bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tools for efficient analysis of neurons in a 3D reference atlas of whole mouse spinal cord
Authors: Fiederling Felix , Hammond Luke A. , Ng David , Mason Carol , Dodd Jane 
Published: May 2021

SummarySpinal neurons are highly heterogeneous in location, transcriptional identity and function. To understand their contributions to sensorimotor circuits, it is essential to map the positions of identified subsets of neurons in relation to others throughout the spinal cord (SC), but we lack tools for whole SC sample preparation, imaging and in toto analysis. To overcome this problem, we have (1) designed scaffolds (SpineRacks) that facilitate efficient and ordered cryo-sectioning of the entire SC in a single block, (2) constructed a 3D reference atlas of adult mouse SC and (3) developed software (SpinalJ) to register images of sections and for standardized analysis of cells and projections in atlas space. We have verified mapping accuracies for known neurons and demonstrated the usefulness of this platform to reveal unknown neuronal distributions. Together, these tools provide high-throughput analyses of whole mouse SC and enable direct comparison of 3D spatial information between animals and studies.
Ongoing neural oscillations predict the post-stimulus outcome of closed loop auditory stimulation during slow-wave sleep
Authors: Navarrete Miguel , Arthur Steven , Treder Matthias S. , Lewis Penelope A. 
Published: May 2021

ABSTRACTThe large slow oscillation (SO, 0.5-2Hz) that characterises slow-wave sleep is crucial to memory consolidation and other physiological functions. Manipulating slow oscillations can enhance sleep and memory, as well as benefitting the immune system. Closed-loop auditory stimulation (CLAS) has been demonstrated to increase the SO amplitude and to boost fast sleep spindle activity (11-16Hz). Nevertheless, not all such stimuli are effective in evoking SOs, even if they are precisely phase-locked. Here, we studied whether it is possible to use ongoing activity patterns to determine which oscillations to stimulate in order to effectively enhance SOs or SO-locked spindle activity. To this end, we trained classifiers using the morphological characteristics of the ongoing SO, as measured by electroencephalography (EEG), to predict whether stimulation would lead to a benefit in terms of the resulting SO and spindle amplitude. Separate classifiers were trained using trials from spontaneous control and stimulated datasets, and we evaluated their performance by applying them to held-out data both within and across conditions. We were able to predict both when large SOs will occur spontaneously, and whether a phase-locked auditory click will effectively enlarge them with an accuracy of ~70%. We were also able to predict when stimulation would elicit spindle activity with an accuracy of ~60%. Finally, we evaluate the importance of the various SO features used to make these predictions. Our results offer new insight into SO and spindle dynamics and provide a new method for online optimisation of stimulation.HIGHLIGHTS- Random forest classifiers can predict spontaneous and stimulated SOs and spindle amplitudes.- Morphological wave features predicted the response of SOs and spindles to CLAS.- SO amplitude during the click is the main predictor for post-stimulus SO amplitude.- Prediction of spindle activity did not differ in accuracy for stimulated vs spontaneous data.
Metagenome-genome-wide association studies reveal human genetic impact on the oral microbiome
Authors: Liu Xiaomin , Tong Xin , Zhu Jie , Tian Liu , Jie Zhuye , Zou Yuanqiang , Lin Xiaoqian , Liang Hewei , Li Wenxi , Ju Yanmei , Qin Youwen , Zou Leying , Lu Haorong , Xu Xun , Yang Huanming , Wang Jian , Zong Yang , Liu Weibin , Hou Yong , Zhu Shida , Jin Xin , Jia Huijue , Zhang Tao 
Published: May 2021

AbstractThe oral microbiota contains billions of microbial cells, which could contribute to diseases in a number of body sites. Challenged by eating, drinking and dental hygiene on a daily basis, the oral microbiota is regarded as highly dynamic. Here, we report significant human genomic associations with the oral metagenome from more than 1,915 individuals, for both the tongue dorsum and saliva. We identified five genetic loci associated with oral microbiota at study-wide significance (p< 3.16 × 10−11). Four of the five associations were well replicated in an independent cohort of 1,439 individuals: rs1196764 atAPPL2withPrevotella jejuni, Oribacterium uSGB 3339andSolobacterium uSGB 315; rs3775944 at the serum uric acid transporterSLC2A9withOribacterium uSGB 1215, OribacteriumuSGB 489 andLachnoanaerobaculum umeaense; rs4911713 nearOR11H1with speciesF0422 uSGB 392;and rs36186689 atLOC105371703withEggerthia. Further analyses confirmed 84% (386/455 for tongue dorsum) and 85% (391/466 for saliva) of genetic-microbiota associations including 6 genome-wide significant associations mutually validated between the two niches. Human genetics accounted for at least 10% of oral microbiome compositions between individuals. Machine learning models showed that polygenetic risk score dominated over oral microbiome in predicting predisposing risk of dental diseases such as dental calculus and gingival bleeding. These findings indicate that human genetic differences are one explanation for a stable or recurrent oral microbiome in each individual.
Reconstruction of dynamic regulatory networks reveals signaling-induced topology changes associated with germ layer specification
Authors: Su Emily Y. , Spangler Abby , Bian Qin , Kasamoto Jessica Y. , Cahan Patrick 
Published: May 2021

AbstractElucidating regulatory relationships between transcription factors (TFs) and target genes is fundamental to understanding how cells control their identity and behavior. Computational gene regulatory network (GRN) reconstruction methods aim to map this control by inferring relationships from transcriptomic data. Unfortunately, existing methods are imprecise, may be computationally burdensome, and do not uncover how networks transition from one topology to another. Here we present Epoch, a computational network reconstruction tool that leverages single cell transcriptomics to infer dynamic network structures. Epoch performs favorably when benchmarked using data derived fromin vivo,in vitro,andin silicosources. To illustrate the usefulness of Epoch, we applied it to identify the dynamic networks underpinning directed differentiation of mouse embryonic stem cells (ESC) guided by multiple primitive streak induction treatments. Our analysis demonstrates that modulating signaling pathways drives topological network changes that shape cell fate potential. We also find that Peg3 is a central contributor to the rewiring of the pluripotency network to favor mesoderm specification. By integrating signaling pathways with GRN structures, we traced how Wnt activation and PI3K suppression govern mesoderm and endoderm specification, respectively. Finally, we compare the networks established inin vitrodirected differentiation of ESCs to those inin vivogastrulation and mesoderm specification. The methods presented here are available in the R package Epoch, and provide a foundation for future work in understanding the biological implications of dynamic regulatory structures.
Coil-to-Helix Transition at the Nup358-BicD2 Interface Activates BicD2 for Dynein Recruitment
Authors: Gibson James M. , Cui Heying , Ali M. Yusuf , Zhao Xiaoxin , Debler Erik W. , Zhao Jing , Trybus Kathleen M. , Solmaz Sozanne R. , Wang Chunyu 
Published: May 2021

AbstractNup358, a nuclear pore protein, facilitates a nuclear positioning pathway that is essential for many biological processes, including neuromuscular and brain development. Nup358 binds and activates the auto-inhibited dynein adaptor Bicaudal D2 (BicD2), which in turn recruits and activates the dynein machinery to position the nucleus. However, the molecular details of the Nup358/BicD2 interaction remain poorly understood. Here, we show that a minimal Nup358 domain activates dynein/dynactin/BicD2 for processive motility on microtubules. Using nuclear magnetic resonance (NMR) titration and chemical exchange saturation transfer (CEST), a Nup358 helix encompassing residues 2162-2184 was identified, which transitioned from random coil to an α-helix upon BicD2-binding and formed the core of the Nup358-BicD2 interface. Mutations in this region of Nup358 decreased the Nup358/BicD2 interaction, resulting in decreased dynein recruitment and impaired motility. BicD2 thus recognizes the cargo adaptor Nup358 though a “cargo recognition α-helix”, a structural feature that may stabilize BicD2 in its activated state and promote processive dynein motility.
Topologically Associating Domain Boundaries are Commonly Required for Normal Genome Function
Authors: Rajderkar Sudha , Barozzi Iros , Zhu Yiwen , Hu Rong , Zhang Yanxiao , Li Bin , Fukuda-Yuzawa Yoko , Kelman Guy , Akeza Adyam , Blow Matthew J. , Pham Quan , Harrington Anne N. , Godoy Janeth , Meky Eman M. , von Maydell Kianna , Novak Catherine S. , Plajzer-Frick Ingrid , Afzal Veena , Tran Stella , Talkowski Michael E. , Kent Lloyd K. C. , Ren Bing , Dickel Diane E. , Visel Axel , Pennacchio Len A. 
Published: May 2021

SummaryTopologically associating domain (TAD) boundaries are thought to partition the genome into distinct regulatory territories. Anecdotal evidence suggests that their disruption may interfere with normal gene expression and cause disease phenotype1–3, but the overall extent to which this occurs remains unknown. Here we show that TAD boundary deletions commonly disrupt normal genome functionin vivo. We used CRISPR genome editing in mice to individually delete eight TAD boundaries (11-80kb in size) from the genome in mice. All deletions examined resulted in at least one detectable molecular or organismal phenotype, which included altered chromatin interactions or gene expression, reduced viability, and anatomical phenotypes. For 5 of 8 (62%) loci examined, boundary deletions were associated with increased embryonic lethality or other developmental phenotypes. For example, a TAD boundary deletion nearSmad3/Smad6caused complete embryonic lethality, while a deletion nearTbx5/Lhx5resulted in a severe lung malformation. Our findings demonstrate the importance of TAD boundary sequences forin vivogenome function and suggest that noncoding deletions affecting TAD boundaries should be carefully considered for potential pathogenicity in clinical genetics screening.
Longitudinal changes in diet cause repeatable and largely reversible shifts in gut microbial communities of laboratory mice and are observed across segments of the entire intestinal tract
Authors: Low Adrian , Soh Melissa , Miyake Sou , Jie Aw Vanessa Zhi , Feng Jian , Wong Adeline , Seedorf Henning 
Published: May 2021

AbstractDietary changes are known to alter the composition of the gut microbiome. However, it is less understood how repeatable and reversible these changes are and how diet-switches affect the microbiota in the various segments of the gastrointestinal tract. Here, a treatment group of conventionally raised laboratory mice is subjected to two periods of western diet (WD) interrupted by a period of standard diet (SD) of the same duration. Beta-diversity analyses show that diet-induced microbiota changes are largely reversible (q= 0.1501; PERMANOVA, weighted-UniFrac comparison of the treatment-SD group to the control-SD group) and repeatable (q= 0.032; PERMANOVA, weighted-UniFrac comparison of both WD treatments). Furthermore, we report that diet switches alter the gut microbiota composition along the length of the intestinal tract in a segment-specific manner, leading to gut segment-specific Firmicutes/Bacteroidota ratios. We identified prevalent and distinct Amplicon Sequencing Variants (ASVs), particularly in genera of the recently describedMuribaculaceae, along the gut as well as ASVs that are differentially abundant between segments of treatment and control groups. Overall, this study provides insights into the reversibility of diet-induced microbiota changes and highlights the importance to expand sampling efforts beyond the collections of fecal samples to characterize diet-dependent and segment-specific microbiome differences.
FliW and CsrA govern flagellin (FliC) synthesis and play pleiotropic roles in virulence and physiology ofClostridioides difficileR20291
Authors: Zhu Duolong , Wang Shaohui , Sun Xingmin 
Published: May 2021

ABSTRACTClostridioides difficileis a Gram-positive, spore-forming, and toxin-producing anaerobe that can cause nosocomial antibiotic-associated intestinal disease. InC. difficile, the expression of flagellar genes is coupled to toxin gene regulation and bacterial colonization and virulence. The flagellin FliC is responsible for pleiotropic gene regulation duringin vivoinfection. However, howfliCexpression is regulated is unclear. InBacillus subtilis, flagellin homeostasis and motility are coregulated by flagellar assembly factor FliW, Flagellin Hag (FliC homolog), and CsrA (Carbon storage regulator A), which is referred to as partner-switching mechanism “FliW-CsrA-Hag”. In this study, we characterized FliW and CsrA functions by deleting or overexpressingfliW, csrA, andfliW-csrAinC. difficileR20291. We showed that bothfliWdeletion orcsrAoverexpression in R20291, andcsrAcomplementation in R20291ΔWA (fliW-csrAcodeletion) dramatically decreased FliC production, however,fliCgene transcription was unaffected. While suppression offliCtranslation bycsrAoverexpression was mostly relieved whenfliWwas coexpressed, and no significant difference in FliC production was detected when onlyfliWwas complemented in R20291ΔWA. Further, loss offliWled to increased biofilm formation, cell adhesion, toxin production, and pathogenicity in a mouse model ofC. difficileinfection (CDI), whilefliW-csrAcodeletion decreased toxin production and mortalityin vivo. Taken together, these data suggest that CsrA negatively modulatesfliCexpression and FliW indirectly affectsfliCexpression through inhibition of CsrA post-transcriptional regulation, which seems similar to the “FliW-CsrA-Hag” switch inB. subtilis. Our data also suggest that “FliW-CsrA-fliC/FliC” can regulate many facets ofC. difficileR20291 pathogenicity.IMPORTANCEC. difficileflagellin FliC is associated with toxin gene expression, bacterial colonization and virulence, and is also involved in pleiotropic gene regulation duringin vivoinfection. However, how fliCexpression is regulated remains unclear. In light of “FliW-CsrA-Hag” switch coregulation mechanism reported inB. subtilis, we showed thatfliWandcsrAplay an important role in flagellin synthesis which affectsC. difficilemotility directly. Our data also suggest that FliW-CsrA-fliC/FliC” can regulate many facets ofC. difficileR20291 pathogenicity. These findings further aid us in understanding the virulence regulation inC. difficile.
Host bioenergetic parameters reveal cytotoxicity of anti-tuberculosis drugs undetected using conventional viability assays
Authors: Cumming Bridgette M. , Baig Zainab , Addicott Kelvin W. , Chen D , Steyn AJC 
Published: May 2021

AbstractHigh attrition rates in tuberculosis (TB) drug development have been largely attributed to safety, which is likely due to the use of endpoint assays measuring cell viability to detect drug cytotoxicity. In drug development of cancer, metabolic and neurological disorders, and antibiotics, cytotoxicity is increasingly being assessed using extracellular flux (XF) analysis, which measures cellular bioenergetic metabolism in real-time. Here, we adopt the XF platform to investigate the cytotoxicity of drugs currently used in TB treatment on the bioenergetic metabolism of HepG2 cells, THP-1 macrophages, and human monocyte derived macrophages (hMDM). We found that the XF analysis reveals earlier drug-induced effects on the cells’ bioenergetic metabolism prior to cell death, measured by conventional viability assays. Furthermore, each cell type has a distinct response to drug treatment, suggesting that more than one cell type should be considered to examine cytotoxicity in TB drug development. Interestingly, chemically unrelated drugs with different modes of action onMycobacterium tuberculosishave similar effects on the bioenergetic parameters of the cells, thus, discouraging the prediction of potential cytotoxicity based on chemical structure and mode of action of new chemical entities. The clustering of the drug-induced effects on the hMDM bioenergetic parameters are reflected in the clustering of the effects of the drugs on cytokine production in hMDMs, demonstrating concurrence between the effects of the drugs on the metabolism and functioning of the macrophages. These findings can be used as a benchmark to establish XF analysis as a new tool to assay cytotoxicity in TB drug development.
Inhibitory concentrations of ciprofloxacin induce an adaptive response promoting the intracellular survival ofSalmonellaTyphimurium
Authors: Sridhar Sushmita , Forrest Sally , Pickard Derek , Cormie Claire , Lees Emily , Thomson Nicholas R , Dougan Gordon , Baker Stephen 
Published: May 2021

AbstractAntimicrobial resistance (AMR) is a pressing global health crisis, which has been fuelled by the sustained use of certain classes of antimicrobials, including fluoroquinolones. While the genetic mutations responsible for decreased fluoroquinolone (ciprofloxacin) susceptibility are known, the implications of ciprofloxacin exposure on bacterial growth, survival, and interactions with host cells are not well described. Aiming to understand the influence of inhibitory concentrations of ciprofloxacinin vitro, we subjected three clinical isolates ofS.Typhimurium to differing concentrations of ciprofloxacin, dependent on their minimum inhibitory concentrations (MIC), and assessed the impact on bacterial growth, morphology, and transcription. We further investigated the differential morphology and transcription that occurred following ciprofloxacin exposure and measured the ability of ciprofloxacin-treated bacteria to invade and replicate in host cells. We found that ciprofloxacin-exposedS.Typhimurium are able to recover from inhibitory concentrations of ciprofloxacin, and that the drug induces specific morphological and transcriptional signatures associated with the bacterial SOS response, DNA repair, and intracellular survival. In addition, ciprofloxacin-treatedS.Typhimurium have increased capacity for intracellular replication in comparison to untreated organisms. These data suggest thatS.Typhimurium undergoes an adaptive response under ciprofloxacin perturbation that promotes cellular survival, a consequence that may justify more measured use of ciprofloxacin forSalmonellainfections. The combination of multiple experimental approaches provides new insights into the collateral effects that ciprofloxacin and other antimicrobials have on invasive bacterial pathogens.ImportanceAntimicrobial resistance is a critical concern in global health. In particular, there is rising resistance to fluoroquinolones, such as ciprofloxacin, a first-line antimicrobial for many Gram-negative pathogens. We investigated the adaptive response of clinical isolates ofSalmonellaTyphimurium to ciprofloxacin, finding that the bacteria adapt in short timespans to high concentrations of ciprofloxacin in a way that promotes intracellular survival during early infection. Importantly, by studying three clinically relevant isolates, we were able to show that individual isolates respond differently to ciprofloxacin, and for each isolate, there was a heterogeneous response under ciprofloxacin treatment. The heterogeneity that arises from ciprofloxacin exposure may drive survival and proliferation ofSalmonelladuring treatment and lead to drug resistance.
Network analysis of large phospho-signalling datasets: application to Plasmodium-erythrocyte interactions
Authors: Adderley Jack D. , O’Donoghue Finn , Doerig Christian , Davis Stephen 
Published: May 2021

AbstractPhosphorylation based signalling is a complicated and intertwined series of pathways critical to all domains of life. This interconnectivity, though essential to life, makes understanding and decoding the interactions difficult. Large datasets of phosphorylation interactions through the activity of kinases on their numerous effectors are now being generated, however interpretation of the network environment remains challenging. In humans, many phosphorylation interactions have been identified across published works to form the known phosphorylation interaction network. We overlayed phosphorylation datasets onto this network which provided information to each of the connections. To analyse the datasets now mapped into a network, we designed a pathway analysis that uses random walks to identify chains of phosphorylation events occurring much more or much less frequently than expected. This analysis highlights pathways of phosphorylation that work synergistically, providing a rapid interpretation of the most critical pathways in a given dataset. Here we used datasets of human red blood cells infected with the notable stages ofPlasmodium falciparumasexual development. The analysis identified several known signalling interactions, and additional interactions which could form the basis of numerous future studies. The network analysis designed here is widely applicable to any comparative phosphorylation dataset across infection and disease and can provide a rapid and reliable analysis to guide validation studies.
Infection, recovery and re-infection of farmed mink with SARS-CoV-2
Authors: Rasmussen Thomas Bruun , Fonager Jannik , Sværke Jørgensen Charlotte , Lassaunière Ria , Hammer Anne Sofie , Quaade Michelle Lauge , Boklund Anette , Lohse Louise , Strandbygaard Bertel , Rasmussen Morten , Michaelsen Thomas Yssing , Mortensen Sten , Fomsgaard Anders , Belsham Graham J. , Bøtner Anette 
Published: May 2021

AbstractMink, on a farm with about 15,000 animals, became infected with SARS-CoV-2. Over 75% of tested animals were positive for SARS-CoV-2 RNA in throat swabs and 100% of tested animals were seropositive. The virus responsible had a deletion of nucleotides encoding residues H69 and V70 within the spike protein gene. The infected mink recovered and after free-testing of the mink, the animals remained seropositive. During follow-up studies, after a period of more than 2 months without virus detection, over 75% of tested animals scored positive again for SARS-CoV-2 RNA. Whole genome sequencing showed that the virus circulating during this re-infection was most closely related to the virus identified in the first outbreak on this farm but additional sequence changes had occurred. Animals had much higher levels of anti-SARS-CoV-2 antibodies after re-infection than at free-testing. Thus, following recovery from an initial infection, seropositive mink rapidly became susceptible to re-infection by SARS-CoV-2.Article Summary LineFollowing widespread infection with SARS-CoV-2 of mink on a farm, all tested animals had seroconverted and the farm was then tested free of infection; however, less than 3 months later, a further round of infection affected more than 75% of tested animals.