bluuebunny/crossref_metadata_2025_split huggingface dataset:
Harnessing Expressed Single Nucleotide Variation and Single Cell RNA Sequencing to Define Immune Cell Chimerism in the Rejecting Kidney Transplant
Authors: Malone Andrew F. , Wu Haojia , Fronick Catrina , Fulton Robert , Gaut Joseph P. , Humphreys Benjamin D. 
Published: March 2020

AbstractIn solid organ transplantation, donor derived immune cells are assumed to decline with time after surgery. Whether donor leukocytes persist within kidney transplants or play any role in rejection is unknown, however, in part because of limited techniques for distinguishing recipient and donor cells. To address this question, we performed paired whole exome sequencing of donor and recipient DNA and single cell RNA sequencing (scRNA-seq) of 5 human kidney transplant biopsy cores. Exome sequences were used to define single nucleotide variations (SNV) across all samples. By analyzing expressed SNVs in the scRNA-seq dataset we could define recipient vs. donor cell origin for all 81,139 cells. The leukocyte donor to recipient ratio varied with rejection status for macrophages and with time post-transplant for lymphocytes. Recipient macrophages were characterized by inflammatory activation and donor macrophages by antigen presentation and complement signaling. Recipient origin T cells expressed cytotoxic and pro-inflammatory genes consistent with an effector cell phenotype whereas donor origin T cells are likely quiescent expressing oxidative phosphorylation genes relative to recipient T cells. Finally, both donor and recipient T cell clones were present within the rejecting kidney, suggesting lymphoid aggregation. Our results indicate that donor origin macrophages and T cells have distinct transcriptional profiles compared to their recipient counterparts and donor macrophages can persist for years post transplantation. This study demonstrates the power of this approach to accurately define leukocyte chimerism in a complex tissue such as the kidney transplant coupled with the ability to examine transcriptional profiles at single cell resolution.
Age-related trajectories of DNA methylation network markers: a parenclitic network approach to a family-based cohort of patients with Down Syndrome
Authors: Krivonosov M. , Nazarenko T. , Bacalini M.G. , Vedunova M.V. , Franceschi C. , Zaikin A. , Ivanchenko M. 
Published: March 2020

AbstractDespite the fact that the cause of Down Syndrome (DS) is well established, the underlying molecular mechanisms that contribute to the syndrome and the phenotype of accelerated aging remain largely unknown. DNA methylation profiles are largely altered in DS, but it remains unclear how different methylation regions and probes are structured into a network of interactions. We develop and generalize the Parenclitic Networks approach that enables finding correlations between distant CpG probes (which are not pronounced as stand-alone biomarkers) and quantifies hidden network changes in DNA methylation. DS and a familybased cohort (including healthy siblings and mothers of persons with DS) are used as a case study. Following this approach, we constructed parenclitic networks and obtained different signatures that indicate (i) differences between individuals with DS and healthy individuals; (ii) differences between young and old healthy individuals; (iii) differences between DS individuals and their age-matched siblings, and (iv) difference between DS and the adult population (their mothers). The Gene Ontology analysis showed that the CpG network approach is more powerful than the single CpG approach in identifying biological processes related to DS phenotype. This includes the processes occurring in the central nervous system, skeletal muscles, disorders in carbohydrate metabolism, cardiopathology, and oncogenes. Our open-source software implementation is accessible to all researchers. The software includes a complete workflow, which can be used to construct Parenclitic Networks with any machine learning algorithm as a kernel to build edges. We anticipate a broad applicability of the approach to other diseases.
The 16S microbiota of Budu, the Malaysian fermented anchovy sauce
Authors: Md Zoqratt Muhammad Zarul Hanifah , Gan Han Ming 
Published: March 2020

ABSTRACTBudu is a Malaysian fermented anchovy sauce produced by immersing small fishes into a brine solution for 6 to 18 months. Fermentation of the anchovy sauce is contributed partly by microbial enzymes, but little is known about the microbial community in Budu. Therefore, a better understanding of the Budu microbiome is necessary to better control the quality, consistency and safety of the product. In this study, we collected 60 samples from twenty bottles of Budu produced by seven different manufacturers. We analyzed their microbiota based on V3-V4 16S rRNA amplicon sequencing at the time of opening the bottle as well as 3- and 7-months post-opening.Tetragenococcuswas the dominant genus in many samples, reaching a maximum proportion of 98.62%, but was found in low abundance, or absent, in other samples. When Budu samples were not dominated by a dominant taxa, we observed a wider genera diversity such asStaphylococcus, Acinetobacter, HalanaerobiumandBacillus. While the taxonomic composition was relatively stable across sampling periods, samples from two brands showed a sudden increase in relative abundance of the genusChromobacteriumin the 7thmonth. Based on prediction of metagenome functions, non-Tetragenococcus-dominated samples were predicted to have enriched functional pathways related to amino acid metabolism and purine metabolism compared toTetragenococcus-dominated microbiome; these two pathways are fundamental fermented quality and health attributes of fish sauce. Within the non-Tetragenococcus-dominated group, contributions towards amino acid metabolism and purine metabolism were biased towards the dominant taxa when species evenness is low, while in samples with higher species evenness, the contributions towards the two pathways were predicted to be evenly distributed between taxa.
Pathogenic LRRK2 R1441C mutation is associated with striatal alterations
Authors: Xenias Harry S. , Chen Chuyu , Kang Shuo , Cherian Suraj , Situ Xiaolei , Shanmugasundaram Bharanidharan , Scesa Giuseppe , Chan C. Savio , Parisiadou Loukia 
Published: March 2020

AbstractLRRK2 mutations are associated with both familial and sporadic forms of Parkinson’s disease (PD). Convergent evidence suggests that LRRK2 plays critical roles in regulating striatal function. Here, by using knock-in mouse lines that express the two most common LRRK2 pathogenic mutations—G2019S and R1441C—we investigated how pathogenic LRRK2 mutations altered striatal physiology. We found that R1441C mice displayed a reduced nigrostriatal dopamine release and hypoexcitability in indirect-pathway striatal projection neurons. These alterations were associated with an impaired striatal-dependent motor learning. This deficit in motor learning was rescued following the subchronic administration of the LRRK2 kinase inhibitor Mli-2. In contrast, though a decreased release of dopamine was observed in the G2019S knock-in mice no concomitant cellular and behavioral alterations were found. In summary, our data argue that the impact of LRRK2 mutations cannot be simply generalized. Our findings offer mechanistic insights for devising treatment strategies for PD patients.
Glucose-dependent activation, activity, and deactivation of beta cell networks in acute mouse pancreas tissue slices
Authors: Stožer Andraž , Klemen Maša Skelin , Gosak Marko , Bombek Lidija Križančić , Pohorec Viljem , Rupnik Marjan Slak , Dolenšek Jurij 
Published: March 2020

AbstractMany details of glucose-stimulated intracellular calcium changes in beta cells during activation, activity and deactivation, as well as their concentration-dependence, remain to be described. Classical physiological experiments indicated that in islets functional differences between individual cells are largely attenuated, but recent findings suggest considerable intercellular heterogeneity, with some cells possibly coordinating the collective responses. To address the above with an emphasis on heterogeneity and describing the relations between classical physiological and functional network properties, we performed functional multicellular calcium imaging in mouse pancreas tissue slices over a wide range of glucose concentrations. During activation, delays to activation of cells and first responder-any cell delays shortened, and the sizes of simultaneously responding clusters increased with increasing glucose. Exactly the opposite characterized deactivation. The frequency of fast calcium oscillations during activity increased with increasing glucose up to 12 mM glucose, beyond which oscillation duration became longer, resulting in a homogenous increase in active time. In terms of functional connectivity, islets progressed from a very segregated network to a single large functional unit with increasing glucose. A comparison between classical physiological and network parameters revealed that the first-responders during activation had longer active times during plateau and the most active cells during the plateau tended to deactivate later. Cells with the most functional connections tended to activate sooner, have longer active times, and deactivate later. Our findings provide a common ground for recent differing views on beta cell heterogeneity and an important baseline for future studies of stimulus-secretion and intercellular coupling.
Inhibition of KDM1A activity restores adult neurogenesis and improves hippocampal memory in a mouse model of Kabuki syndrome
Authors: Zhang Li , Pilarowski Genay , Pich Emilio Merlo , Nakatani Atsushi , Dunlop John , Baba Rina , Matsuda Satoru , Daini Masaki , Hattori Yasushi , Matsumoto Shigemitsu , Ito Mitsuhiro , Kimura Haruhide , Bjornsson Hans Tomas 
Published: March 2020

AbstractKabuki syndrome (KS) is a rare cause of intellectual disability primarily caused by loss of function mutations in lysine-specific methyltransferase 2D (KMT2D), which normally adds methyl marks to lysine 4 on histone 3. Previous studies have shown that a mouse model of KS (Kmt2d+/βGeo) demonstrates disruption of adult neurogenesis and hippocampal memory. Proof-of-principle studies have shown postnatal rescue of neurological dysfunction following treatments that promote chromatin opening, however, these strategies are non-specific and do not directly address the primary defect of histone methylation. Since lysine-specific demethylase 1A (LSD1/KDM1A) normally removes the H3K4 methyl marks added by KMT2D, we hypothesize that inhibition of KDM1A demethylase activity may ameliorate molecular and phenotypic defects stemming from KMT2D loss. To test this hypothesis, we evaluated a recently developed KDM1A inhibitor (TAK-418) inKmt2d+/βGeomice. We find that orally administered TAK-418 increases the numbers of newly born Doublecortin (DCX)+cells and processes in hippocampus in a dose dependent manner. We also observe TAK-418-dependent rescue of histone modification defects in hippocampus both by Western blot and ChIP-Seq. Treatment rescues gene expression abnormalities including those of immediate early genes such as FBJ osteosarcoma oncogene (Fos)and FBJ osteosarcoma oncogene homolog B (Fosb). After 2 weeks of TAK-418,Kmt2d+/βGeomice demonstrate normalization of hippocampal memory defects. In summary, our data suggest that KDM1A inhibition is a plausible treatment strategy for KS and support the hypothesis that the epigenetic dysregulation secondary to KMT2D dysfunction plays a major role in the postnatal neurological disease phenotype in KS.
Hough transform implementation to evaluate the morphological variability of the moon jellyfish (Aureliaspp.)
Authors: Lacaux Céline , Desolneux Agnès , Gadreaud Justine , Martin-Garin Bertrand , Thiéry Alain 
Published: March 2020

AbstractVariations of the animal body plan morphology and morphometry can be used as prognostic tools of their habitat quality. The potential of the moon jellyfish (Aureliaspp.) as a new model organism has been poorly tested. However, as a tetramerous symmetry organism, it exhibits some variations in radial symmetry number. A pertinent list of morphological – number of gonads – and morphometric characteristics – e.g. ratio of the gonads area on the umbrella area – has been established to describe the morphology of 19 specimens through an image analysis. The method uses for the first time the Hough transform to approximate the gonads and the umbrella by ellipses and automatically extracts the morphometric data. A statistical comparison has been done to compare the morphometric characteristics of tetramerous jellyfish and of jellyfish with 5 gonads: it is only provided as a first step for testing biological hypotheses, since the small size of the data set leads to relativize its conclusions. It suggests that two parameters are discriminant: distance between the center of the gonads and the center of the umbrella, and the individual variability of the gonad eccentricity, both higher in jellyfish with 5 gonads. Additionally, the relative size of the gonads does not seem to be different between tetramerous and non-tetramerous. Combined to ecotoxicological bioassays to better understand the causes of this developmental alteration, this optimizable method can become a powerful tool in the symmetry description of anin situpopulation.
An Assay for Apoptosis detection based on Quantification of Multi nuclei feature and Nucleus to Cytoplasm ratio inS. cerevisiaecells treated with Acetic Acid and Hydrogen peroxide
Authors: Bairwa Narendra K , Shoket Heena , Pandita Monika , Sharma Meenu 
Published: March 2020

AbstractThe programmed cell death, apoptosis is a complex universal biological process in all types of eukaryotes ranging from single cell to multi-cellular organisms. The markers for apoptosis have been studied by assays based on both biochemical as well as microscopy however most assays are not affordable for many smaller labs. Acetic acid and hydrogen peroxide both induce apoptosis at higher concentrations inS. cerevisiae.Here we describe an assay system for the detection of apoptosis features based on DAPI staining followed by fluorescence microscopy in the cells treated with apoptosis inducing concentration of acetic acid and hydrogen peroxide. In this assay both untreated and cells treated with acetic acid and hydrogen peroxide were stained with DAPI and observed for the late stage apoptosis feature, Nuclear DNA fragmentation based multi nuclei centers and increase in the nuclear region enlargement. Further the multi nuclei feature and enlarged nuclei region as nucleus to cytoplasm ratio was quantified using Image J software. We report thatS. cerevisiaestrain BY4741 cells when treated with apoptosis inducing doses of acetic acid (140mM) and hydrogen peroxide (10mM) for 200 minutes, showed apoptosis marker feature such as nuclear region enlargement with multi-nuclei feature due to nuclear DNA fragmentation and increased nucleus to cytoplasm ratio when compared with untreated cells. We propose that this assay can be utilized for scoring the quantitative apoptotic feature as increase in multi-nuclei centers due to DNA fragmentation and nucleus to cytoplasm ratio as an indicator of apoptosis inS. cerevisiaeupon treatment with apoptosis inducing agents. The assay system described here is easy to perform and affordable for the smaller lab to analyze the apoptotic features inS. cerevisiaecells which can be applied to other system as well.
Endogenous retroviruses drive species-specific germline transcriptomes in mammals
Authors: Sakashita Akihiko , Maezawa So , Alavattam Kris G. , Yukawa Masashi , Barski Artem , Pavlicev Mihaela , Namekawa Satoshi H. 
Published: March 2020

AbstractGene regulation in the germline ensures the production of high-quality gametes, long-term maintenance of the species, and speciation. Germline transcriptomes undergo dynamic changes after the mitosis-to-meiosis transition in males and have been subject to evolutionary divergence among mammals. However, the mechanism that underlies germline regulatory divergence remains undetermined. Here, we show that endogenous retroviruses influence species-specific germline transcriptomes in mammals. We show that the expression of endogenous retroviruses, particularly the evolutionarily young K family (ERVK), is associated with gene activation after the mitosis-to-meiosis transition in male mice. We demonstrate that accessible chromatin and H3K27ac, a marker of active enhancers, are tightly associated with ERVK loci as well as with the activation of neighboring evolutionarily young germline genes. Thus, ERVKs serve as evolutionarily novel enhancers in mouse spermatogenesis. These ERVK loci bear binding motifs for critical regulators of spermatogenesis such as A-MYB. The genome-wide transposition of ERVKs might have rewired germline gene expression in a species-specific manner. Notably, these features are present in human spermatogenesis, but independently evolved ERVs are associated with expression of germline genes, demonstrating the prevalence of ERV-driven mechanisms in mammals. Together, we propose a model whereby species-specific transcriptomes are fine-tuned by endogenous retroviruses in the mammalian germline.
Membrane-proximal external region is a superior target for mediating effector activity of HIV-1 specific chimeric antigen receptor modified T cells
Authors: Kranz Emiko , Chan Joshua , Hashimoto Maya , Kanazawa Toshio , Wang Hanlu , Kamata Masakazu 
Published: March 2020

AbstractThe use of chimeric antigen receptor modified-T (CAR-T) cells in adoptive immunotherapy has been popularized through recent success in the field of cancer treatment research. CD4ζ CAR, which targets HIV-1-infected cells, has been developed and evaluated in patients. Though well-tolerated for over a decade, efficacy was disappointingly limited. This result encourages us to develop a novel CAR more effective than CD4ζ CAR. To quantitatively compare anti-HIV-1 activity of different CAR constructs in a highly sensitive and reproducible manner, we developed a multicolor flow cytometry method for assessing anti-HIV-1 effector T-cell activity. “Target” Jurkat cells inducibly expressing an HIV-1HXBC2envelope protein and “Non-target” control cells were genetically labeled with red and blue fluorescent protein, respectively, and co-incubated with human primary T cells transduced with anti-HIV-1 “Effector” CARs at various Effector vs Target cell ratios. Absolute cell numbers of each population were collected by MACSQuant Analyzer and used for calculation of relative cytotoxicity. We successfully ranked the cytotoxicity of three previously reported single chain-antibody CARs and six newly developed single-domain antibody CARs in comparison to CD4ζ CAR. Interestingly, three CARs—10E8, 2E7, and 2H10—which demonstrate high cytotoxic activity were all known to target the membrane-proximal external region. Use of this novel assay will simplify assessment of new CAR constructs and in turn accelerate the development of new effective CARs against HIV-1.Author SummaryAdoptive immunotherapies that utilize autologous T cells expressing a desired antigen-specific CAR aim to elicit directed immune responses. In recent years, CAR immunotherapies have been promoted extensively in B cell malignancy treatments. The HIV-1-targeting CAR, known as CD4ζ, was developed over 20 years ago and has been widely and longitudinally tested in patients. However, its effectiveness was hindered by poor survival and functionality of the transduced cells. To conduct quantitative evaluation of newly designed anti-HIV-1 CARs, we developed a novel multicolor flow-based assay for HIV-1-specific cytotoxicity, enabling sensitive and quantitative assessment in a high-throughput fashion. This assay would be also useful in screening HIV-1-targeting immune receptors—including CARs and T cell receptors—and other immunotherapeutic drugs such as anti-HIV-1 antibodies.
An approach to stress assessment during hunting: Cortisol levels of wild boar (Sus scrofa) during drive hunts
Authors: Güldenpfennig Justine , Schmicke Marion , Hoedemaker Martina , Siebert Ursula , Keuling Oliver 
Published: March 2020

AbstractOnly little is known about the effect of stress (both short-term and long-term) on wildlife species. To get an idea of stress in wildlife, we investigated the cortisol level of wild boar during drive hunts in Lower Saxony, Germany. Cortisol as one of the main stress hormone in mammals is considered to have negative impacts on the animal’s well-being if expressed excessively (repeatedly over a longer period). We analysed serum cortisol levels of 115 samples using a radioimmunoassay and compared sampling month, hunting grounds, age classes and sexes, as well as possible correlations between cortisol level and weight and pregnancy status of female wild boar. We found that cortisol levels during these drive hunts exhibit wide variation. The mean cortisol level was 411.16 nmol/L with levels ranging from 30.60 nmol/L (minimum) to 1,457.92 nmol/L (maximum). Comparing age groups and sexes, we found significant differences between the sexes, with females having a higher cortisol levels than males. After grouping age groups and sexes together, we also found significant differences based on the age-sex group. We found no correlation between cortisol levels and weight, but significantly higher cortisol levels in pregnant females compared to non-pregnant females. No differences were found between sampling months and locations, respectively. These results show the impact of drive hunts on stress in wild boar; nevertheless, this impact of drive hunts as performed in most parts of Central Europe seems to be not as high as imagined. Still, we need more information about cortisol levels and stress in (hunted) wildlife species.
Network Organisation and the Dynamics of Tubules in the Endoplasmic Reticulum
Authors: Perkins H. , Ducluzaux P. , Woodman P. , Allan V. , Waigh T. 
Published: March 2020

ABSTRACTThe endoplasmic reticulum (ER) is a eukaryotic subcellular organelle composed of tubules and sheet-like areas of membrane connected at junctions. The tubule network is highly dynamic and undergoes rapid and continual rearrangement. There are currently few tools to evaluate network organisation and dynamics. We quantified ER network organisation in Vero and MRC5 cells, and developed a classification system for ER dynamics in live cells. The persistence length, tubule length, junction coordination number and angles of the network were quantified. Hallmarks of imbalances in ER tension, indications of interactions with microtubules and other subcellular organelles, and active reorganisation and dynamics were observed. Live cell ER tubule dynamics were classified using a Gaussian mixture model, defining tubule motion asactiveorthermaland conformational phase space analysis allowed this classification to be refined by tubule curvature states.STATEMENT OF SIGNIFICANCEThe endoplasmic reticulum (ER), a subcellular organelle, is an underexplored real-world example of active matter. Many processes essential to cell survival are performed by the ER, the efficacy of which may depend on its organisation and dynamics. Abnormal ER morphology is linked to diseases such as hereditary spastic paraplegias and it is possible that the dynamics are also implicated. Therefore, analysing the ER network in normal cells is important for the understanding of disease-related alterations. In this work, we outline the first thorough quantification methods for determining ER organisation and dynamics, deducing that tubule motion has a binary classification as active or thermal. Active reorganisation and dynamics along with indications of tension imbalances and membrane contact sites were observed.