bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of the microbiota associated with 12-week-old bovine fetuses exposed to divergent in utero nutrition
Authors: Amat Samat , Holman Devin B. , Schmidt Kaycie , McCarthy Kacie L. , Dorsam Sheri T. , Ward Alison K. , Borowicz Pawel P. , Reynolds Lawrence P. , Caton Joel S. , Sedivec Kevin K. , Dahlen Carl R.
Published: September 2021

A recent study reported the existence of a diverse microbiota in 5-to-7-month-old calf fetuses, suggesting that colonization of the bovine gut with so-called “pioneer” microbiota may begin during mid-gestation. In the present study, we investigated 1) the presence of microbiota in bovine fetuses at early gestation (12 weeks), and 2) whether the fetal microbiota is influenced by the maternal rate of gain or dietary supplementation with vitamins and minerals (VTM) during early gestation. Amniotic and allantoic fluids, and intestinal and placental (cotyledon) tissue samples obtained from fetuses (n = 33) on day 83 of gestation were processed for the assessment of fetal microbiota using 16S rRNA gene sequencing. The sequencing results revealed that a diverse and complex microbial community was present in each of these fetal compartments evaluated. Allantoic and amniotic fluids, and fetal intestinal and placenta microbiota each had distinctly different (0.047 ≥ R2 ≥ 0.019, P ≤ 0.031) microbial community structures. Allantoic fluid had a greater (P < 0.05) microbial richness (number of OTUs) (Mean 122) compared to amniotic fluid (84), intestine (63) and placenta (66). Microbial diversity (Shannon index) was similar for the intestinal and placental samples, and both were less diverse compared with fetal fluid microbiota (P < 0.05). Thirty-nine different archaeal and bacterial phyla were detected across all fetal samples, with Proteobacteria (55%), Firmicutes (16.2%), Acidobacteriota (13.6%) and Bacteroidota (5%) predominating. Among the 20 most relatively abundant bacterial genera, Acidovorax, Acinetobacter, Brucella, Corynebacterium, Enterococcus, Exiguobacterium and Stenotrophomonas differed by fetal sample type (P < 0.05). A total of 55 taxa were shared among the four different microbial communities. qPCR of bacteria in the intestine and placenta samples as well as scanning electron microscopy imaging of fetal fluids provided additional evidence for the presence of a microbiota in these samples. Minor effects of maternal rate of gain and VTM supplementation, and their interactions on microbial richness and composition were detected. Overall, the results of this study indicate that colonization with pioneer microbiota may occur during early gestation in bovine fetuses, and that that the maternal nutritional regime during gestation may influence the early fetal microbiota.
GABA and IA Independently Regulate rNST Responses to Afferent Input
Authors: Chen Z. , Terman D.H. , Travers S.P. , Travers J.B.
Published: September 2021

Taste responses in the rostral nucleus of the solitary tract (rNST) influence motivated ingestive behavior via ascending pathways, and consummatory reflex behavior via local, brainstem connections. Modifications to the afferent signal within the rNST include changes in gain (the overall rate of neuron activity) and changes in gustatory tuning (the degree to which individual neurons respond to divergent gustatory qualities). These alterations of the sensory signal derive from both synaptic interactions within the nucleus and the constitutive cellular membrane properties of rNST neurons. GABA neurons are well represented within the rNST, as is expression of KV4.3, a channel for a rapidly inactivating outward K+ current (IA). GABAergic synapses suppress rNST responses to afferent input and previous studies showed that this suppression is greater in cells expressing IA, suggesting a possible interaction. Here, we examine the potential interaction between GABAergic inhibition and IA channels in a series of patch clamp experiments. Optogenetic release of GABA suppressed rNST responses to afferent (electrical) stimulation and this effect was greater in cells with IA, confirming an earlier report. We further observed that the composite inhibitory postsynaptic potential was larger in IA positive cells, suggesting one mechanism for the greater afferent suppression. Blocking IA with the channel blocker AmmTX3, enhanced the response to afferent stimulation, suggesting a suppressive role for this channel in regulating afferent input at rest. However, pharmacologic blockade of IA did not suppress GABAergic inhibition, indicating that IA and GABA independently regulate excitatory afferent input.
Ancestral chromosomes for the Peronosporaceae inferred from a telomere-to-telomere genome assembly of Peronospora effusa
Authors: Fletcher Kyle , Shin Oon-Ha , Clark Kelley J. , Feng Chunda , Putman Alexander I. , Correll James C. , Klosterman Steven J. , Van Deynze Allen , Michelmore Richard
Published: September 2021

We report the first telomere-to-telomere genome assembly for an oomycete. This assembly has extensive synteny with less complete genome assemblies of other oomycetes and will therefore serve as a reference genome for this taxon. Downy mildew disease of spinach, caused by the oomycete Peronospora effusa, causes major losses to spinach production. The 17 chromosomes of P. effusa were assembled telomere-to-telomere using Pacific Biosciences High Fidelity reads. Sixteen chromosomes are complete and gapless; Chromosome 15 contains one gap bridging the nucleolus organizer region. Putative centromeres were identified on all chromosomes. This new assembly enables a re-evaluation of the genomic composition of Peronospora spp.; the assembly was almost double the size and contained more repeat sequences than previously reported for any Peronospora spp. Genome fragments consistently under-represented in six previously reported assemblies of P. effusa typically encoded repeats. Some genes annotated as encoding effectors were organized into multigene clusters on several chromosomes. At least two effector-encoding genes were annotated on every chromosome. The intergenic distances between annotated genes were consistent with the two-speed genome hypothesis, with some effectors located in gene-sparse regions. The near-gapless assembly revealed apparent horizontal gene transfer from Ascomycete fungi. Gene order was highly conserved between P. effusa and the genetically oriented assembly of the oomycete Bremia lactucae. High levels of synteny were also detected with Phytophthora sojae. Many oomycete species may have similar chromosome organization; therefore, this genome assembly provides the foundation for genomic analyses of diverse oomycetes.
Dynamic and stationary brain connectivity during movie watching as revealed by functional MRI
Authors: Di Xin , Zhang Zhiguo , Xu Ting , Biswal Bharat B.
Published: September 2021

Spatially remote brain regions show synchronized activity as typically revealed by correlated functional MRI (fMRI) signals. An emerging line of research has focused on the temporal fluctuations of connectivity; however, its relationships with stationary connectivity have not been clearly illustrated. We examined dynamic and stationary connectivity when the participants watched four different movie clips. We calculated point-by-point multiplication between two regional time series to estimate the time-resolved dynamic connectivity, and estimated the inter-individual consistency of the dynamic connectivity time series. Widespread consistent dynamic connectivity was observed for each movie clip, which also showed differences between the clips. For example, a cartoon movie clip, Wall-E, showed more consistent of dynamic connectivity with the posterior cingulate cortex and supramarginal gyrus, while a court drama clip, A Few Good Men, showed more consistent of dynamic connectivity with the auditory cortex and temporoparietal junction, which might suggest the involvement of specific brain processing for different movie contents. In contrast, the stationary connectivity as measured by the correlations between regional time series was highly similar among the movie clips, and showed fewer statistically significant differences. The patterns of consistent dynamic connectivity could be used to classify different movie clips with higher accuracy than the stationary connectivity and regional activity. These results support the functional significance of dynamic connectivity in reflecting functional brain changes, which could provide more functionally relevant information than stationary connectivity.
Naturalistic stimuli reveal a critical period in visual cortex development: Evidence from adult-onset blindness
Authors: Musz Elizabeth , Loiotile Rita , Chen Janice , Cusack Rhodri , Bedny Marina
Published: September 2021

How do life experiences impact cortical function? In people who are born blind, the “visual” cortices are recruited for nonvisual tasks such as Braille reading and sound localization (e.g., Collignon et al., 2011; Sadato et al., 1996). The mechanisms of this recruitment are not known. Do visual cortices have a latent capacity to respond to nonvisual information that is equal throughout the lifespan? Alternatively, is there a sensitive period of heightened plasticity that makes visual cortex repurposing possible during childhood? To gain insight into these questions, we leveraged naturalistic auditory stimuli to quantify and compare cross-modal responses congenitally blind (CB, n=22), adult-onset blind (vision loss >18 years-of-age, AB, n=14) and sighted (n=22) individuals. Participants listened to auditory excerpts from movies; a spoken narrative; and matched meaningless auditory stimuli (i.e., shuffled sentences, backwards speech) during fMRI scanning. These rich naturalistic stimuli made it possible to simultaneous engage a broad range of cognitive domains. We correlated the voxel-wise timecourses of different participants within each group. For all groups, all stimulus conditions induced synchrony in auditory cortex and for all groups only the narrative stimuli synchronized responses in higher-cognitive fronto-parietal and temporal regions. Inter-subject synchrony in visual cortices was high in the CB group for the movie and narrative stimuli but not for meaningless auditory controls. In contrast, visual cortex synchrony was equally low among AB and sighted blindfolded participants. Even many years of blindness in adulthood fail to enable responses to naturalistic auditory information in visual cortices of people who had sight as children. These findings suggest that cross-modal responses in visual cortex of people born blind reflect the plasticity of developing visual cortex during a sensitive period.
A Role for Visual Areas in Physics Simulations
Authors: Ahuja Aarit , Desrochers Theresa M. , Sheinberg David L.
Published: September 2021

To engage with the world, we must regularly make predictions about the outcomes of physical scenes. How do we make these predictions? Recent evidence points to simulation - the idea that we can introspectively manipulate rich, mental models of the world - as one possible explanation for how such predictions are accomplished. While theories based on simulation are supported by computational models, neuroscientific evidence for simulation is lacking and many important questions remain. For instance, do simulations simply entail a series of abstract computations? Or are they supported by sensory representations of the objects that comprise the scene being simulated? We posit the latter and suggest that the process of simulating a sequence of physical interactions is likely to evoke an imagery-like envisioning of those interactions. Using functional magnetic resonance imaging, we demonstrate that when participants predict how a ball will fall through an obstacle-filled display, motion-sensitive brain regions are activated. We further demonstrate that this activity, which occurs even though no motion is being sensed, resembles activity patterns that arise while participants perceive the ball’s motion. This finding suggests that the process of simulating the ball’s movement is accompanied by a sensory representation of this movement. These data thus demonstrate that mental simulations recreate sensory depictions of how a physical scene is likely to unfold.
Defective endosome-TGN retrograde transport promotes NLRP3 inflammasome activation
Authors: Zhang Zhirong , Ran Li , Venditti Rossella , Liu Zengzhen , Schürmann Annette , Bonifacino Juan S. , De Matteis Maria Antonietta , Ricci Romeo
Published: September 2021

Inflammasome complexes are pivotal in the innate immune response to pathogens and other danger signals1–4. The NLRP3 inflammasome is activated in response to a broad variety of cellular stressors. Most of the stimuli act in a potassium efflux-dependent manner but a primary and converging sensing mechanism by the NLRP3 receptor initiating inflammasome assembly remains ill-defined. Here we show that NLRP3 activators disrupt endosome-TGN retrograde transport (ETRT) and lead to localization of NLRP3 to endosomal vesicles. Genetic and pharmacologic perturbation of ETRT leads to accumulation of phosphoinositol-4-phosphate (PI4P) in endosomes to which NLRP3 is recruited. Disruption of ETRT potentiates NLRP3 inflammasome activation in murine and human macrophages in vitro. Mice with defects in ETRT in the myeloid compartment are more susceptible to LPS-induced sepsis showing enhanced mortality and IL-1β serum levels as compared to control animals. Our study thus uncovers that changes in endocytic trafficking mediate NLRP3-dependent inflammatory responses.
Single cell infection with influenza A virus using drop-based microfluidics
Authors: Loveday Emma Kate , Sanchez Humberto S. , Thomas Mallory M. , Chang Connie B.
Published: September 2021

Influenza A virus (IAV) is an RNA virus with high genetic diversity which necessitates the development of new vaccines targeting emerging mutations each year. As IAV exists in genetically heterogeneous populations, current studies focus on understanding population dynamics at the single cell level. These studies include novel methodology that can be used for probing populations at the single cell level, such as single cell sequencing and microfluidics. Here, we introduce a drop-based microfluidics method to study IAV infection at a single cell level by isolating infected host cells in microscale drops. Single human alveolar basal epithelial (A549), Madin-Darby Canine Kidney cells (MDCK) and MDCK + human siat7e gene (Siat7e) cells infected with the pandemic A/California/07/2009 (H1N1) strain were encapsulated within 50 μm radii drops and incubated at 37°C. We demonstrate that drops remain stable over 24 hours, that 75% of cells remain viable, and that IAV virus can propagate within the drops. Drop-based microfluidics therefore enables single cell analysis of viral populations produced from individually infected cells.
Exploring the effects of CO2elevation on seedlings’ growth of Acacia senegal in the era of changes
Authors: Attaelmanan Abdelmoniem A. , Siddig Ahmed A. H. , Warrag Essam I.
Published: September 2021

Acacia senegalis a priority and important C3tree species in drylands of Sudan and across the gum belt. Investigation of its seedlings response to elevated carbon dioxide (eCO2) is important as atmospheric ([CO2]) has increased and predicted to continue to rise. Many studies showed that eCO2causes increased photosynthesis in plants, which leads to greater production of carbohydrates and biomass, and increased soil organic matter and carbon content. This study investigated the effects of eCO2onA. senegalseedlings grown in sand and silt soils under irrigation intervals of every day and every two days. Seven days old seedlings were assigned to the treatments in Split - spilt plot design for 4 weeks. The main plot is eCO2(600-800 ppm) and ambient (≤400 ppm) under Free Air CO2Enrichment (FACE) system. Subplots are irrigation intervals and soil types. Seedling height and number of leaves were measured weekly, and seedlings were harvested after 4 weeks where growth parameters and soil properties were measured. The eCO2showed no effect on the measured parameters except the significant increase in tap-root length. However, the irrigation every day showed significant increase than every two days in seedling’s height, number of leaves, root length and seedling’s dry weight but not seedling’s and soil C% & N%. Soil treatment showed effects on stem height, leaf number, seedling’s dry weight, leaves and root N% and soil C% but not root length, seedling C% and soil N%. The results indicate the importance of soil moisture, physical and chemical properties that reflects adaptation of the species to its dry land environment.
Signatures of adaptive evolution during human to mink SARS CoV2 cross-species transmission inform estimates of the COVID19 pandemic timing
Authors: Tai Jui-Hung , Chaw Shu-Miaw , Sun Hsiao-Yu , Tseng Yi-Cheng , Li Guanghao , Chang Sui-Yuan , Yeh Shiou-Hwei , Chen Pei-Jer , Wang Hurng-Yi
Published: September 2021

One of the unique features of SARS-CoV-2 is that it mainly evolved neutrally or under purifying selection during the early pandemic. This contrasts with the preceding epidemics of the closely related SARS-CoV and MERS-CoV, both of which evolved adaptively. It is possible that the SARS-CoV-2 exhibits a unique or adaptive feature which deviates from other coronaviruses. Alternatively, the virus may have been cryptically circulating in humans for a sufficient time to have acquired adaptive changes for efficient transmission before the onset of the current pandemic. In order to test the above scenarios, we analyzed the SARS-CoV-2 sequences from minks (Neovision vision) and parenteral human strains. In the early phase of the mink epidemic (April to May 2020), nonsynonymous to synonymous mutation ratios per site within the spike protein was 2.93, indicating a selection process favoring adaptive amino acid changes. In addition, mutations within this protein concentrated within its receptor binding domain and receptor binding motif. Positive selection also left a trace on linked neutral variation. An excess of high frequency derived variants produced by genetic hitchhiking was found during middle (June to July 2020) and early late (August to September 2020) phases of the mink epidemic, but quickly diminished in October and November 2020. Strong positive selection found in SARS-CoV-2 from minks implies that the virus may be not unique in super-adapting to a wide range of new hosts. The mink study suggests that SARS-CoV-2 already went through adaptive evolution in humans, and likely been circulating in humans at least six months before the first case found in Wuhan, China. We also discuss circumstances under which the virus can be well-adapted to its host but fail to induce an outbreak.
Molecular architecture and dynamics of SARS-CoV-2 envelope by integrative modeling
Authors: Pezeshkian Weria , Grünewald Fabian , Narykov Oleksandr , Lu Senbao , Arkhipova Valeria , Solodovnikov Alexey , Wassenaar Tsjerk A , Marrink Siewert J. , Korkin Dmitry
Published: September 2021

Despite tremendous efforts by the research community during the COVID-19 pandemic, the exact structure of SARS-CoV-2 and related betacoronaviruses remains elusive. Being a key structural component of the SARS-CoV-2 virion, the envelope encapsulates viral RNA and is composed of three structural proteins, spike (S), membrane (M), and envelope (E), which interact with each other and with the lipids acquired from the host membranes. Here, we developed and applied an integrative multiscale computational approach to model the envelope structure of SARS-CoV-2 with near atomistic detail, focusing on studying the dynamic nature and molecular interactions of its most abundant, but largely understudied, M protein. The molecular dynamics simulations allowed us to test the envelope stability under different configurations and revealed that the M dimers agglomerated into large, filament-like, macromolecular assemblies with distinct molecular patterns formed by M’s transmembrane and intravirion (endo) domains. These results are in good agreement with current experimental data, demonstrating a generic and versatile integrative approach to model the structure of a virus de novo. We anticipate our work to provide insights into critical roles of structural proteins in the viral assembly and integration, proposing new targets for the antiviral therapies.
Droplet-based Single-cell Total RNA-seq Reveals Differential Non-Coding Expression and Splicing Patterns during Mouse Development
Authors: Salmen Fredrik , De Jonghe Joachim , Kaminski Tomasz S. , Alemany Anna , Parada Guillermo , Verity-Legg Joe , Yanagida Ayaka , Kohler Timo N. , Battich Nicholas , van den Brekel Floris , Ellermann Anna L. , Arias Alfonso Martinez , Nichols Jennifer , Hemberg Martin , Hollfelder Florian , van Oudenaarden Alexander
Published: September 2021

In recent years, single-cell transcriptome sequencing has revolutionized biology, allowing for the unbiased characterization of cellular subpopulations. However, most methods amplify the termini of polyadenylated transcripts capturing only a small fraction of the total cellular transcriptome. This precludes the detection of many long non-coding, short non-coding and non-polyadenylated protein-coding transcripts. Additionally, most workflows do not sequence the full transcript hindering the analysis of alternative splicing. We therefore developed VASA-seq to detect the total transcriptome in single cells. VASA-seq is compatible with both plate-based formats and droplet microfluidics. We applied VASA-seq to over 30,000 single cells in the developing mouse embryo during gastrulation and early organogenesis. The dynamics of the total single-cell transcriptome result in the discovery of novel cell type markers many based on non-coding RNA, an in vivo cell cycle analysis and an improved RNA velocity characterization. Moreover, it provides the first comprehensive analysis of alternative splicing during mammalian development.
Dynamic behavior of cell-free mitochondrial DNA in human saliva
Authors: Trumpff Caroline , Rausser Shannon , Haahr Rachel , Karan Kalpita R. , Gouspillou Gilles , Puterman Eli , Kirschbaum Clemens , Picard Martin
Published: September 2021

Mitochondria contain their own genome that can be released in multiple biofluids such as blood and cerebrospinal fluid, as cell-free mitochondrial DNA (cf-mtDNA). In clinical studies, single measures of blood cf-mtDNA predict mortality, and higher cf-mtDNA levels are associated with mental and physical stress. However, the dynamics of cf-mtDNA has not been defined, and whether it can be measured non-invasively like other neuroendocrine markers in saliva has not been examined. Here we report cf-mtDNA in human saliva and establish its natural within-person dynamic behavior across multiple weeks. In a small proof-of-principle cohort of healthy adults, we first develop an approach to rapidly quantify salivary cf-mtDNA without DNA extraction, and demonstrate the existence of saliva cf-mtDNA. We then deploy this approach to perform an intensive repeated-measures analysis of two healthy men studied at 4 daily timepoints over 53-60 consecutive days (n=212-220 observations each) with parallel measures of steroid hormones, self-reported daily mood, and health-related behaviors. Salivary cf-mtDNA exhibited a robust awakening response reaching up to two orders of magnitude 30-45 minutes after awakening, varied from day-to-day, and moderately correlated with the cortisol awakening response. No consistent association with self-reported daily mood/health-related behaviors were found, although this requires further examination in more extensive studies. Dynamic variation in cf-mtDNA was inversely related with salivary interleukin 6 (IL6), inconsistent with a pro-inflammatory effect of salivary cf-mtDNA. The highly dynamic behavior of salivary cf-mtDNA opens the door to non-invasive studies examining the relevance of mtDNA signaling in relation to human health.
Integrated gene analyses ofde novomutations from 46,612 trios with autism and developmental disorders
Authors: Wang Tianyun , Kim Chang , Bakken Trygve E. , Gillentine Madelyn A. , Henning Barbara , Mao Yafei , Gilissen Christian ,   The SPARK Consortium, Nowakowski Tomasz J. , Eichler Evan E.
Published: September 2021

Most genetic studies consider autism spectrum disorder (ASD) and developmental disorder (DD) separately despite overwhelming comorbidity and shared genetic etiology. Here we analyzedde novomutations (DNMs) from 15,560 ASD (6,557 are new) and 31,052 DD trios independently and combined as broader neurodevelopmental disorders (NDD) using three models. We identify 615 candidate genes (FDR 5%, 189 potentially novel) by one or more models, including 138 reaching exome-wide significance (p < 3.64e-07) in all models. We find no evidence for ASD-specific genes in contrast to 18 genes significantly enriched for DD. There are 53 genes show particular mutational-bias including enrichments for missense (n=41) or truncating DNM (n=12). We find 22 genes with evidence of sex-bias including five X chromosome genes also with significant female burden (DDX3X, MECP2, SMC1A, WDR45, andHDAC8). NDD risk genes group into five functional networks associating with different brain developmental lineages based on single-cell nuclei transcriptomic data, which provides important insights into disease subtypes and future functional studies.
Construction of a solid Cox model for AML patients based on multiomics bioinformatic analysis
Authors: Li Fu , Cai Jiao , Liu Jia , Yu Shi-cang , Zhang Xi , Su Yi , Gao Lei
Published: September 2021

Acute myeloid leukemia (AML) is a highly heterogeneous hematological malignancy. The bone marrow (BM) microenvironment in AML plays an important role in leukemogenesis, drug resistance and leukemia relapse. In this study, we aimed to identify reliable immune-related biomarkers for AML prognosis by multiomics analysis. We obtained expression profiles from The Cancer Genome Atlas (TCGA) database and constructed a LASSO-Cox regression model to predict the prognosis of AML using multiomics bioinformatic analysis data. This was followed by independent validation of the model in the GSE106291 (n=251), GSE12417 (n=163) and GSE37642 (n=137) datasets and mutated genes in clinical samples for predicting overall survival (OS). Molecular docking was performed to predict the most optimal ligands to these hub genes. The single-cell RNA sequence dataset GSE116256 was used to clarify the expression of the hub genes in different immune cell types. According to their significant differences in immune gene signatures and survival trends, we concluded that the immune infiltration-lacking subtype (IL type) is associated with better prognosis than the immune infiltration-rich subtype (IR type). Using the LASSO model, we built a classifier based on 5 hub genes to predict the prognosis of AML (risk score = −0.086×ADAMTS3 + 0.180×CD52 + 0.472×CLCN5 - 0.356×HAL + 0.368×ICAM3). In summary, we constructed a prognostic model of AML using integrated multiomics bioinformatic analysis that could serve as a therapeutic classifier.
IPMK physically binds to the SWI/SNF complex and modulates BRG1 occupancy
Authors: Beon Jiyoon , Han Sungwook , Park Seung Eun , Hyun Kwangbeom , Lee Song-Yi , Rhee Hyun-Woo , Seo Jeong Kon , Kim Jaehoon , Kim Seyun , Lee Daeyoup
Published: September 2021

Inositol polyphosphate multikinase (IPMK), a key enzyme in the inositol polyphosphate (IP) metabolism, is a pleiotropic signaling factor involved in major biological events including transcriptional control. In yeasts, IPMK and its IP products were known to promote the activity of SWI/SNF chromatin remodeling complex, which plays a critical role in gene expression by regulating chromatin accessibility. However, the direct linkage between IPMK and chromatin remodelers remains unclear, raising a question on how IPMK contributes to the transcriptional regulation in mammals. By employing unbiased screenings and in vivo/in vitro immunoprecipitations, here we demonstrated that IPMK physically associates with native mammalian SWI/SNF complexes by directly binding to SMARCB1, BRG1, and SMARCC1. Furthermore, we identified the specific domains required for the IPMK-SMARCB1 binding. Notably, using CUT&RUN and ATAC-seq assays, we discovered that IPMK co-localizes with BRG1 and regulates BRG1 localization as well as BRG1-mediated chromatin accessibility in a genome-wide manner (including promoter-TSS) in mouse embryonic stem cells. Finally, our mRNA-seq analyses revealed that IPMK and SMARCB1 regulate common gene sets, validating a functional link between IPMK and SWI/SNF complex. Together, these findings establish an importance of IPMK in promoter targeting of the SWI/SNF complex, thereby contributing to SWI/SNF-meditated chromatin accessibility and transcription.
Mitochondrial translation occurs preferentially in the peri-nuclear mitochondrial network of cultured human cells
Authors: Albus Christin , Berlinguer-Palmini Rolando , Caroline Caroline , McFarlane Fiona , Savu Elisabeta-Ana , Lightowlers Robert N. , Chrzanowska-Lightowlers Zofia M. , Zorkau Matthew
Published: September 2021

Human mitochondria are highly dynamic organelles, fusing and budding to maintain reticular networks throughout many cell types. Although extending to the extremities of the cell, the majority of the network is concentrated around the nucleus in most of the commonly cultured cell lines. This organelle harbours its own genome, mtDNA, with a different gene content to the nucleus, but the expression of which is critical for maintaining oxidative phosphorylation. Recent advances in click chemistry have allowed us to visualise sites of mitochondrial protein synthesis in intact cultured cells. We show that the majority of translation occurs in the peri-nuclear region of the network. Further analysis reveals that whilst there is a slight peri-nuclear enrichment in the levels of mitoribosomal protein and mitochondrial rRNA, it is not sufficient to explain this substantial heterogeneity in distribution of translation. Finally, we also show that in contrast, a mitochondrial mRNA does not show such a distinct gradient in distribution. These data suggest that the relative lack of translation in the peripheral mitochondrial network is not due to an absence of mitoribosomes or an insufficient supply of the mt-mRNA transcripts.
Revealing spatio-temporal dynamics with long-term trypanosomatid live-cell imaging
Authors: Muniz Richard S. , Campbell Paul C. , Sladewski Thomas E. , Renner Lars D. , de Graffenried Christopher L.
Published: September 2021

Trypanosoma brucei, the causative agent of human African trypanosomiasis, employs a flagellum for dissemination within the parasite’s mammalian and insect hosts.T. bruceicells are highly motile in culture and must be able to move in all three dimensions for reliable cell division. These characteristics have made long-term microscopic imaging of liveT. bruceicells challenging, which has limited our understanding of a variety of important cell-cycle events. To address this issue, we have devised an imaging approach that confines cells to small volumes that can be imaged continuously for up to 24 h. This system employs cast agarose microwells generated using a PDMS stamp that can be made with different dimensions to maximize cell viability and imaging quality. Using this approach, we have imaged individualT. bruceithrough multiple rounds of cell division with high spatial and temporal resolution. We have employed this method to study the differential rate ofT. bruceidaughter cell division and show that the approach is compatible with loss-of-function experiments such as small molecule inhibition and RNAi. We have also developed a strategy that employs in-well “sentinel” cells to monitor potential toxicity due to imaging. This live-cell imaging method will provide a novel avenue for studying a wide variety of cellular events in trypanosomatids that have previously been inaccessible.

Importance

Trypanosoma bruceicauses severe diseases that affect humans and livestock in Sub-Saharan Africa. Efficient strategies for manipulating theT. bruceigenome have provided a wealth of information about protein localization and function in diverse cellular processes. However, employing live-cell imaging for phenotypic analysis inT. bruceiremains a significant challenge because immobilization of this highly motile parasite rapidly leads to morphologic defects and cell death. While fixed-cell imaging can provide snapshots of cellular events, it cannot provide the direct causal link or precise timing of events that comes from watching a living cell change over time. Our strategy using agarose microwells now allows long-term live cellT. bruceiimaging with a simple apparatus that can be adapted for a wide range of experimental conditions.
Effect of sodium silicate on drinking water biofilm development
Authors: Munoz Sebastian , Trueman Benjamin F. , Li Bofu , Gagnon Graham A.
Published: September 2021

Sodium silicates have been studied for sequestration of iron, coagulation, and corrosion control, but their impact on biofilm formation has not been documented in detail. This study investigated the impact of sodium silicate corrosion control on biomass accumulation in drinking water systems in comparison to orthophosphate, a common corrosion inhibitor. Biofilm growth was measured by determining ATP concentrations, and the bacterial community was characterized using 16S ribosomal RNA (rRNA) sequencing. A pilot-scale study with cast-iron pipe loops, annular reactors (ARs), and polycarbonate coupons demonstrated significantly lower biofilm ATP concentrations in the sodium silicate-treated AR than the orthophosphate-treated AR when the water temperature exceeded 20°C. However, an elevated sodium silicate dose (48 mg L-1 of SiO2) disturbed and dispersed the biofilm formed inside the AR, resulting in elevated effluent ATP concentrations. Two separate experiments confirmed that biomass accumulation was higher in the presence of orthophosphate at high water temperatures (20°C) only. No significant differences were identified in biofilm ATP concentrations at lower water temperatures (below 20°C). Differences in bacterial communities between the orthophosphate- and sodium silicate-treated systems were not statistically significant, even though orthophosphate promoted higher biofilm growth. However, the genera Halomonas and Mycobacterium—which include opportunistic pathogens—were present at greater relative abundances in the orthophosphate-treated system compared to the sodium silicate system.

Graphical abstract

Orthophosphate promotes more biofilm growth in comparison to sodium silicates at water temperatures above 20°C.

Water impact statement

Sodium silicates have been used in drinking water treatment for decades, both as sequestrants and as corrosion inhibitors. However, their impact on biofilm formation is poorly understood, and this risks drinking water quality. This study aims to further clarify the effects of corrosion inhibitors on biofilm development, including inhibitors that are not phosphate-based.
Gram-negative bacterial infection increases lung cancer metastasis via Toll-like receptor activation and increased cancer cell proliferation post-tumor adhesion
Authors: Rayes Roni F. , Wilson Marnie Goodwin , Gowing Stephen D. , Bourdeau France , Giannias Betty , Camilleri-Broet Sophie , Fiset Pierre-Olivier , Najmeh Sara , Spicer Jonathan D. , Ferri Lorenzo E. , Cools-Lartigue Jonathan J.
Published: September 2021

Background

Lung cancer is a leading cause of death partially due to high recurrence rates after surgical resection. Clinical data suggest that post-operative infections may increase the risk of recurrence. Our previous work indicated that increased adhesion of circulating tumors in the context of infection is partially responsible for this phenotype. However, cancer metastasis is a multi-step process, and it is likely that other events following tumor adhesion also play a role.

Methods

In vivo intrasplenic injection of murine lung cancer cells into wild type (WT) and Toll-like receptor 4 knockout (TLR4-/-) mice followed by cecal-ligation and puncture (CLP) as a model of post-operative infection or sham surgery were used. H&E staining and immunohistochemistry analysis of Ki67+ cells in the livers of those mice were performed. In vitro proliferation assays were performed on human lung cancer cells using combinations of TLR blockade.

Results

We found a 5-fold increase in hepatic metastases in WT CLP mice compared to WT sham mice. TLR4-/- CLP mice had a significant decreased tumor burden compared to WT CLP mice. This indicated an important mechanistic role for the TLR4-initiated host response to gram negative infection post-tumor cell adhesion. By analyzing the livers of those mice, we observed an increase in proliferation of tumor micrometastases in vivo in WT CLP mice as compared to WT sham mice. Here again, CLP TLR4 -/- mice had significantly fewer replicating micrometastases than CLP WT mice. Indeed, we found that direct stimulation of lung cancer cells with heat-inactivated E.Coli resulted in increased proliferation of tumor growth in vitro. These effects were partially abrogated by tumor TLR4 blockade; combined TLR2, 4 and 5 blockades led to a more prominent decrease. Conditioned media from bronchoalveolar epithelial cells treated with lipopolysaccharide lead to increased lung cancer proliferation; these changes were reversed with TLR blockade, indicating that the host response to infection is TLR mediated.

Conclusions

Overall, these results imply a more complex mechanistic role of post-operative infection in metastasis. From a clinical standpoint, this evidence strengthens the case for the use of TLR blockade as a potential therapeutic target in the prevention of metastasis.
VGLL2-NCOA2 leverages developmental programs for pediatric sarcomagenesis
Authors: Watson Sarah , LaVigne Collette , Xu Lin , Murchison Whitney , Surdez Didier , Rakheja Dinesh , Tirode Franck , Delattre Olivier , Amatruda James , Kendall Genevieve
Published: September 2021

Clinical sequencing efforts are uncovering numerous fusion genes in childhood solid tumors, yet few methods exist to delineate fusion-oncogenes from structural changes of unknown significance. One such novel fusion gene is VGLL2-NCOA2, which was described by us and others in patients with congenital sarcomas but has lacked functional validation. To determine if this fusion is an oncogene, and how it is driving disease, we developed a vertebrate zebrafish model and mouse allograft model of human VGLL2-NCOA2 driven sarcomagenesis. We found that VGLL2-NCOA2 is indeed an oncogene and is sufficient to generate mesenchymal tumors that recapitulate the human disease at the histological and transcriptional level. Zebrafish VGLL2-NCOA2 tumors display features of arrested skeletal muscle development, and a subset transcriptionally cluster with somitogenesis in developing embryos. By comparing tumor and embryonic gene expression signatures, we identified developmentally regulated targets that VGLL2-NCOA2 potentially leverages for tumorigenesis. These targets highlight the core biology of the disease and could represent therapeutic opportunities. Specifically, a RAS family GTPase, arf6/ARF6, involved in actin remodeling and rapid cycling of endocytic vesicles at the plasma membrane, is highly expressed during zebrafish somitogenesis and in VGLL2-NCOA2 tumors. In zebrafish tumors, arf6 protein is highly expressed and is absent from mature skeletal muscle. In VGLL2-NCOA2 mouse allograft models and patient tumors, ARF6 mRNA is overexpressed as compared to skeletal muscle or normal controls. More broadly, ARF6 is overexpressed in adult and pediatric sarcoma subtypes as compared to mature skeletal muscle. Overall, our cross-species comparative oncology approach provides evidence that VGLL2-NCOA2 is an oncogene which leverages developmental programs for tumorigenesis, and that one of these programs, the reactivation or persistence of arf6/ARF6, could represent a therapeutic opportunity.
Divergent encoding of active avoidance behavior in corticostriatal and corticolimbic projections
Authors: Kajs Bridget L. , Loewke Adrienne C. , Dorsch Jeffrey M. , Vinson Leah T. , Gunaydin Lisa A.
Published: September 2021

Active avoidance behavior, in which an animal performs an action to avoid a stressor, is crucial for survival and may provide insight into avoidance behaviors seen in anxiety disorders. Active avoidance requires the dorsomedial prefrontal cortex (dmPFC), which is thought to regulate avoidance via downstream projections to the striatum and amygdala. However, the endogenous activity of projection-defined dmPFC subpopulations during active avoidance learning remains unexplored. Here we utilized fiber photometry to record from the dmPFC and its downstream projections to the dorsomedial striatum (DMS) and the basolateral amygdala (BLA) during active avoidance learning in mice. We examined neural activity during conditioned stimulus (CS) presentations, active avoidance, and cued freezing. Both prefrontal projections showed learning-related increases in activity during CS onset throughout active avoidance training. The dmPFC as a whole showed increased activity during avoidance and decreased activity during cued freezing. Finally, dmPFC-DMS and dmPFC-BLA projections showed divergent encoding of active avoidance behavior, with the dmPFC-DMS projection showing increased activity and the dmPFC-BLA showing decreased activity during active avoidance. Our results identify differential prefrontal encoding of active and passive coping behaviors in the same behavioral paradigm and demonstrate divergent encoding of active avoidance in projection-specific dmPFC subpopulations.
Hypoxia promotes a perinatal-like progenitor state in the adult murine epicardium
Authors: Sayed Angeliqua , Turoczi Szimonetta , Soares-da-Silva Francisca , Marazzi Giovanna , Hulot Jean-Sébastien , Sassoon David , Valente Mariana
Published: September 2021

The epicardium is a reservoir of progenitors that give rise to coronary vasculature and stroma during development and mediates cardiac vascular repair in lower vertebrates. However, its role as a source of progenitors in the adult mammalian heart remains unclear due to lack of clear lineage markers and single-cell culture systems to elucidate epicardial progeny cell fate. We found that in vivo exposure of mice to physiological hypoxia induced adult epicardial cells to re-enter the cell cycle and to express a subset of developmental genes. Multiplex transcriptional profiling revealed a lineage relationship between epicardial cells and smooth muscle, stromal, and endothelial fates, and that physiological hypoxia promoted an endothelial cell fate. In vitro analyses of purified epicardial cells showed that cell growth and subsequent differentiation is dependent upon hypoxia, and that resident epicardial cells retain progenitor identity in the adult mammalian heart with self-renewal and multilineage differentiation potential. These results point to a source of progenitor cells in the adult heart that can promote heart revascularization, providing an invaluable in vitro model for further studies.
Cdc48 targets INQ-localized Mrc1 to facilitate recovery from replication stress
Authors: Colding Camilla , Autzen Jacob , Pfander Boris , Lisby Michael
Published: September 2021

DNA replication stress is a source of genome instability and a replication checkpoint has evolved to enable fork stabilisation and completion of replication during stress. Mediator of the replication checkpoint 1 (Mrc1) is the primary mediator of this response in Saccharomyces cerevisiae. Mrc1 is partially sequestered in the intranuclear quality control compartment (INQ) upon methyl methanesulfonate (MMS)-induced replication stress. Here we show that Mrc1 re-localizes from the replication fork to INQ during replication stress. Sequestration of Mrc1 in INQ is facilitated by the Btn2 chaperone and the Cdc48 segregase is required to release Mrc1 from INQ during recovery from replication stress. Consistently, we show that Cdc48 colocalizes with Mrc1 in INQ and we find that Mrc1 is recognized by the Cdc48 cofactors Ufd1 and Otu1, which contribute to clearance of Mrc1 from INQ. Our findings suggest that INQ localization of Mrc1 and Cdc48 function to facilitate replication stress recovery by transiently sequestering the replication checkpoint mediator Mrc1 and explains our observation that Btn2 and Cdc48 are required for efficient replication restart following MMS-induced replication stress.
Blood flow modeling reveals improved collateral artery performance during mammalian heart regeneration
Authors: Anbazhakan Suhaas , Rios Coronado Pamela E. , Sy-Quia Ana Natalia L. , Seow Anson , Hands Aubrey M. , Zhao Mingming , Dong Melody L. , Pfaller Martin , Raftrey Brian C. , Cook Christopher K. , Bernstein Daniel , Nieman Koen , Pașca Anca M. , Marsden Alison L. , Red-Horse Kristy
Published: September 2021

Collateral arteries are a vessel subtype that bridges two artery branches, forming a natural bypass that can deliver blood flow downstream of an occlusion. These bridges in the human heart are associated with better outcomes during coronary artery disease. We recently found that their rapid development in neonates supports heart regeneration, while the non-regenerative adult heart displays slow and minimal collateralization. Thus, inducing robust collateral artery networks could serve as viable treatment for cardiac ischemia, but reaching this goal requires more knowledge on their developmental mechanisms and functional capabilities. Here, we use whole-organ imaging and 3D computational fluid dynamics (CFD) modeling to identify the spatial architecture of and predict blood flow through collaterals in neonate and adult hearts. We found that neonate collaterals are more numerous, larger in diameter, and, even when similar in size/number, are predicted to more effectively re-perfuse an occluded coronary network when compared to adults. CFD analysis revealed that collaterals perform better in neonates because of decreased differential pressures along their coronary artery tree. Furthermore, testing of various collateral configurations indicated that larger, more proximal collaterals are more beneficial than many smaller ones, identifying a target architecture for therapeutic interventions. Morphometric analysis revealed how the coronary artery network expands during postnatal growth. Vessel diameters do not scale with cardiac muscle growth. Instead, the coronary tree expands solely by adding additional branches of a set length, a burst of which occurs during murine puberty. Finally, we compared mouse structural and functional data to human hearts. Surprisingly, fetal human hearts possessed a very large number of small, but mature, smooth muscle cell covered collaterals while angiogram data indicated adult patients with chronic coronary occlusions contained at least two. Comparing size ratios with modeled mouse data suggested low re-perfusion capabilities of the embryonic collaterals but higher functional benefits of those in diseased adults. Our unique interdisciplinary approach allowed us to quantify the functional significance of collateral arteries during heart regeneration and repair–a critical step towards realizing their therapeutic potential.