tillage (including no-tillage, NT, and reduced tillage, RT) are common conservation tillage practices that have been extensively practised for improving soil health and reducing the negative environmental impact caused by intensive farming. However, the complex effect of conservation tillage practices on soil organic carbon (SOC) storage has not been systematically analyzed, and particularly, the synergistic effect of crop residue retention and minimum tillage on SOC storage remains nonexistent. We conducted a global meta-analysis using a dataset consisting of 823 pairs of data points from 164 studies. We analyzed the effect of crop residue retention and minimum tillage on SOC storage and how the above effects were influenced by various soil/environmental (soil sampling depth, soil texture, and climate) and management conditions (cropping intensity and treatment duration). We found that either residue retention or minimum tillage alone increased SOC stock, while the former increased SOC more. The NT and RT increased SOC stock by 10 and 6%, respectively, in comparison to conventional tillage (CT). The NT plus residue retention (NTS) and RT plus residue retention (RTS) resulted in 20 and 26% more increase in SOC than NT and RT, respectively. Compared with CT, NTS and RTS further increased SOC stock by 29 and 27%, respectively. The above effects were greater in the topsoil than in the subsoil. Availability of initial soil nutrient played a greater role in affecting SOC stock than climatic conditions and management practices. Both residue retention and NT increased SOC rapidly in the first 6 years regardless of soil texture or climate condition, followed by a period of slower sequestration phase before reaching a slow steady rate. Double cropping generally increased SOC stock across all conservation tillage practices as compared to single or multiple cropping. Therefore, we conclude that minimum tillage coupled with residue retention in a double cropping system is the most beneficial management system for increasing cropland SOC storage, which can inform sustainable soil management practices aimed at increasing global C sequestration.
The CTCF Anatomy of Topologically Associating Domains
Authors: Nanni Luca , Wang Cheng , Manders Freek , Groh Laszlo , Haro Paula , Oldenkamp Roel , Ceri Stefano , Logie Colin 
Published: August 2019

AbstractTopologically associated domains (TADs) are defined as regions of self-interaction. To date, it is unclear how to reconcile TAD structure with CTCF site orientation, which is known to coordinate chromatin loops anchored by Cohesin rings at convergent CTCF site pairs. We first approached this problem by 4C analysis of the FKBP5 locus. This uncovered a CTCF loop encompassing FKBP5 but not its entire TAD. However, adjacent CTCF sites were able to form ‘back-up’ loops and these were located at TAD boundaries. We then analysed the spatial distribution of CTCF patterns along the genome together with a boundary identity conservation ‘gradient’ obtained from primary blood cells. This revealed that divergent CTCF sites are enriched at boundaries and that convergent CTCF sites mark the interior of TADs. This conciliation of CTCF site orientation and TAD structure has deep implications for the further study and engineering of TADs and their boundaries.
The physiological level of rNMPs present in mtDNA does not compromise its stability
Authors: Wanrooij Paulina H. , Tran Phong , Thompson Liam J. , Sharma Sushma , Kreisel Katrin , Navarrete Clara , Feldberg Anna-Lena , Watt Danielle L. , Nilsson Anna Karin , Engqvist Martin K. M. , Clausen Anders R. , Chabes Andrei 
Published: August 2019

AbstractRibonucleotides (rNMPs) incorporated in the nuclear genome are a well-established threat to genome stability and can result in DNA strand breaks when not removed in a timely manner. However, the presence of a certain level of rNMPs is tolerated in mitochondrial DNA (mtDNA), although aberrant mtDNA rNMP content has been identified in disease models. We investigated the effect of incorporated rNMPs on mtDNA stability over the mouse lifespan and found that the mtDNA rNMP content increased during early life. The rNMP content of mtDNA varied greatly across different tissues and was defined by the rNTP/dNTP ratio of the tissue. Accordingly, mtDNA rNMPs were nearly absent in SAMHD1−/− mice that have increased dNTP pools. The near absence of rNMPs did not, however, appreciably affect mtDNA copy number or the levels of mtDNA molecules with deletions or strand breaks in aged animals near the end of their lifespan. The physiological rNMP load therefore does not contribute to the progressive loss of mtDNA quality that occurs as mice age.
The absence of C-5 DNA methylation in Leishmania donovani allows DNA enrichment from complex samples
Authors: Cuypers B , Dumetz F , Meysman P , Laukens K , De Muylder G , Dujardin J-C , Domagalska MA 
Published: August 2019

AbstractCytosine C5 methylation is an important epigenetic control mechanism in a wide array of Eukaryotic organisms and generally carried out by proteins of C-5 DNA methyltransferase family (DNMTs). In several protozoans the status of this mechanism remains elusive, such as in Leishmania, the causative agent of the disease leishmaniasis in humans and a wide array of vertebrate animals. In this work, we show that the Leishmania donovani genome contains a C-5 DNA methyltransferase (DNMT) from the DNMT6 subfamily, of which the function is still unclear, and verified its expression at RNA level. We created viable overexpressor and knock-out lines of this enzyme and characterised their genome-wide methylation patterns using whole-genome bisulfite sequencing, together with promastigote and amastigote control lines. Interestingly, despite DNMT6 presence, we found that methylation levels were equal to or lower than 0.0003% at CpG sites, 0.0005% at CHG sites and 0.0126% at CHH sites at genome scale. As none of the methylated sites were retained after manual verification, we conclude that there is no evidence for DNA methylation in this species. We demonstrate that this difference in DNA methylation between the parasite (no detectable DNA methylation) and the vertebrate host (DNA methylation), allows enrichment of parasite versus host DNA using Methyl-CpG-binding domain columns, readily available in commercial kits. As such, we depleted methylated DNA from mixes of Leishmania promastigote and amastigote DNA with human DNA, resulting in average Leishmania:human enrichments from 62x up to 263x. These results open a promising avenue for unmethylated DNA enrichment as a pre-enrichment step before sequencing Leishmania clinical samples.
Developmental regulation of fear memories by an obesogenic high-saturated fat/high-sugar diet
Authors: Vega-Torres Julio David , Reyes-Rivera Arsenio L. , Figueroa Johnny D. 
Published: August 2019

ABSTRACTBackgroundAnxiety and stress-related disorders are strongly linked with obesity and the consumption of obesogenic diets. Paralleling clinical findings, we showed that the consumption of an obesogenic diet during adolescence disrupts the structural integrity of amygdalar and prefrontal cortex circuits underlying emotional responses to stress. These abnormalities were associated with a PTSD-like phenotype, including heightened stress reactivity to predator odor trauma, anxiety-like behaviors, and profound learning deficits. The present follow-up study investigates how an obesogenic diet alters aversion-related associative memories across adolescence.MethodsAdolescent Lewis rats were fed for eight weeks with an experimental Western-like high-saturated fat/high-sugar diet (WD, 41% kcal from fat) or a matched control diet (CD, 13% kcal from fat). Acoustic fear-potentiated startle (FPS) responses were assessed longitudinally at weeks 1, 4, and 8 after commencing the diets to determine the effects of the WD on cued fear conditioning, fear extinction learning, and fear extinction retention.ResultsWe found that the rats that consumed the WD exhibited substantial attenuation of fear extinction and fear extinction retention when remote memory was tested. One-week WD consumption was sufficient to induce impairments in fear extinction learning. This phenotype was associated with reduced dopamine receptor 1 mRNA levels in the prefrontal cortex. Interestingly, our reconditioning paradigm revealed that early-acquired fear memories were resistant to the disruptive effects of chronic WD consumption on cued fear learning.ConclusionsOur findings demonstrate that consumption of an obesogenic WD during adolescence heightens behavioral vulnerabilities associated with risk for anxiety and stress-related disorders. Given that fear extinction promotes resilience and that fear extinction principles are the foundation of psychological treatments for PTSD, understanding how obesity and obesogenic diets affect the acquisition and expression of fear extinction memories is of tremendous clinical relevance.HIGHLIGHTSAcute WD consumption impairs cued fear extinction learning in a fear-potentiated startle paradigm.WD consumption attenuates fear extinction memory retentionWD consumption during adolescence increases acoustic startle responsivity over timeChronic WD consumption decreases dopamine receptor D1 mRNA levels in the prefrontal cortex.
System-wide analyses of the fission yeast poly(A)+ RNA interactome reveal insights into organisation and function of RNA-protein complexes
Authors: Kilchert Cornelia , Kecman Tea , Priest Emily , Hester Svenja , Kus Krzysztof , Castello Alfredo , Mohammed Shabaz , Vasiljeva Lidia 
Published: August 2019

AbstractProduction, function, and turnover of mRNA are orchestrated by multi-subunit machineries that play a central role in gene expression. Within these molecular machines, interactions with the target mRNA are mediated by RNA-binding proteins (RBPs), and the accuracy and dynamics of these RNA-protein interactions are essential for their function. Here, we show that fission yeast whole cell poly(A)+ RNA-protein crosslinking data provides system-wide information on the organisation and function of the RNA-protein complexes. We evaluate relative enrichment of cellular RBPs on poly(A)+ RNA to identify interactors with high RNA-binding activity and provide key information about the RNA-binding properties of large multi-protein complexes, such as the mRNA 3’ end processing machinery (cleavage and polyadenylation factor, CPF) and the RNA exosome. We demonstrate that different functional modules within CPF differ in their ability to interact with RNA. Importantly, we reveal that CPF forms additional contacts with RNA via the Fip1 subunit of the polyadenylation module and two subunits of the nuclease module. In addition, our data highlights the central role of the RNA helicase Mtl1 in RNA degradation by the exosome as mutations in Mtl1 lead to disengagement of the exosome from RNA. We examine how routes of substrate access to the complex are affected upon mutation of exosome subunits. Our results provide important insights into how different components of the exosome contribute to engagement of the complex with substrate RNA. Overall, our data uncover how multi-subunit cellular machineries interact with RNA, on a proteome-wide scale.
BRD2 regulation of sigma-2 receptor expression upon cytosolic cholesterol deprivation
Authors: Shen Hongtao , Li Jing , Xie Xiujie , Yang Huan , Zhang Mengxue , Wang Bowen , Kent K. Craig , Plutzky Jorge , Guo Lian-Wang 
Published: August 2019

AbstractTraditionally a pharmacologic target for antipsychotic treatment, the sigma-2 receptor (S2R) was recently implicated in cholesterol homeostasis. Here we investigated the transcriptional regulation of S2R by the Bromo/ExtraTerminal epigenetic reader family (BETs, including BRD2, 3, 4) upon cholesterol perturbation.Cytosolic cholesterol deprivation was induced using an export blocker of lysosomal cholesterol in ARPE19 cells. This condition upregulated mRNA and protein levels of S2R, and of SREBP2 but not SREBP1, transcription factors key to cholesterol/fatty acid metabolism. Silencing BRD2 but not BRD4 (though widely deemed as a master regulator) or BRD3 prevented S2R upregulation induced by cholesterol deprivation. Silencing SREBP2 but not SREBP1 diminished S2R expression. Furthermore, BRD2 co-immunoprecipitated with the SREBP2 transcription-active N-terminal domain, and chromatin immunoprecipitation-qPCR showed a BRD2 occupancy at the S2R gene promoter.In summary, this study reveals a novel BRD2/SREBP2 cooperative regulation of S2R transcription in response to cytosolic cholesterol deprivation, thus shedding new light on epigenetic control of cholesterol biology.
Subcellular metabolic pathway kinetics are revealed by correcting for artifactual post harvest metabolism
Authors: Trefely Sophie , Liu Joyce , Huber Katharina , Doan Mary T. , Jiang Helen , Singh Jay , von Krusenstiern Eliana , Bostwick Anna , Xu Peining , Bogner-Strauss Juliane , Wellen Kathryn E. , Snyder Nathaniel W. 
Published: August 2019

AbstractOBJECTIVEThe dynamic regulation of metabolic pathways can be monitored by stable isotope tracing. Yet, many metabolites are part of distinct processes within different subcellular compartments. Standard isotope tracing experiments relying on analyses in whole cells may not accurately reflect compartmentalized metabolic processes. Analysis of compartmentalized metabolism and the dynamic interplay between compartments can potentially be achieved by stable isotope tracing followed by subcellular fractionation. Although it is recognized that metabolism can take place during biochemical fractionation of cells, a clear understanding of how such post-harvest metabolism impacts the interpretation of subcellular isotope tracing data and methods to correct for this are lacking. We set out to directly assess artifactual metabolism, enabling us to develop and test strategies to correct for it. We apply these techniques to examine the compartment-specific metabolic kinetics of 13C-labeled substrates targeting central metabolic pathways.METHODSWe designed a stable isotope tracing strategy to interrogate post-harvest metabolic activity during subcellular fractionation using liquid chromatography-mass spectrometry (LC-MS).RESULTSWe show that post-harvest metabolic activity occurs rapidly (within seconds) upon cell harvest. With further characterization we reveal that this post-harvest metabolism is enzymatic, and reflects the metabolic capacity of the sub-cellular compartment analyzed; but is limited in the extent of its propagation into downstream metabolites in metabolic pathways. We also propose and test a post-labeling strategy to assess the amount of post-harvest metabolism occurring in an experiment and then to adjust data to account for this. We validate this approach for both mitochondrial and cytosolic metabolic analyses.CONCLUSIONSOur data indicate that isotope tracing coupled with sub-cellular fractionation can reveal distinct and dynamic metabolic features of cellular compartments, and that confidence in such data can be improved by applying a post-labeling correction strategy. We examine compartmentalized metabolism of acetate and glutamine and show that acetyl-CoA is turned over rapidly in the cytosol and acts as a pacemaker of anabolic metabolism in this compartment.