bluuebunny/crossref_metadata_2025_split huggingface dataset:
Respiratory depression and analgesia by opioid drugs in freely-behaving larval zebrafish
Authors: Zaig Shenhab , Scarpellini Carolina , Montandon Gaspard 
Published: October 2020

AbstractAn opioid epidemic is spreading in North America with millions of opioid overdoses annually. Opioid drugs, like fentanyl, target the mu opioid receptor system and induce potentially lethal respiratory depression. The challenge in opioid research is to find a safe pain therapy with analgesic properties but no respiratory depression. Current discoveries are limited by lack of amenable animal models to screen candidate drugs. Zebrafish (Danio rerio) is an emerging animal model with high reproduction and fast development, which shares remarkable similarity in their physiology and genome to mammals. However, it is unknown whether zebrafish possesses similar opioid system, respiratory and analgesic responses to opioids than mammals. In freely-behaving larval zebrafish, fentanyl depresses the rate of respiratory mandible movements and induces analgesia, effects reversed by mu-opioid receptor antagonists. Zebrafish presents evolutionary conserved mechanisms of action of opioid drugs, also found in mammals, and constitute amenable models for phenotype-based drug discovery.
Model-guided design of mammalian genetic programs
Authors: Muldoon Joseph J. , Kandula Viswajit , Hong Mihe , Donahue Patrick S. , Boucher Jonathan D. , Bagheri Neda , Leonard Joshua N. 
Published: October 2020

ABSTRACTGenetically engineering cells to perform customizable functions is an emerging frontier with numerous technological and translational applications. However, it remains challenging to systematically engineer mammalian cells to execute complex functions. To address this need, we developed a method enabling accurate genetic program design using high-performing genetic parts and predictive computational models. We built multi-functional proteins integrating both transcriptional and post-translational control, validated models for describing these mechanisms, implemented digital and analog processing, and effectively linked genetic circuits with sensors for multi-input evaluations. The functional modularity and compositional versatility of these parts enable one to satisfy a given design objective via multiple synonymous programs. Our approach empowers bioengineers to predictively design mammalian cellular functions that perform as expected even at high levels of biological complexity.
The role of cation diffusion facilitator CDF-1 in lipid metabolism inCaenorhabditis elegans
Authors: Hu Ying , Wang Yanli , Wang Xuanjun , Wu Xiaoyun , Fu Lin , Liu Xiayu , Wen Yu , Sheng Jun , Zhang Jingjing 
Published: October 2020

AbstractZinc is one of the most important trace elements that plays a vital role in many biological processes, and aberrant zinc metabolism has been implicated in lipid-related metabolic diseases. Previously, we showed that zinc antagonizes iron to regulate sterol regulatory element-binding proteins and stearoyl-CoA desaturase (SREBP-SCD) pathway in lipid metabolism in model organismCaenorhabditis elegans. Here, we further identified another cation diffusion facilitator CDF-1 in addition to SUR-7 in response to zinc to regulate lipid metabolism. Inactivation of SBP-1, the only homolog of SREBPs, leads to increased zinc level but decreased lipid accumulation reversely. However, eithercdf-1(n2527)orsur-7(tm6523)mutation could successfully restore the altered fatty acid profile, fat content and zinc level ofsbp-1(ep79)mutant. Furthermore, we found that CDF-1/SUR-7 may function bypass SBP-1 to directly affect the conversion activity of SCD in the biosynthesis of unsaturated fatty acids and lipid accumulation. Collectively, these results consistently support the link between zinc homeostasis and lipid metabolism via SREBP-SCD axis by cation diffusion facilitators CDF-1 and SUR-7.
Novel genetic tools to model functional enzyme restoration in succinic semialdehyde dehydrogenase deficiency (SSADHD)
Authors: Cheong Lee Henry Hing , Pearl Phillip , Rotenberg Alexander 
Published: October 2020

AbstractSSADHD is a rare inborn metabolic disorder caused by the functional impairment of SSADH (encoded by the aldh5a1 gene), an enzyme essential for breaking down the inhibitory neurotransmitterγ-aminobutyric acid (GABA). In SSADHD, pathologic accumulation of GABA results in broad spectrum encephalopathy including developmental delay, ataxia, seizures and a risk of sudden unexpected death in epilepsy (SUDEP). Proof-of-concept systemic SSADH restoration via enzyme replacement therapy (ERT) or aldh5a1 gene transfer increased survival of SSADH knockout mice, suggesting that SSADH restoration might be a viable cure for SSADHD. However, before testing SSADH restoration therapy in patients, we must consider its safety and feasibility in context of the unique SSADHD pathophysiology. Specifically, a profound use-dependent down-regulation of GABAAreceptors in SSADHD indicates a risk that sudden SSADH restoration might diminish GABAergic tone and provoke seizures. Such risk may be mitigated by gradual, rather than abrupt, SSADH restoration, or by restoration that is confined to critical cell types and brain regions. We therefore describe early work to construct a novel SSADHD mouse model that allows ‘on-demand’ SSADH restoration for the systematic investigation of the rate, timing and cell-specific parameters of SSADH-restoring therapies. We aim to understand the clinical readiness of specific SSADH restoration protocols on brain physiology for purposes of accelerating the bench to bed-side development of ERT or gene therapy for SSADHD patients.
High-dimensional mass cytometry analysis of NK cell alterations in Acute Myeloid Leukemia identifies a subgroup with adverse clinical outcome
Authors: Chretien Anne-Sophie , Devillier Raynier , Granjeaud Samuel , Cordier Charlotte , Demerle Clemence , Salem Nassim , Wlosik Julia , Orlanducci Florence , Gregori Emilie , Paul Magali , Rochigneux Philippe , Pagliardini Thomas , Morey Mathieu , Fauriat Cyril , Dulphy Nicolas , Toubert Antoine , Luche Herve , Malissen Marie , Blaise Didier , Nunès Jacques A. , Vey Norbert , Olive Daniel 
Published: October 2020

ABSTRACTNatural killer (NK) cells are major anti-leukemic immune effectors. Leukemic blasts have a negative impact on NK cell function and promote the emergence of phenotypically and functionally impaired NK cells. In the present work, we highlight an accumulation of CD56-CD16+unconventional NK cells in acute myeloid leukemia (AML), an aberrant subset initially described as being elevated in patients chronically infected with HIV-1. Deep phenotyping of NK cells was performed using peripheral blood from patients with newly-diagnosed AML (N=48, HEMATOBIO cohort,NCT02320656) and healthy subjects (N=18) by mass cytometry. We evidenced a moderate to drastic accumulation of CD56-CD16+unconventional NK cells in 27% of patients. These NK cells displayed decreased expression of NKG2A as well as the triggering receptors NKp30, and NKp46, in line with previous observations in HIV-infected patients. High-dimensional characterization of these NK cells highlighted a decreased expression of three additional major triggering receptors required for NK cell activation, NKG2D, DNAM-1, and CD96. A high proportion of CD56-CD16+NK cells at diagnosis was associated with an adverse clinical outcome, with decreased overall survival (HR=0.13; P=.0002) and event-free survival (HR=0.33; P=.018), and retained statistical significance in multivariate analysis. Pseudo-time analysis of the NK cell compartment highlighted a disruption of the maturation process, with a bifurcation from conventional NK cells toward CD56-CD16+NK cells. Overall, our data suggest that the accumulation of CD56-CD16+NK cells may be the consequence of immune escape from innate immunity during AML progression.SignificanceThis work provides the first report of accumulation of unconventional CD56-CD16+ NK cells in non-virally induced malignancies. Pseudotime analysis highlights a bifurcation point occurring during the course of NK cell maturation, providing elements regarding the possible origin of CD56-CD16+ NK cells. Increased frequency of CD56-CD16+ NK cells is associated with adverse clinical outcome in AML and might contribute, as well as other maturation defects, to a defective control of AML progression. Overall, accumulation of CD56-CD16+ NK cells could be an important feature of immune escape from innate immunity.Graphical abstractKey pointsA disruption in the maturation process of NK cells leads to accumulation of unconventional CD56-CD16+NK cells in patients with AMLHigh frequency of CD56-CD16+NK cells is associated with adverse clinical outcome
Single Cell Analysis Reveals Multi-faceted miR-375 Regulation of the Intestinal Crypt
Authors: Shanahan Michael T. , Kanke Matt , Singh Ajeet P. , Villanueva Jonathan W. , McNairn Adrian J. , Oyesola Oyebola O. , Bonfini Alessandro , Hung Yu-Han , Sheahan Breanna , Bloom Jordana C. , Cubitt Rebecca L. , Curry Ennessa G. , Pitman Wendy A. , Rinaldi Vera D. , Dekaney Christopher M. , Ding Shengli , Peck Bailey C.E. , Schimenti John C. , Dow Lukas E. , Buchon Nicolas , Tait-Wojno Elia D. , Sethupathy Praveen 
Published: October 2020

SummaryThe role of individual miRNAs in small intestinal (SI) epithelial homeostasis is under-explored. In this study, we discovered that miR-375 is among the most enriched miRNAs in intestinal crypts and stem cells (ISCs), especially facultative ISCs. We then showed by multiple manipulations, including CRISPR/Cas9 editing, that miR-375 is strongly suppressed by Wnt-signaling. Single-cell RNA-seq analysis of SI crypt-enriched cells from miR-375 knockout (375-KO) mice revealed elevated numbers of tuft cells and increased expression of pro-proliferative genes in ISCs. Accordingly, the genetic loss of miR-375 promoted resistance to helminth infection and enhanced the regenerative response to irradiation. The conserved effects of miR-375 were confirmed by gain-of-function studies in Drosophila midgut stem cellsin vivo.Moreover, functional experiments in enteroids uncovered a regulatory relationship between miR-375 and Yap1 that controls cell survival. Finally, analysis of mouse model and clinical data revealed an inverse association between miR-375 levels and intestinal tumor development.HighlightsmiR-375 is one of the most enriched miRNAs in ISCs, especially facultative ISCs.miR-375 modifies tuft cell abundance and pro-proliferative gene expression in ISCs.Loss of miR-375 in mice enhances the host response to helminth infection and crypt regeneration.Mouse and human intestinal cancer are associated with reduced miR-375 expression.eTOC BlurbSethupathy and colleagues show that miR-375 is a Wnt-responsive, ISC-enriched miRNA that serves as a break on intestinal crypt proliferation. They also show that miR-375 modulates tuft cell abundance and pro-proliferative gene expression in ISCs, that miR-375 loss enhances the host response to helminth infection as well as crypt regeneration post-irradiation, and its reduced expression is associated with intestinal cancer.
Inorganic Pyrophosphate Promotes Osteoclastogenic Commitment and Survival of Bone Marrow Derived Monocytes mediated byEgr-1up-regulation and MITF phosphorylation
Authors: Abdelmagid Samir M. , Zajac Allison , Salhab Imad , Nah Hyun-Duck 
Published: October 2020

ABSTRACTSeveral reports emphasized the importance of inorganic pyrophosphate (PPi) in hindering osteoblast differentiation and bone matrix mineralization. Its ubiquitous presence is thought to prevent “soft” tissue calcification, whereas its degradation to Piin bones and teeth by alkaline phosphatase (ALP) may facilitate crystal growth. While the inhibiting role of PPion osteoblast differentiation and function is largely understood, less is known about its effects on osteoclast determination and activity. In this study, we investigated the role of PPiin bone resorption using calverial organ culturesex vivo. We present an evidence that PPistimulated calvarial bone resorption marked by calcium (Ca2+) release in the condition media (CM). We then examined PPieffects on osteoclast differentiation using mouse bone marrow-derived monocytes (BMMs). Our results revealed that PPienhanced osteoclast differentiationex vivo, marked by increased number and size of TRAP-stained mature osteoclasts. Moreover, PPistimulated osteoclastogenesis in BMMs co-cultured with osteoblasts. These data supported the increased osteoclast activity in bone resorption using functional osteo-assays. The finding of PU.1-Egr-1 dependent up-regulation of c-FMS and RANK receptors in BMMs supported the enhanced pre-osteoclast commitment and differentiation. Moreover, osteoclast survival was enhanced by activation of MITF-BCL-2 pathway that was mediated by MAPK-ERK1/2 signaling. Last, our data showed that PPiup-regulated ANK; PPitransporter, during osteoclast differentiation through ERK1/2 phosphorylation whereas mutation of ANK inhibited osteoclastogenesis. Collectively, our data suggest that PPipromotes osteoclast differentiation, survival, and function through PU.1 up-regulation and MITF phosphorylation whereas ANK loss-of-function inhibited osteoclastogenesis.
The effect of maternal HMB supplementation on bone mechanical and geometrical properties, as well as histomorphometry and immunolocalization of VEGF, TIMP2, MMP13, BMP2 in the bone and cartilage tissue of the humerus of their newborn piglets
Authors: Tomczyk-Warunek Agnieszka , Blicharski Tomasz , Jarecki Jaromir , Dobrowolski Piotr , Muszyński Siemowit , Tomaszewska Ewa , Rovati Lucio C. 
Published: October 2020

AbstractThe presented experiment focuses on assessing the impact of HMB (hydroxy-β-methobutyrate) supplementation of mothers during pregnancy on the development of the skeletal system of their offspring. For this purpose, an experiment was carried out on 12 clinically healthy sows of the Great White Poland breed, which were divided randomly into two groups the control and the HMB group. All animals were kept under standard conditions and received the same feed for pregnant females. In contrast, females from the HMB group between 70 and 90 days were supplemented with 3-hydroxy-3-methylbutyle in the amount of 0.2g/kg b.w/day. Immediately after birth, the piglets were also divided into groups based on: sex, and presence or lack HMB supplementation, and subsequently were euthanized and humerus bones from all piglets were collected.Mother’s HMB supplementation during pregnancy affected the multiple index of their offspring. The higher humerus mass and length was observed with the greater effect in males. Maternal supplementation also influenced on the geometrical and mechanical properties of the humerus as in the case of mass, this effect was higher in males. Also, the collagen structure of the compacted and trabecular bone changed under the HMB addition. Maternal supplementation also affected the expression of selected proteins in growth cartilage and trabecular bone. The obtained results show that the administration to the mother during pregnancy by the HMB significantly affects the development of the humerus in many ways. The obtained results also confirm the utility of such experiments in understanding of the importance of the pregnancy diet as an develop and adaptable factor of offspring organisms and are the base for further research in that area as well as in the protein markers expression area.
DamageProfiler: Fast damage pattern calculation for ancient DNA
Authors: Neukamm Judith , Peltzer Alexander , Nieselt Kay 
Published: October 2020

AbstractIn ancient DNA research, the authentication of ancient samples based on specific features remains a crucial step in data analysis. Because of this central importance, researchers lacking deeper programming knowledge should be able to run a basic damage authentication analysis. Such software should be user-friendly and easy to integrate into an analysis pipeline. Here, we present DamageProfiler, a Java based, stand-alone software to determine damage patterns in ancient DNA. The results are provided in various file formats and plots for further processing. DamageProfiler has an intuitive graphical as well as command line interface that allows the tool to be easily embedded into an analysis pipeline.
Single cell transcriptional and functional analysis of human dopamine neurons in 3D fetal ventral midbrain organoid like cultures
Authors: Birtele Marcella , Sharma Yogita , Storm Petter , Kajtez Janko , Wahlestedt Jenny Nelander , Sozzi Edoardo , Nilsson Fredrik , Stott Simon , He Xiaoling L , Mattsson Bengt , Ottosson Daniella Rylander , Barker Roger A , Fiorenzano Alessandro , Parmar Malin 
Published: October 2020

SUMMARYTransplantation of midbrain dopamine (DA) neurons for the treatment of Parkinson’s disease (PD) is a strategy that has being extensively explored and clinical trials using fetal and stem cell-derived DA neurons are ongoing. An increased understanding of the mechanisms promoting the generation of distinct subtypes of midbrain DA during normal development will be essential for guiding future efforts to precisely generate molecularly defined and subtype specific DA neurons from pluripotent stem cells. In this study, we used droplet-based scRNA-seq to transcriptionally profile a large number of fetal cells from human embryos at different stages of ventral midbrain (VM) development (6, 8, and 11 weeks post conception). This revealed that the emergence of transcriptionally distinct cellular populations was evident already at these early timepoints. To study late events of human DA differentiation and functional maturation, we established a primary fetal 3D culture system that recapitulates key molecular aspects of late human DA neurogenesis and sustains differentiation and functional maturation of DA neurons in a physiologically relevant cellular context. This approach allowed us to define the molecular identities of distinct human DA progenitors and neurons at single cell resolution and construct developmental trajectories of cell types in the developing fetal VM.Overall these findings provide a unique transcriptional profile of developing fetal VM and functionally mature human DA neurons, which can be used to quality control stem cell-derived DA neurons and guide stem cell-based therapies and disease modeling approaches in PD.
A conserved cell division protein directly regulates FtsZ dynamics in filamentous and unicellular actinobacteria
Authors: Ramos-Léon Felix , Bush Matthew J. , Sallmen Joseph W. , Chandra Govind , Richardson Jake , Findlay Kim C. , McCormick Joseph R. , Schlimpert Susan 
Published: October 2020

AbstractBacterial cell division is driven by the polymerization of the GTPase FtsZ into a contractile structure, the so-called Z-ring. This essential process involves proteins that modulate FtsZ dynamics and hence the overall Z-ring architecture. Actinobacteria, likeStreptomycesandMycobacteriumlack known key FtsZ-regulators. Here we report the identification of SepH, a conserved actinobacterial protein that directly regulates FtsZ dynamics. We show that SepH is crucially involved in cell division inStreptomycesand that it binds FtsZ via a conserved helix-turn-helix motif, stimulating the assembly of FtsZ protofilaments. Comparativein vitrostudies using the SepH homolog fromMycobacteriumfurther reveal that SepH can also bundle FtsZ protofilaments, indicating an additional Z-ring stabilizing functionin vivo. We propose that SepH plays a crucial role at the onset of cytokinesis in actinobacteria by promoting the rapid assembly of FtsZ filaments into division-competent Z-rings that can go on to mediate septum synthesis.
Gut metabolites are more predictive of disease- and cohoused- states than gut bacterial features in a mouse model of polycystic ovary syndrome
Authors: Ho Bryan , Ryback Daniel , Benson Basilin , Torres Pedro J. , Quinn Robert A , Thackray Varykina G. , Kelley Scott T. 
Published: October 2020

ABSTRACTPolycystic ovary syndrome (PCOS) impacts ∼10% of reproductive-aged women worldwide. In addition to infertility, women with PCOS suffer from metabolic dysregulation which increases their risk of developing type 2 diabetes, cardiovascular disease and non-alcoholic fatty liver disease. Studies have shown differences in the gut microbiome of women with PCOS compared to controls, a pattern replicated in mouse models. Recently, using a letrozole-induced mouse model of PCOS, we demonstrated that cohousing was protective against development of metabolic and reproductive phenotypes and showed via 16S amplicon sequencing that this protection correlated with time-dependent shifts in gut bacteria. Here, we applied untargeted metabolomics and shotgun metagenomics approaches to further analyze the longitudinal samples from the cohousing experiment. Analysis of beta diversity found that untargeted metabolites had the strongest correlation to both disease and cohoused states and that shifts in metabolite diversity were detected prior to shifts in bacterial diversity. In addition, log2-fold analyses found numerous metabolite features, particularly bile acids (BA), to be highly differentiated between placebo (P) and letrozole (LET), as well as cohoused LET versus LET. Our results indicate that changes in gut metabolites, particularly BAs, are associated with a PCOS-like phenotype in the LET mouse model as well as the protective effect of cohousing. Our results also suggest that transfer of metabolites via coprophagy occurs rapidly and may precipitate changes in bacterial diversity. This study joins a growing body of research highlighting changes in primary and secondary bile acids that may provide a link between host metabolism and gut microbes relevant to the pathology of PCOS.IMPORTANCEUsing a combination of untargeted metabolomics and metagenomics, we performed a comparative longitudinal analysis of the feces collected in a cohousing study with a PCOS mouse model. Our results showed that gut metabolite composition experienced earlier and more pronounced differentiation in both the disease model and cohoused mice compared with the microbial composition. Notably, statistical and machine learning approaches identified shifts in the relative abundance of primary and secondary BA, which have been implicated as modifiers of gut microbial growth and diversity. Network correlation analysis showed strong associations between particular BA and bacterial species, particularly members ofLactobacillus, and that these correlations were time and treatment dependent. Our results provide novel insights into host/microbe relationships related to hyperandrogenism in females and indicate that focused research into small molecule control of gut microbial diversity and host physiology may provide new therapeutic options for the treatment of PCOS.
Cross-compartment signal propagation in the Mitotic Exit Network
Authors: Zhou Xiaoxue , Li Wenxue , Liu Yansheng , Amon Angelika 
Published: October 2020

ABSTRACTIn budding yeast, the Mitotic Exit Network (MEN), a GTPase signaling cascade integrates spatial and temporal cues to promote exit from mitosis. This signal integration requires transmission of a signal generated on the cytoplasmic face of spindle pole bodies (SPBs; yeast equivalent of centrosomes) to the nucleolus, where the MEN effector protein Cdc14 resides. Here, we show that the MEN activating signal at SPBs is relayed to Cdc14 in the nucleolus through the dynamic localization of its terminal kinase complex Dbf2-Mob1. Cdc15, the protein kinase that activates Dbf2-Mob1 at SPBs, also regulates its nuclear access. Once in the nucleus, priming phosphorylation of Cfi1/Net1, the nucleolar anchor of Cdc14, by the Polo-like kinase Cdc5 targets Dbf2-Mob1 to the nucleolus. Nucleolar Dbf2-Mob1 then phosphorylates Cfi1/Net1 and Cdc14, activating Cdc14. The kinase-primed transmission of the MEN signal from the cytoplasm to the nucleolus exemplifies how signaling cascades can bridge distant inputs and responses.