bluuebunny/crossref_metadata_2025 huggingface dataset:
Perinatal High Fat Diet Exposure Alters Oxytocin and Corticotropin Releasing Factor Inputs onto Vagal Neurocircuits Controlling Gastric Motility
Authors: Carson Kaitlin E. , Alvarez Jared , Mackley Jasmine , Travagli R. Alberto , Browning Kirsteen N.
Published: November 2022

Perinatal high fat diet (pHFD) exposure alters the development of vagal neurocircuits that control gastrointestinal (GI) motility and reduce stress resiliency in offspring. Descending oxytocin (OXT; prototypical anti-stress peptide) and corticotropin releasing factor (CRF; prototypical stress peptide) inputs from the paraventricular nucleus (PVN) of the hypothalamus to the dorsal motor nucleus of the vagus (DMV) modulate the GI stress response. How these descending inputs, and their associated changes to GI motility and stress responses, are altered following pHFD exposure are, however, unknown. The present study used retrograde neuronal tracing experiments,in vivorecordings of gastric tone, motility, and gastric emptying rates, andin vitroelectrophysiological recordings from brainstem slice preparations to investigate the hypothesis that pHFD alters descending PVN-DMV inputs and dysregulates vagal brain-gut responses to stress. Compared to controls, rats exposed to pHFD had slower gastric emptying rates and did not respond to acute stress with the expected delay in gastric emptying. Neuronal tracing experiments demonstrated that pHFD reduced the number of PVNOXTneurons that project to the DMV, but increased PVNCRFneurons. Bothin vitroelectrophysiology recordings of DMV neurons andin vivorecordings of gastric motility and tone demonstrated that, following pHFD, PVNCRF-DMV projections were tonically active, and that pharmacological antagonism of brainstem CRF1 receptors restored the appropriate gastric response to brainstem OXT application. These results suggest that pHFD exposure disrupts descending PVN-DMV inputs, leading to a dysregulated vagal brain-gut response to stress.

Summary Figure

Keypoints

Maternal high fat diet exposure is associated with gastric dysregulation and stress sensitivity in offspring

The present study demonstrates that perinatal high fat diet exposure downregulates hypothalamic-vagal oxytocin (OXT) inputs but upregulates hypothalamic-vagal corticotropin releasing factor (CRF) inputs

Both in vitro and in vivo studies demonstrated that, following perinatal high fat diet, CRF receptors were tonically active at NTS-DMV synapses, and that pharmacological antagonism of these receptors restored appropriate gastric response to OXT

The current study suggests that perinatal high fat diet exposure disrupts descending PVN-DMV inputs, leading to a dysregulated vagal brain-gut response to stress.
Eosinophilic esophagitis-associated epithelial remodeling may limit esophageal carcinogenesis
Authors: Fuller Annie D. , Karami Adam L. , Kabir Mohammad Faujul , Klochkova Alena , Jackson Jazmyne L. , Mu Anbin , Tan Yinfei , Klein-Szanto Andres , Whelan Kelly A.
Published: November 2022

Under homeostatic conditions, esophageal epithelium displays a proliferation/differentiation gradient that is generated as proliferative basal cells give rise to suprabasal cells then terminally differentiated superficial cells. This proliferation/differentiation gradient is perturbed in esophageal pathologies both benign and malignant. Esophageal cancer is among the deadliest forms of human malignancy with 5-year survival rates of <20%. Esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC) are the two most common subtypes of esophageal cancer. Gastroesophageal reflux disease (GERD) is a primary risk factor for EAC. Although GERD and the food allergy-mediated condition eosinophilic esophagitis (EoE) are both associated with chronic esophageal inflammation and epithelial remodeling, including basal cell hyperplasia, epidemiological evidence suggests that EoE patients do not develop esophageal malignancy. Here, we perform single cell RNA-sequencing in murine models of EoE and ESCC to delineate the effects that these two conditions have specifically upon the cellular landscape of esophageal epithelium. In mice with EoE or ESCC, we find expansion of cell populations as compared to normal esophageal epithelium. In mice with EoE, we detect expansion of 4 suprabasal populations coupled with depletion of 4 basal cell populations. By contrast, mice with ESCC display expansion of 4 basal populations as well as depletion of 3 superficial populations. We further evaluated modules of co-expressed genes in EoE- and ESCC-enriched epithelial cell clusters. Senescence, glucocorticoid receptor signaling, and granulocyte-macrophage colony-stimulating factor pathways were associated with EoE-enriched clusters while pathways associated with cell proliferation and metabolism were identified in ESCC-enriched clusters. Finally, by pairing murine models of EoE and ESCC, we demonstrate that exposure to EoE inflammation limits esophageal carcinogenesis. Our findings provide the first functional investigation of the relationship between EoE and esophageal cancer and suggest that esophageal epithelial remodeling events occurring in response to EoE inflammation may limit act to esophageal carcinogenesis which may have future implications for leveraging allergic inflammation-associated alterations in epithelial biology to prevent and/or treat esophageal cancer.
Spontaneous confinement of mRNA at RNP granule interfaces
Authors: Perelman Rebecca T. , Schmidt Andreas , Khan Umar , Walter Nils G.
Published: November 2022

Cellular membraneless organelles termed ribonucleoprotein (RNP) granules often are enriched in messenger RNA (mRNA) molecules relative to the surrounding cytoplasm. Yet, the spatial localization and diffusion of mRNAs in close proximity to phase separated RNP granules is not well understood. In this study, we performed single molecule fluorescence imaging experiments of mRNAs in live cells in the presence of two types of RNP granules, stress granules (SG) and processing bodies (PB), which are distinct in their molecular composition and function. We developed a new colocalization imaging algorithm that was employed to determine the accurate positions of individual mRNAs relative to the granule’s boundaries. We found that mRNA is often localized at granule boundaries, an observation consistent with recently published data1,2. We suggest that mRNA molecules become spontaneously confined at the RNP granule boundary similar to the adsorption of polymer molecules at liquid-liquid interfaces, which is observed in various technological and biological processes.
Mitotic bookmarking redundancy by nuclear receptors mediates robust post-mitotic reactivation of the pluripotency network
Authors: Chervova Almira , Molliex Amandine , Baymaz H. Irem , Papadopoulou Thaleia , Mueller Florian , Hercul Eslande , Fournier David , Dubois Agnès , Gaiani Nicolas , Beli Petra , Festuccia Nicola , Navarro Pablo
Published: November 2022

Mitotic bookmarking transcription factors (TFs) are thought to mediate rapid and accurate post-mitotic gene reactivation. However, the loss of individual bookmarking TFs often leads to the deregulation of only a small proportion of their mitotic targets, raising doubts on the significance and importance of their bookmarking function. Here, we used targeted proteomics of the mitotic bookmarking TF ESRRB, an orphan nuclear receptor, to discover an unexpected redundancy among members of the protein superfamily of nuclear receptors. Focusing on the nuclear receptor NR5A2, which together with ES-RRB is essential for mouse pluripotency, we demonstrate conjoint bookmarking activity of both factors on promoters and enhancers of a large fraction of active genes, particularly the most rapidly and strongly reactivated ones. Upon fast and simultaneous degradation of both factors during mitotic exit, hundreds of mitotic targets of ESRRB/NR5A2, including key players of the pluripotency network, display attenuated transcriptional reactivation. We propose that redundancy in mitotic bookmarking TFs, especially by nuclear receptors, confers robustness to the reestablishment of gene regulatory networks after mitosis.
Macrophage and neutrophil heterogeneity at single-cell spatial resolution in inflammatory bowel disease
Authors: Garrido-Trigo Alba , Corraliza Ana M. , Veny Marisol , Dotti Isabella , Melon-Ardanaz Elisa , Rill Aina , Crowell Helena L. , Corbí Ángel , Gudiño Victoria , Esteller Miriam , Álvarez-Teubel Iris , Aguilar Daniel , Masamunt M Carme , Killingbeck Emily , Kim Youngmi , Leon Michael , Visvanathan Sudha , Marchese Domenica , Caratù Ginevra , Martin-Cardona Albert , Esteve Maria , Panés Julian , Ricart Elena , Mereu Elisabetta , Heyn Holger , Salas Azucena
Published: November 2022

Ulcerative colitis (UC) and Crohn’s disease (CD) are chronic inflammatory intestinal diseases that show a perplexing heterogeneity in manifestations and response to treatment. The molecular basis for this heterogeneity remains uncharacterized. We applied single-cell RNA sequencing and CosMx™ Spatial Molecular Imaging to human colon and found the highest diversity in cellular composition in the myeloid compartment of UC and CD patients. Besides resident macrophage subsets (M0 and M2), patients showed a variety of activated macrophages including classical (M1 CXCL5 and M1 ACOD1) and new inflammation-dependent alternative (IDA) macrophages. In addition, we captured intestinal neutrophils in three transcriptional states. Subepithelial IDA macrophages expressedNRG1, which promotes epithelial differentiation. In contrast,NRG1lowIDA macrophages were expanded within the submucosa and in granulomas, in proximity to abundant inflammatory fibroblasts, which we suggest may promote macrophage activation. We conclude that macrophages sense and respond to unique tissue microenvironments, potentially contributing to patient-to-patient heterogeneity.
Distinct Differences in Gene Expression Profiles in Early and Late Stage Rhodesiense HAT Individuals in Malawi
Authors: Nambala Peter , Mulindwa Julius , Noyes Harry , Namulondo Joyce , Nyangiri Oscar , Matovu Enock , MacLeod Annette , Musaya Janelisa
Published: November 2022

T. b. rhodesienseis the causative agent of rhodesian Human African trypanosomiasis (r-HAT) in Malawi. Clinical presentation of r-HAT in Malawi varies between the different foci and differs from East African HAT clinical phenotypes. The purpose of this study was to gain more insights into the transcriptomic profiles of patients with early stage 1 and late stage 2 HAT disease in Malawi. Whole blood from individuals infected withT. b. rhodesiensewas used for RNA-Seq. Control samples were from healthy trypanosome negative individuals matched on sex, age range, and disease focus. Illumina sequence FASTQ reads were aligned to the GRCh38 release 84 human genome sequence using HiSat2 and differential analysis was done in R using the DESeq2 package. XGR, ExpressAnalyst and InnateDB algorithms were used for functional annotation and gene enrichment analysis of significant differentially expressed genes. RNA-seq was done on 25 healthy controls and 23 r-HAT case samples of which 3 case samples were excluded for downstream analysis as outliers. 4519 genes were significantly differentially expressed (p adjusted <0.05) in individuals with early stage 1 r-HAT disease (n = 12) and 1824 genes in individuals with late stage 2 r-HAT disease (n = 8). Enrichment of innate immune response genes through neutrophil activation was identified in individuals with both early and late stages of the disease. Additionally, lipid metabolism genes were enriched in late stage 2 disease. We further identified uniquely upregulated genes (log2 Fold Change 1.4 - 2.0) in stage 1 (ZNF354C) and stage 2 (TCN1 and MAGI3) blood. Our data brings new insight into the human transcriptome landscape duringT. b. rhodesienseinfection. We have further identified key biological pathways and transcripts during stage 1 and stage 2 r-HAT. Lastly, we have identified potential diagnostic biomarkers that may be used for staging of r-HAT disease.
Euphorbia yadgirensis sp. nov., (Euphorbiaceae) from Karnataka state, India
Authors: Sarojini Devi N , Raja Kullayiswamy K
Published: November 2022

Euphorbia yadgirensisis a new species from the scrub forest of Royangole village, Yadgiri district of Karnataka, India is described and illustrated here. It belongs to the genusEuphorbia,subg.Chamaesyce,sect.Longistylaeand resemblesEuphorbia kadapensis. However, it differs in its decumbent habit (vs. erect), sympodial monochasium (vs. dichotomous), laciniate stipules (vs. scaly), sutures absent on capsule (vs. present).
Exploring the Neural Processes behind Narrative Engagement: An EEG Study
Authors: Dini Hossein , Simonetti Aline , Bruni Luis Emilio
Published: November 2022

Past cognitive neuroscience studies using naturalistic stimuli have considered narratives holistically and focused on cognitive processes. In this study, we incorporated the narrative structure—the dramatic arc—as an object of investigation, to examine how engagement levels fluctuate across a narrative-aligned dramatic arc. We explored the possibility of predicting self-reported engagement ratings from neural activity and investigated the idiosyncratic effects of each phase of the dramatic arc on brain responses as well as the relationship between engagement and brain responses. We presented a movie excerpt following the six-phase narrative arc structure to female and male participants while collecting EEG signals. We then asked this group of participants to recall the excerpt, another group to segment the video based on the dramatic arc model, and a third to rate their engagement levels while watching the movie. The results showed that the self-reported engagement ratings followed the pattern of the narrative dramatic arc. Moreover, whilst EEG amplitude could not predict group-averaged engagement ratings, other features comprising dynamic inter-subject correlation, dynamic functional connectivity patterns and graph features were able to achieve this. Furthermore, neural activity in the last two phases of the dramatic arc significantly predicted engagement patterns. This study is the first to explore the cognitive processes behind the dramatic arc and its phases. By demonstrating how neural activity predicts self-reported engagement, which itself aligns with the narrative structure, this study provides insights on the interrelationships between narrative structure, neural responses, and viewer engagement.

Significance statement

Dramatic narratives follow a complex structure termed as the narrative arc. Here, we addressed the complexity of this structure in order to explore brain responses during narrative cognition. We examined the link between the narrative arc and its six phases with self-reported engagement, and whether brain responses elicited by a narrative can predict engagement levels. Our results showed that the group-averaged engagement ratings followed the dramatic arc model. EEG features predicted group-averaged engagement patterns and also engagement levels in the last two phases. This is the first study to characterize the narrative dramatic arc phases at the neural level. It contributes to the fields of cognitive narratology and neuroscience by extending current knowledge on how the brain responds to narratives.
Genomic footprints of bottleneck in landlocked salmon population
Authors: Subramanian Sankar , Kumar Manoharan
Published: November 2022

At the end of the last ice age, several Atlantic salmon populations got caught up in the lakes and other small waterbodies of the Northern Hemisphere. Therefore, the pattern of evolution shaping the landlocked salmon populations is different from the other anadromous salmons, which migrate between the sea and rivers. According to the theories of population genetics, the effect of genetic drift is expected to be more pronounced in the former compared to the latter. Here we examined this using the whole genome data of landlocked and anadromous salmon populations of Norway. Our results showed a 50-80% reduction in the genomic heterozygosity in the landlocked compared to anadromous salmon populations. The number and total size of the runs of homozygosity (RoH) segments of landlocked salmons were 2 to 8-fold higher than those of their anadromous counterparts. We found the former had a higher ratio of nonsynonymous-to-synonymous diversities than the latter. The investigation also revealed a significant elevation of homozygous deleterious Single Nucleotide Variants (SNVs) in the landlocked salmon compared to the anadromous populations. All these results point to a significant reduction in the population size of the landlocked salmons, which might have started after the last glacial epoch. Previous studies on terrestrial vertebrates observed similar signatures of a bottleneck when the populations from Island and the mainland were compared. Since landlocked waterbody such as ponds and lakes are geographically analogous to Islands for fish populations, the findings of this study suggest the similarity in the patterns of evolution between the two.
Computational deconvolution of fifteen leukocyte subtypes from DNA methylation microarrays trained on flow cytometry data in the Health and Retirement Study
Authors: Heiss Jonathan A. , Bakulski Kelly M. , Thyagarajan Bharat , Crimmins Eileen M. , Faul Jessica D. , Fisher Jonah D. , Just Allan C.
Published: November 2022

Adjusting for cell composition is critical in epigenome-wide association studies of whole blood samples. Using DNA methylation of whole blood samples (as opposed to purified cell types) and complete blood counts/flow cytometry data from 2530 participants in the Health and Retirement Study, we trained and tested a computational model that extends the number of estimated leukocyte subtypes to fifteen compared to established models with six or seven cell types. Our model, which can be applied to both Illumina 450k and EPIC microarrays, explained a larger proportion of the observed variance in whole blood DNA methylation levels than popular reference-based cell deconvolution approaches, and vastly reduced the number of false-positive findings in a reanalysis of an epigenome-wide association study of chronological age.
Transcriptional signals of dedifferentiation in human cancer
Authors: Kildisiute Gerda , Kalyva Maria , Elmentaite Rasa , van Dongen Stijn , Thevanesan Christine , Piapi Alice , Ambridge Kirsty , Prigmore Elena , Haniffa Muzlifah , Teichmann Sarah A. , Straathof Karin , Cortés-Ciriano Isidro , Behjati Sam , Young Matthew D.
Published: November 2022

As normal cells transform into cancers, their cell state changes (or “dedifferentiates”), which may drive cancer cells into a stem-like or more primordial, foetal or embryonic cell state. Here, we used single cell atlases to study dedifferentiation in transcriptional terms across a wide spectrum of adult and childhood cancers. At the level of the whole transcriptome, we find that adult cancers rarely return to an embryonic state, but rather that a foetal state is a near-universal feature of childhood cancers. We extend these bulk transcriptomic findings to a single cell resolution analysis of colorectal and liver cancers, confirming the lack of reversion to a primordial state in adult tumours and the retention of foetal signals in childhood cancers. Our findings provide a nuanced picture of dedifferentiation in these two groups of neoplasms, indicating cancer-specific rather than universal patterns of dedifferentiation pervade adult epithelial cancers.
Early but not late exercise training in mice exacerbates hepatic inflammation in early NAFLD
Authors: Kovynev Artemiy , Ying Zhixiong , Lambooij Joost , Guigas Bruno , Rensen Patrick C.N. , Schönke Milena
Published: November 2022

Exercise effectively prevents obesity-related disorders, but it is unclear whether the beneficial health effects of exercise are restricted to unique circadian windows. Therefore, we aimed to study whether timing of exercise training differentially modulates the development and progression of non-alcoholic fatty liver disease (NAFLD), a disease currently estimated to affect over two billion people worldwide. We endurance-trained high fat-high cholesterol-fed NAFLD-prone male APOE*3-Leiden.CETP mice five times per week for eight weeks either in the early (ZT13) or in the late (ZT22) active phase and assessed the NAFLD score (histology) and hepatic inflammation compared to sedentary mice. Exercise training prevented an increase in body fat mass and fasting plasma glucose as expected, but neither early nor late training affected liver triglyceride or cholesterol content compared to sedentary mice, likely due to a very early stage of hepatic steatosis. In line, hepatic expression of de novo lipogenesis genes (e.g., Fasn, Srebp1c) was similarly downregulated by early and late training. However, exercise had a distinct time-dependent effect on hepatic inflammation, as only early training promoted an influx of pro-inflammtory cells into the liver paired with increased expression of the pro-inflammatory cytokines (e.g. Tnfa, Il1b). This data suggests that the timing of exercise is a critical factor for the effect on cardiometabolic disease development.
Remodelled Ribosomes Synthesise a Specific Proteome in Proliferating Plant Tissue during Cold
Authors: Martinez-Seidel Federico , Suwanchaikasem Pipob , Gentry-Torfer Dione , Rajarathinam Yogeswari , Ebert Alina , Erban Alexander , Pereira Firmino Alexandre Augusto , Nie Shuai , Leeming Michael G. , Williamson Nicholas A. , Roessner Ute , Kopka Joachim , Boughton Berin A.
Published: November 2022

Plant acclimation to low temperatures occurs through system-wide mechanisms that include proteome shifts, some of which occur at the level of protein synthesis. All proteins are synthesised by ribosomes. Rather than being monolithic, transcript-to-protein translation machines, ribosomes can be selective and cause effective proteome shifts required for successful temperature acclimation. Here, we use apical root meristems of germinating seedlings of the monocotyledonous plant barley as a model to study changes in protein abundance and synthesis rates during cold acclimation. We measure metabolic and physiological parameters that allow us to compare protein synthesis rates in different physiological states, e.g., in cold acclimation compared to the optimal temperature state. We show that ribosomal proteins are independently synthesised and assembled into ribosomal complexes in root proliferative tissue, and assess how the ribo-proteome shifts during cold may be associated with changes in synthesis and accumulation of macromolecular complexes. We demonstrate that translation initiation is the limiting step during cold acclimation and based on our data propose a model of a ribosomal code that depends on a reconfigured ribosome population, where as a mode of cold acclimation, specific ribosomal protein compositions may confer selective association capabilities between 60S subunits and 48S initiation complexes.
A new theoretical framework jointly explains behavioral and neural variability across subjects performing flexible decision-making
Authors: Pagan Marino , Tang Vincent D , Aoi Mikio C. , Pillow Jonathan W. , Mante Valerio , Sussillo David , Brody Carlos D.
Published: November 2022

The ability to flexibly switch our response to external stimuli according to contextual information is critical for successful interactions with a complex world. Context-dependent computations are necessary across many domains1–3, yet their neural implementations remain poorly understood. Here we developed a novel behavioral task in rats to study context-dependent selection and accumulation of evidence for decision-making4–6. Under assumptions supported by both monkey and rat data, we first show mathematically that a network can solve this problem through a combination of three defined components. These components can be identified and tested directly with experimental data. We further show that existing electrophysiological and modeling data are compatible with the full variety of possible combinations of these components, suggesting that different individuals could use different component combinations. To study variability across individual subjects, we developed automated, high-throughput methods to train rats on our task, and we trained many subjects on it. Consistent with theoretical predictions, neural and behavioral analyses revealed substantial heterogeneity across rats, despite uniformly good task performance. Our theory further predicts a specific link between behavioral and neural signatures, which was robustly supported in the data. In summary, our results provide a new experimentally-supported theoretical framework to analyze individual variability in biological and artificial systems performing flexible decision-making tasks, they open the door to cellular-resolution studies of individual variability in higher cognition, and they provide insights into neural mechanisms of context-dependent computation more generally.
Imputation of low-coverage sequencing data from 150,119 UK Biobank genomes
Authors: Rubinacci Simone , Hofmeister Robin , da Mota Bárbara Sousa , Delaneau Olivier
Published: November 2022

Recent work highlights the advantages of low-coverage whole genome sequencing (lcWGS), followed by genotype imputation, as a cost-effective genotyping technology for statistical and population genetics. The release of whole genome sequencing data for 150,119 UK Biobank (UKB) samples represents an unprecedented opportunity to impute lcWGS with high accuracy. However, despite recent progress1,2, current methods struggle to cope with the growing numbers of samples and markers in modern reference panels, resulting in unsustainable computational costs. For instance, the imputation cost for a single genome is 1.11£ using GLIMPSE v1.1.1 (GLIMPSE1) on the UKB research analysis platform (RAP) and rises to 242.8£ using QUILT v1.0.4. To overcome this computational burden, we introduce GLIMPSE v2.0.0 (GLIMPSE2), a major improvement of GLIMPSE, that scales sublinearly in both the number of samples and markers. GLIMPSE2 imputes a low-coverage genome from the UKB reference panel for only 0.08£ in compute cost while retaining high accuracy for both ancient and modern genomes, particularly at rare variants (MAF < 0.1%) and for very low-coverage samples (0.1x-0.5x).
TheStreptococcus mutansRhamnose-glucose Polysaccharide Plays an Important Role in Oxidative Stress Resistance and Iron Homeostasis
Authors: Bischer Andrew P. , Faustoferri Roberta C. , Kovacs Christopher J. , Gill Steven R. , Quivey Robert G.
Published: November 2022

The rhamnose-glucose polysaccharide (RGP) ofStreptococcus mutansis known to play an essential role in cell division and biofilm formation. It has become increasingly apparent that the structure plays a role in protection against external stress, including an undefined role in oxidative stress. In this study, we demonstrate that the loss of RGP impairs the uptake of glucose and the susceptibility ofS. mutansto lethal concentrations of iron, while at the same time, generates elevated content of intracellular iron, a prominent producer of reactive oxygen species. Intracellular iron levels were significantly higher in a strain lacking rhamnose production (ΔrmlD), compared to a strain deficient in components of the RGP production pathway (ΔrgpG). The seemingly paradoxical discrepancy between iron uptake and iron susceptibility may be partially explained by increased expression ofdprandsod, genes that protect against oxidative stress and primeS. mutansagainst oxidative stressors such as H2O2and superoxide. Analysis of the promoter of the rhamnose biosynthesis genermlDindicated the presence of regulatory motifs, including Rex and PerR, which we have shown control expression for the genes responsible for rhamnose biosynthesis and RGP production. These results provide initial insights into the role that RGP plays in toleration of oxidative stress and suggest a complexity in regulation of the genes responsible for production of the RGP.

Importance

Dental caries, a disease caused byStreptococcus mutans, imposes significant healthcare burdens and productivity losses in the US. The outer structure ofS. mutans, which is primarily composed of the rhamnose-glucose polysaccharide (RGP), is understudied, though it plays a crucial role in survival of the organism in response to environmental stress. Elucidating the protective role of RGP and the regulatory mechanisms that control the synthesis of RGP inS. mutanswill lead to insights into the structure and function of cell wall polysaccharides in other streptococci. This study reveals a role for L-rhamnose, the building block of RGP, in mediating homeostasis of iron uptake, while the loss of rhamnose biosynthesis causes alterations in transcription ofsodanddpr.
Generative network modeling reveals quantitative definitions of bilateral symmetry exhibited by a whole insect brain connectome
Authors: Pedigo Benjamin D. , Powell Mike , Bridgeford Eric W. , Winding Michael , Priebe Carey E. , Vogelstein Joshua T.
Published: November 2022

Comparing connectomes can help explain how neural connectivity is related to genetics, disease, development, learning, and behavior. However, making statistical inferences about the significance and nature of differences between two networks is an open problem, and such analysis has not been extensively applied to nanoscale connectomes. Here, we investigate this problem via a case study on the bilateral symmetry of a larvalDrosophilabrain connectome. We translate notions of “bilateral symmetry” to generative models of the network structure of the left and right hemispheres, allowing us to test and refine our understanding of symmetry. We find significant differences in connection probabilities both across the entire left and right networks and between specific cell types. By rescaling connection probabilities or removing certain edges based on weight, we also present adjusted definitions of bilateral symmetry exhibited by this connectome. This work shows how statistical inferences from networks can inform the study of connectomes, facilitating future comparisons of neural structures.
Increasing Ciliary ARL13B Expression Drives Active and Inhibitor-Resistant SMO and GLI into Glioma Primary Cilia
Authors: Shi Ping , Tian Jia , Mallinger Julianne C. , Deleyrolle Loic P. , McIntyre Jeremy C. , Caspary Tamara , Breunig Joshua J , Sarkisian Matthew R.
Published: November 2022

ADP-ribosylation factor-like protein 13B (ARL13B), a regulatory GTPase and guanine exchange factor (GEF) enriches in primary cilia and promotes tumorigenesis in part by regulating Smoothened (SMO), GLI, and Sonic hedgehog (SHH) signaling. Gliomas with increasedARL13B, SMOandGLI2expression are more aggressive but the relationship to cilia is unclear. Previous studies showed increasing ARL13B in glioblastoma cells promoted ciliary SMO accumulation, independent of exogenous SHH addition. Here we show SMO accumulation is due to increased ciliary, but not extraciliary ARL13B. Increasing ARL13B expression promotes the accumulation of both activated SMO and GLI2 in glioma cilia, but not in NIH3T3 fibroblast cilia. ARL13B-driven increases in ciliary SMO and GLI2 are resistant to SMO inhibitors, GDC-0449 and cyclopamine. Finally, temozolomide chemotherapy which increases ARL13B expression in glioma, stimulates SMO and GLI2 into glioma cilia, but not fibroblast cilia. Collectively, our data suggest factors that elevate ARL13B may drive drug-resistant SMO and GLI into cilia. This suggests the ARL13B-associated mechanism that leads to ciliary SMO/GLI recruitment may promote treatment resistance in glioma.
Age-related differences in prefrontal glutamate are associated with increased working memory decay that gives the appearance of learning deficits
Authors: Rmus Milena , He Mingjian , Baribault Beth , Walsh Edward G. , Festa Elena K. , Collins Anne G.E. , Nassar Matthew R.
Published: November 2022

The ability to use past experience to effectively guide decision making declines in older adulthood. Such declines have been theorized to emerge from either impairments of striatal reinforcement learning systems (RL) or impairments of recurrent networks in prefrontal and parietal cortex that support working memory (WM). Distinguishing between these hypotheses has been challenging because either RL or WM could be used to facilitate successful decision making in typical laboratory tasks. Here we investigated the neurocomputational correlates of age-related decision making deficits using an RL-WM task to disentangle these mechanisms, a computational model to quantify them, and magnetic resonance spectroscopy to link them to their molecular bases. Our results reveal that task performance is worse in older age, in a manner best explained by working memory deficits, as might be expected if cortical recurrent networks were unable to sustain persistent activity across multiple trials. Consistent with this, we show that older adults had lower levels of prefrontal glutamate, the excitatory neurotransmitter thought to support persistent activity, compared to younger adults. Individuals with the lowest prefrontal glutamate levels displayed the greatest impairments in working memory after controlling for other anatomical and metabolic factors. Together, our results suggest that lower levels of prefrontal glutamate may contribute to failures of working memory systems and impaired decision making in older adulthood.
Learning from the unknown: exploring the range of bacterial functionality
Authors: Mahlich Yannick , Zhu Chengsheng , Chung Henri , Velaga Pavan K. , De Paolis Kaluza M. Clara , Radivojac Predrag , Friedberg Iddo , Bromberg Yana
Published: November 2022

Determining the repertoire of a microbe’s molecular functions is a central question in microbial biology. Modern techniques achieve this goal by comparing microbial genetic material against reference databases of functionally annotated genes/proteins or known taxonomic markers such as 16S rRNA. Here we describe a novel approach to exploring bacterial functional repertoires without reference databases. OurFusionscheme establishes functional relationships between bacteria and assigns organisms to Fusion-taxa that differ from otherwise defined taxonomic clades. Three key findings of our work stand out. First, bacterial functional comparisons outperform marker genes in assigning taxonomic clades. Fusion profiles are also better for this task than other functional annotation schemes. Second, Fusion-taxa are robust to addition of novel organisms and are, arguably, able to capture the environment-driven bacterial diversity. Finally, our alignment-free nucleic acid-based Siamese Neural Network model, created using Fusion functions, enables finding shared functionality of very distant, possibly structurally different, microbial homologs. Our work can thus help annotate functional repertoires of bacterial organisms and further guide our understanding of microbial communities.
IL-17C is a driver of damaging inflammation duringNeisseria gonorrhoeaeinfection of human Fallopian tube
Authors: Garcia Erin M. , Lenz Jonathan D. , Hackett Kathleen T. , Salgado-Pabón Wilmara , Dillard Joseph P.
Published: November 2022

The human-restricted pathogenNeisseria gonorrhoeaeascends into the upper female reproductive tract to cause damaging inflammation within the Fallopian tubes (salpingitis) and pelvic inflammatory disease (PID), increasing the risk of infertility and life-threatening ectopic pregnancy. The loss of ciliated cells from the epithelium is thought to be both a consequence of inflammation and a cause of the associated adverse sequelae. However, the links between infection, inflammation, and ciliated cell extrusion remain unresolved. With the use ofex vivocultures of human Fallopian tube paired with RNA sequencing we defined the tissue response to gonococcal challenge, identifying cytokine, chemokine, cell adhesion, and apoptosis related transcripts not previously recognized as potentiators of gonococcal PID. Unexpectedly, the cytokine IL-17C was one of the most highly induced genes. Yet, this cytokine has no previous association with gonococcal disease nor any sexually transmitted infection and thus it was selected for further characterization in our model. We show that human Fallopian tubes express the IL-17C receptor (IL-17RE) on the epithelial surface and that treatment with purified IL-17C induces pro-inflammatory cytokine secretion in addition to sloughing of the epithelium and generalized tissue damage. These results demonstrate a previously unrecognized but critical role of IL-17C in the damaging inflammation induced by gonococci in a human explant model of PID.

Significance

We performed untargeted transcriptional analysis of the human Fallopian tube response toNeisseria gonorrhoeae. Focusing on one upregulated transcript not previously identified in any context of gonococcal infection, we show that the human Fallopian tube secretes the inflammation amplifying cytokine IL-17C in response toN. gonorrhoeaechallenge. IL-17C treatment of human Fallopian tubes stimulated pro-inflammatory cytokine secretion and was sufficient to elicit epithelial cell pathologies characteristic of pelvic inflammatory disease (sloughing, exfoliation). Thus, we identify IL-17C as a previously unrecognized component of the host response to gonococci that promotes inflammation and tissue damage within the human Fallopian tube.
Bioavailability of Schisandrin B and its effect on 5-Fluorouracil metabolism in a xenograft mouse model of colorectal cancer
Authors: Lee Pui-Kei , Co Vanessa Anna , Yang Yang , Wan Murphy Lam Yim , El-Nezami Hani , Zhao Danyue
Published: November 2022

Schisandrin B (Sch-B) is a predominant bioactive lignan in the fruit of a traditional Chinese medicinal plantSchisandra Chinensiswith widely reported anti-cancer properties. Using a xenograft mouse model of colorectal cancer (CRC), we showed potent anti-tumor effects of Sch-B and synergistic effects when co-treated with the chemotherapy drug, fluorouracil (5-FU). To explore the underlying anti-tumor mechanism of Sch-B, we first compared the bioavailability, metabolism and tissue distribution of Sch-B and its metabolites among healthy and tumor-bearing mice. To understand the drug-phytochemical interactions associated with the synergy between Sch-B and 5-FU, we examined their reciprocal influence on drug metabolism, tissue distribution, and multidrug resistance (MDR) gene expression in tumor-bearing mice. Using a targeted metabolomics approach, three Sch-B metabolites and two bioactive 5-FU metabolites were quantified and found to reach tumor tissue. Generally, Sch-B metabolites were present at higher levels in tumor-bearing than healthy mice, whereas 5-FU metabolite accumulation was remarkably higher in the co-treatment than 5-FU alone group. Moreover, MDR genes were significantly downregulated upon co-treatment, demonstrating the capacity of Sch-B to reverse MDR in chemotherapy. This study showed that Sch-B may serve as a promising adjuvant to chemotherapy drugs via favorably modulating drug metabolism and bioavailability, and attenuating MDR.
1Arche: An Advanced Flexible Tool for High-throuput Annotation of Functions on Microbial Contigs
Authors: Alonso-Reyes Daniel Gonzalo , Albarracin Virginia Helena
Published: November 2022

The growing amount of genomic data has prompted a need for less demanding and user friendly functional annotators. At the present, it’s hard to find a pipeline for the annotation of multiple functional data, such as both enzyme commission numbers (E.C.) and orthologous identifiers (KEGG and eggNOG), protein names, gene names, alternative names, and descriptions. In this work, we provide a new solution which combines different algorithms (BLAST, DIAMOND, HMMER3) and databases (UniprotKB, KOfam, NCBIFAMs, TIGRFAMs, and PFAM), and also overcome data download challenges. The software framework, Arche, herein demonstrated competitive results overEscherichia coliK-12 genome, the metagenome-assembled genome ofFerrovum myxofaciensS2.4, and a freshwater metagenome when compared to other annotators. Finally, Arche provides an analysis pipeline that can accommodate advanced tools in a unique order, creating several advantages regarding to other commonly used annotators.
Structural Elucidation of a Protective B cell Epitope on Outer Surface Protein C (OspC) of the Lyme disease spirochete,Borreliella burgdorferi
Authors: Rudolph Michael J. , Davis Simon A. , Haque H M Emranul , Weis David D. , Vance David J , Piazza Carol Lyn , Ejemel Monir , Cavacini Lisa , Wang Yang , Mbow M. Lamine , Gilmore Robert D. , Mantis Nicholas J
Published: November 2022

Outersurfaceprotein C (OspC) plays a pivotal role in mediating tick-to-host transmission and infectivity of the Lyme disease spirochete,Borreliella burgdorferi. OspC is a helical-rich homodimer that interacts with tick salivary proteins, as well as components of the mammalian immune system. Several decades ago, it was shown that the OspC-specific monoclonal antibody, B5, was able to passively protect mice from experimental tick-transmitted infection byB. burgdorferistrain B31. However, B5’s epitope has never been elucidated, despite widespread interest in OspC as a possible Lyme disease vaccine antigen. Here we report the crystal structure of B5 antigen-binding fragments (Fabs) in complex with recombinant OspC type A (OspCA). Each OspC monomer within the homodimer was bound by a single B5 Fab in a side-on orientation, with contact points along OspC’s α-helix 1 and α-helix 6, as well as interactions with the loop between a-helices 5 and 6. In addition, B5’s complementarity-determining region (CDR) H3 bridged the OspC-OspC’ homodimer interface, revealing the quaternary nature of the protective epitope. To provide insight into the molecular basis of B5 serotype specificity, we solved the crystal structures of recombinant OspC types B and K and compared them to OspCA. This study represents the first structure of a protective B cell epitope on OspC and will aid in the rational design of OspC-based vaccines and therapeutics for Lyme disease.

IMPORTANCE

The spirochete,Borreliella burgdorferi, is the causative agent of Lyme borreliosis, the most common tickborne disease in the United States. The spirochete is transmitted to humans during the course of a tick taking a bloodmeal. AfterB. burgdorferiis deposited into the skin of a human host, it replicates locally and spreads systemically, often resulting in clinical manifestations involving the central nervous system, joints, and/or heart. Antibodies directed againstB. burgdorferi’s outer surface protein C (OspC) are known to block tick-to-host transmission, as well as dissemination of the spirochete within a mammalian host. In this report, we reveal the first atomic structure of one such antibody in complex with OspC. Our results have implications for the design of a Lyme disease vaccine capable to interfering with multiple stages inB. burgdorferiinfection.
Long-range inhibitory axons from medial entorhinal cortex target lateral entorhinal neurons projecting to the hippocampus
Authors: Nilssen Eirik S. , Jacobsen Bente , Doan Thanh P. , Girão Paulo J. B. , Witter Menno P.
Published: November 2022

Functionally distinct information encoded by the two main divisions of the entorhinal cortex (EC), the lateral EC (LEC) and the medial EC (MEC), is thought to be first integrated at the level of the hippocampus. Here we examine a circuit connecting MEC to LEC that supports functional interplay at the level of the two entorhinal domains. Using a combination of anatomical,in vitroelectrophysiological and behavioral experiments in the mouse, we report that axons from MEC somatostatin-expressing GABAergic neurons densely distribute in layer I of LEC, where they drive strong and near selective inhibition of principal neurons in layer IIa. This inhibitory pathway is accompanied by MEC glutamatergic axons that innervate multiple layers of LEC and preferentially synapse onto principal neurons in layers IIb and III. Our findings indicate that excitatory and inhibitory projections from MEC may separately regulate the activity of different populations of hippocampal-projecting principal neurons in LEC.
Human Gasdermin D and MLKL disrupt mitochondria, endocytic traffic and TORC1 signaling in budding yeast
Authors: Valenti Marta , Molina María , Cid Víctor J
Published: November 2022

Gasdermin D (GSDMD) and mixed lineage kinase domain-like protein (MLKL) are the pore-forming effectors of pyroptosis and necroptosis, respectively, with the capacity to disturb plasma membrane selective permeability and induce programmed cell death. The budding yeastSaccharomyces cerevisiaehas long been used as a simple eukaryotic model for the study of proteins associated with human diseases by heterologous expression. In this work, we expressed in yeast both GSDMD and its N-terminal domain [GSDMD(NT)] to characterize their cellular effects, and compare them to those of MLKL. GSDMD(NT) and MLKL inhibited yeast growth, formed cytoplasmic aggregates, and fragmented mitochondria. Loss-of-function point mutants of GSDMD(NT) showed affinity for this organelle. Besides, GSDMD(NT) and MLKL caused an irreversible cell cycle arrest through TORC1 inhibition, and disrupted endosomal and autophagic vesicular traffic. Our results provide a basis for a humanized yeast platform to study GSDMD and MLKL, a useful tool for structure-function assays and drug discovery.