bluuebunny/crossref_metadata_2025 huggingface dataset:
Brain functional connectivity correlates of response in the 7.5% CO2inhalational model of generalized anxiety disorder: a pilot study
Authors: Huneke Nathan T.M. , Broulidakis M. John , Darekar Angela , Baldwin David S. , Garner Matthew
Published: October 2019

The 7.5% CO2inhalational model (‘CO2challenge’) can be used to explore potential treatments for generalized anxiety disorder. However, it remains unknown how inter-individual variability in the functional architecture of negative affective valence systems might relate to the anxiogenic response to CO2challenge. In this pilot study, we explored how connectivity in systems associated with processing potential threat (“anxiety”) correlated with behavioural measures of anxiety following prolonged CO2inhalation.

The negative affective valence system was identified using a passive emotional face perception task. Spherical regions of interest were created from peak voxels of significant brain activation when 100 young adult participants viewed emotional faces compared with black and white concentric circles during a functional MRI scan. Using these regions of interest, generalized psychophysiological interaction (gPPI) analysis was undertaken to explore task-evoked functional connectivity in a separate group of 13 healthy volunteers. Within 7 days of the scan, these participants underwent CO2challenge and results from the gPPI analysis were correlated with CO2outcome measures.

Exposure to CO2challenge significantly increased subjective anxiety, negative affect, systolic blood pressure and heart rate. Functional connectivity between the ventromedial prefrontal cortex and right amygdala was positively correlated with heart rate. Increased connectivity between the vmPFC and the right amygdala, and decreased connectivity between the midcingulate cortex (MCC) and the left amygdala, correlated with subjective anxiety during CO2challenge.

Response to CO2challenge was related to task-evoked functional connectivity between regions known to be important in processing potential threat. Further studies are required to assess whether this translates into clinical populations. Measures of functional connectivity within emotional processing networks could be potential biomarkers to enable stratification of healthy volunteers, and to examine correlates of response, in trials using experimental medicine models.
Steering Molecular Dynamics Simulations of Membrane-Associated Proteins with Neutron Reflection Results
Authors: Treece Bradley W. , Heinrich Frank , Ramanathan Arvind , Lösche Mathias
Published: October 2019

We present a method to incorporate structural results from neutron reflectometry, a technique that determines interfacial structures such as protein-membrane complexes at a solid surface, into molecular dynamics simulations. By analyzing component volume occupancy profiles, which describe the one-dimensional distribution of a particular molecular component within an interfacial architecture, we construct a real-space constraint in the form of a biasing potential for the simulation that vanishes when the simulated and experimental profiles agree. This approach improves the correspondence between simulation and experiment, as shown for an earlier investigation where an NR-derived structure was well captured by an independent MD simulation, and may lead to faster equilibration of ensemble structures. We further show that time averaging of the observable when biasing with this approach permits fluctuations about the average, which are necessary for conformational exploration of the protein. The method described here also provides insights into systems that are characterized by NR and MD when the two show slight differences in their profiles. This is particularly valuable for studies of proteins at interfaces that contain disordered regions since the conformation of such regions is difficult to judge from the analysis of one-dimensional experimental profiles and take prohibitively long to equilibrate in simulations.
The realised velocity of climate change reveals remarkable idiosyncrasy of species’ distributional shifts
Authors: Pearse William D. , Davies T. Jonathan
Published: October 2019

To date, our understanding of how species have shifted in response to recent climate warming has been based on a few studies with a limited number of species. Here we present a comprehensive, global overview of species’ distributional responses to changing climate across a broad variety of taxa (animals, plants, and fungi). We characterise species’ responses using a metric that describes the realised velocity of climate change: how closely species’ responses have tracked changing climate through time. In contrast to existing ‘climate velocity’ metrics that have focused on space, we focus on species and index their responses to a null expectation of change in order to examine drivers of inter-specific variation. Here we show that species are tracking climate on average, but not sufficiently to keep up with the pace of climate change. Further, species responses are highly idiosyncratic, and thus highlight that projections assuming uniform responses may be misleading. This is in stark contrast to species’ present-day and historical climate niches, which show strong evidence of the imprint of evolutionary history and functional traits. Our analyses are a first step in exploring the vast wealth of empirical data on species’ historic responses to recent climate change.
Cortical functional connectivity indexes arousal state during sleep and anesthesia
Authors: Banks Matthew I. , Krause Bryan M. , Endemann Christopher M. , Campbell Declan I. , Kovach Christopher K. , Dyken M. Eric , Kawasaki Hiroto , Nourski Kirill V.
Published: October 2019

Disruption of cortical connectivity likely contributes to loss of consciousness (LOC) during both sleep and general anesthesia, but the degree of overlap in the underlying mechanisms is unclear. Both sleep and anesthesia comprise states of varying levels of arousal and consciousness, including states of largely maintained consciousness (sleep: N1, REM; anesthesia: sedated but responsive) as well as states of substantially reduced consciousness (sleep: N2/N3; anesthesia: unresponsive). Here, we tested the hypotheses that (1) cortical connectivity will reflect clear changes when transitioning into states of reduced consciousness, and (2) these changes are similar for arousal states of comparable levels of consciousness during sleep and anesthesia. Using intracranial recordings from five neurosurgical patients, we compared resting state cortical functional connectivity (as measured by weighted phase lag index) in the same subjects across arousal states during natural sleep [wake (WS), N1, N2, N3, REM] and propofol anesthesia [pre-drug wake (WA), sedated/responsive (S) and unresponsive (U)]. In wake states WS and WA, alpha-band connectivity within and between temporal, parietal and occipital regions was dominant. This pattern was largely unchanged in N1, REM and S. Transitions into states of reduced consciousness N2, N3 and U were characterized by dramatic and strikingly similar changes in connectivity, with dominant connections shifting to frontal cortex. We suggest that shifts from temporo-parieto-occipital to frontal cortical connectivity may reflect impaired sensory processing in states of reduced consciousness. The data indicate that functional connectivity can serve as a biomarker of arousal state and suggest common mechanisms of LOC in sleep and anesthesia.
Hypoxia inducible factor-2α increases sensitivity of colon cancer cells towards oxidative cell death
Authors: Singhal Rashi , Mitta Sreedhar R , Olive Kenneth P. , Lyssiotis Costas A. , Shah Yatrik M.
Published: October 2019

Colorectal cancer (CRC) is the second leading cause of cancer-related deaths in the US. Hypoxia is a hallmark of solid tumors which promotes tumor cell growth, survival, metastasis and confers resistance to chemo and radiotherapies. Targeting hypoxic cells has been difficult. Moreover, inhibitors for the major transcription factors, hypoxia inducible factor (HIF)-1α and HIF-2α have not shown long-term efficacy in most cancers. We have previously shown that HIF-2α is essential for colon tumorigenesis. Using an unbiased screen, we show a significant increase in synthetic lethality of HIF-2α overexpressing tumor enteroids to oxidative cell death activators. The treatment with hypoxia mimetic FG4592 (Roxadustat), led to a robust increase in erastin-, RSL3-, and dimethyl fumarate-induced cell death in a dose- and time-dependent manner. Further, our in-vitro data shows that HIF-2α knock-down cells are completely resistant to these drugs. HIF activation promotes upregulation of lipid synthesis genes in vitro and in vivo leading to oxidative stress. Taken together, our results suggest that this intrinsic sensitivity towards oxidative stress associated with hypoxia could be utilized as a persistent and dynamic form of cell death for colon cancer treatment.
Chemotherapy induced immunogenic cell death alters response to exogenous activation of STING pathway and PD-L1 immune checkpoint blockade in a syngeneic murine model of ovarian cancer
Authors: Nersesian Sarah , Shakfa Noor , Peterson Nichole , Vidotto Thiago , AfriyieAsante Afrakoma , Lightbody Elizabeth , Koti Madhuri
Published: October 2019

Poor response to platinum/taxane-based chemotherapy has remained a major hurdle in the management of high grade serous carcinoma of the ovary (HGSC). Recurrent HGSC is often treated with liposomal doxorubicin as a second line chemotherapy. Unfortunately, HGSC patients have not benefited from immunotherapies targeting the PD-1/PD-L1 immune checkpoint axis. In a pre-clinical study evaluating the efficacy of a “Stimulator of Interferon Genes” (STING) agonist, we demonstrated the synergistic potential of STING pathway activation in enhancing response to carboplatin chemotherapy and sensitization to PD-1 immune checkpoint blockade (ICB). Since carboplatin and doxorubicin exhibit distinct immunogenic cell death (ICD) inducing potential, we investigated the chemotherapy specific effect in the magnitude of response to exogenous STING pathway activation. Immunocompetent C57/BL6 mice were implanted with ID8-Trp53−/−cells followed by treatment with carboplatin or doxorubicin. Towards rationalized addition of STING agonist with or without PD-L1 blockade, we first determined the expression of 60 known ICD associated genes at an early time point following the initial treatment with carboplatin or doxorubicin with or without STING agonist. Doxorubicin treated tumours showed significantly higher expression of ICD genes,Cxcl10, Cd274, Isg15, Psmb9andCalr. Expression changes were further amplified following the addition of STING agonist. Significantly higher expression ofCxcl10andIsg15were observed in the doxorubicin + STING agonist treated mice compared to carboplatin + STING agonist combination. Interestingly,Ccl5gene expression was higher in the tumours from carboplatin or carboplatin and STING agonist combination treated mice compared to those treated with doxorubicin. Plasma cytokine analysis showed distinct profiles of CXCL10, CCL5, MCP-1 and IL6 post treatment with each chemotherapy type. Doxorubicin monotherapy treated mice showed significantly longer overall survival compared to their carboplatin counterparts with further increases following addition of either STING agonist or PD-L1 ICB. However, despite the stronger ICD inducing ability of doxorubicin, overall survival of mice treated with carboplatin + STING agonist + PD-L1 ICB was the longest. Findings from our pre-clinical study provide novel insights for rationalized combinations of immune sensitizing agents such as STING pathway activators to improve response of HGSC patients to chemotherapy and ICB in the primary and recurrent settings.
DG-CA3 circuitry mediates hippocampal representations of latent information
Authors: Keinath Alexandra T. , Nieto-posadas Andres , Robinson Jennifer C. , Brandon Mark P.
Published: October 2019

Survival in complex environments necessitates a flexible navigation system that incorporates memory of recent behavior and associations. Yet, how the hippocampal spatial circuit represents latent information independent of sensory inputs and future goals has not been determined. To address this, we imaged the activity of large ensembles in subregion CA1 via wide-field fluorescent microscopy during a novel behavioral paradigm. Our results demonstrated that latent information is represented through reliable firing rate changes during unconstrained navigation. We then hypothesized that the representation of latent information in CA1 is mediated by pattern separation/completion processes instantiated upstream within the dentate gyrus (DG) and CA3 subregions. Indeed, CA3 ensemble recordings revealed an analogous code for latent information. Moreover, selective chemogenetic inactivation of DG-CA3 circuitry completely and reversibly abolished the CA1 representation of latent information. These results reveal a causal and specific role of DG-CA3 circuitry in the maintenance of latent information within the hippocampus.
scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data
Authors: Yu Wenbao , Uzun Yasin , Zhu Qin , Chen Changya , Tan Kai
Published: October 2019

Single cell chromatin accessibility sequencing (scCAS) has become a powerful technology for understanding epigenetic heterogeneity of complex tissues. The development of several experimental protocols has led to a rapid accumulation of scCAS data. In contrast, there is a lack of open-source software tools for comprehensive processing, analysis and visualization of scCAS data generated using all existing experimental protocols. Here we present scATAC-pro for quality assessment, analysis and visualization of scCAS data. scATAC-pro provides flexible choice of methods for different data processing and analytical tasks, with carefully curated default parameters. A range of quality control metrics are computed for several key steps of the experimental protocol. scATAC-pro generates summary reports for both quality assessment and downstream analysis. It also provides additional utility functions for generating input files for various types of downstream analyses and data visualization. With the rapid accumulation of scCAS data, scATAC-pro will facilitate studies of epigenomic heterogeneity in healthy and diseased tissues.
Evolution in novel environments: do restored prairie populations experience strong selection?
Authors: Magnoli Susan M. , Lau Jennifer A.
Published: October 2019

When populations colonize new habitats, they are likely to experience novel environmental conditions, and as a consequence may experience strong selection. While selection and the resulting evolutionary responses may have important implications for establishment success in colonizing populations, few studies have estimated selection in such scenarios. Here we examined evidence of selection in recently established plant populations in two prairie restorations in close proximity (< 15 km apart) using two approaches: 1) we tested for evidence of past selection on a suite of traits in twoChamaecrista fasciculatapopulations by comparing the restored populations to each other and their shared source population in common gardens to quantify evolutionary responses and 2) we measured selection in the field. We found evidence of past selection on flowering time, specific leaf area, and root nodule production in one of the populations, but detected contemporary selection on only one trait (plant height). This demonstrates that while selection can occur in colonizing populations, resulting in significant evolutionary responses in less than 6 generations, rapid evolutionary responses may be weak in even nearby populations sown with the same source population. Because contemporary measures of selection rarely predicted observed evolutionary responses, it also suggests that selection likely differs over the early stages of succession that characterize young prairies.
Mapping the Immune Landscape of Clear Cell Renal Cell Carcinoma by Single-Cell RNA-seq
Authors: Vishwakarma Ajaykumar , Bocherding Nicholas , Chimenti Michael S. , Vishwakarma Purshottam , Nepple Kenneth , Salem Aliasger , Jenkins Russell W. , Zhang Weizhou , Zakharia Yousef
Published: October 2019

The immune cells within the tumor microenvironment are considered key determinants of response to cancer immunotherapy. Immune checkpoint blockade (ICB) has transformed the treatment of clear cell renal cell carcinoma (ccRCC), although the role of specific immune cell states remains unclear. To characterize the tumor microenvironment (TME) of ccRCC, we applied single-cell RNA sequencing (scRNA-seq) along with paired T cell receptor sequencing to map the transcriptomic heterogeneity of 24,904 individual CD45+lymphoid and myeloid cells in matched tumor and blood from patients with ccRCC. We identified multiple distinct immune cell phenotypes for B and T (CD4 and CD8) lymphocytes, natural kill (NK) cells, and myeloid cells. Evaluation of T cell receptor (TCR) sequences revealed limited shared clonotypes between patients, whereas tumor-infiltrating T cell clonotypes were frequently found in peripheral blood, albeit in lower abundance. We further show that the circulating CD4+T cell clonality is far less diverse than peripheral CD8+. Evaluation of myeloid subsets revealed unique gene programs defining monocytes, dendritic cells and tumor-associated macrophages. In summary, here we have leveraged scRNA-seq to refine our understanding of the relative abundance, diversity and complexity of the immune landscape of ccRCC. This report represents the first characterization of ccRCC immune landscape using scRNA-seq. With further characterization and functional validation, these findings may identify novel sub-populations of immune cells amenable to therapeutic intervention.

One Sentence Summary

Single-cell RNA-sequencing reveals unique lymphoid and myeloid gene programs with putative functions in clear cell renal cancer patients
Genome sequence and analysis of the eggplant (Solanum melongenaL.)
Authors: Li Dandan , Qian Jun , Li Wenjia , Jiang Yaqin , Gan Guiyun , Li Weiliu , Chen Riyuan , Yu Ning , Li Yan , Wu Yongguan , Kang Dexian , Lian Jinmin , Niu Yongchao , Wang Yikui
Published: October 2019

The eggplant (Solanum melongenaL.) is one of the most important Solanaceae crops, ranking third in the total production and economic value in the genusSolanum. Here, we report a high-quality, chromosome-scale eggplant reference genome sequence of 1,155.8 Mb, with N50 of 93.9 Mb, which was assembled by combining PacBio long reads and Hi-C sequencing data. Repetitive sequences occupied 70.1% of the assembly length, and 35,018 high-confidence protein-coding genes were annotated based on multiple evidence. Comparative analysis revealed 646 species-specific families and 364 positive selection genes, conferring distinguishing traits to the eggplant. We performed genome-wide identification of disease resistance genes and discovered an expanded gene family of bacterial spot resistance in the eggplant and pepper but not in tomato and potato. The genes involved in chlorogenic acid synthesis were comprehensively characterized. Highly similar chromosomal distribution patterns of polyphenol oxidase genes were observed in the eggplant, tomato, and potato genomes. The eggplant reference genome sequence will not only facilitate evolutionary studies in the Solanaceae but also facilitate their breeding and improvement.
The table-top visual search ability test for children and young people: normative response time data from typically developing children
Authors: Waddington Jonathan , Pickering Jade , Hodgson Timothy
Published: October 2019

Five table-top tasks were developed to test the visual search ability of children and young people in a real-world context, and to assess the transfer of training related improvements in visual search on computerised tasks to real-world activities. Each task involved searching for a set of target objects among distracting objects on a table-top. Performance on the Table-top Visual Search Ability Test for Children (TVSAT-C) was measured as the time spent searching for targets divided by the number of targets found. 108 typically developing children (3-11 years old) and 8 children with vision impairment (7-12 years old) participated in the study. A significant correlation was found between log-transformed age and log-transformed performance (R2 = 0.65, p = 4 × 10−26) in our normative sample, indicating a monomial power law relationship between age and performance with an exponent of −1.67, 95% CI [−1.90, −1.43]. We calculated age-dependent percentiles and receiver operating characteristic curve analysis indicated the 3rd percentile as the optimal cut-off for detecting a visual search deficit, giving a specificity of 97.2%, 95% CI [92.2%, 99.1%] and sensitivity of 87.5%, 95% CI [52.9%, 97.8%] for the test. Further studies are required to calculate measures of reliability and external validity, to confirm sensitivity for visual search deficits, and to investigate the most appropriate response modes for participants with conditions that affect manual dexterity. Additionally, more work is needed to assess construct validity where semantic knowledge is required that younger children may not have experience with. We have made the protocol and age-dependent normative data available for those interested in using the test in research or practice, and to illustrate the smooth developmental trajectory of visual search ability during childhood.
Increasing vitrification temperature improves the cryo-electron microscopy reconstruction
Authors: Shi Huigang , Ling Wuchun , Zhu Dongjie , Zhang Xinzheng
Published: October 2019

At the initial stage of the cryo-electron microcopy (cryo-EM) samples irradiated by electrons, the cryo-EM samples suffer from a rapid “burst” phase (first 3~4 e−/Å2) of beam induced motion (BIM) which is too fast to be corrected by existing motion correction software, and lowers the quality of the initial frames. Therefore, these least radiation damaged, but ruined frames are commonly excluded or down-weighted during data processing, which reduces the undamaged signals in the reconstruction and decreases the reconstruction resolution by weakening the averaging power. Here, we show that increasing the freezing temperature of cryo-EM samples suppresses the BIM in this phase. The quality of initial frames is partially recovered after BIM correction and is better than that of subsequent frames in certain frames. Incorporating these initial frames into the reconstruction increases the resolution, at an equivalent of ~60% extra data. Moreover, these frames are least radiation damaged, thus preserves the high quality cryo-EM density of radiation sensitive residues. Such density is usually damaged or very weak in the canonical 3D reconstruction. In addition, we found that a different kind of radiation damage neglected previously occurs in the per-frame reconstruction after the exposure of 2.5 e−/Å2. Such radiation damage distorts the density of atoms. The deformation can be avoided by only including the frames from the first 2.5 e−/Å2into the reconstruction. Overall, the high temperature freezing not only provides extra undamaged signal to the reconstruction, but also increases the resolution of the reconstruction.
Chromatin structure changes inDaphniapopulations upon exposure to environmental cues – or – The discovery of Wolterecks “Matrix”
Authors: de Carvalho Augusto Ronaldo , Minoda Aki , Rey Oliver , Cosseau Céline , Chaparro Cristian , Vidal-Dupiol Jérémie , Allienne Jean-François , Duval David , Pinaud Silvain , Tönges Sina , Andriantsoa Ranja , Luquet Emilien , Aubret Fabien , Dia Sow Mamadou , David Patrice , Thomson Vicki , Federico Déborah , Joly Dominique , Lima Mariana Gomes , Danchin Etienne , Grunau Christoph
Published: October 2019

Phenotypic plasticity is an important feature of biological systems that is likely to play a major role in the future adaptation of organisms to the ongoing global changes. It may allow an organism to produce alternative phenotypes in responses to environmental cues. Modifications in the phenotype can be reversible but are sometimes enduring and can even span over generations. The notion of phenotypic plasticity was conceptualized in the early 20thcentury by Richard Woltereck. He introduced the idea that the combined relations of a phenotypic character and all environmental gradients that influence on it can be defined as “norm of reaction”. Norms of reaction are specific to species and to lineages within species, and they are heritable. He postulated that reaction norms can progressively be shifted over generations depending on the environmental conditions. One of his biological models was the water-fleedaphnia. Woltereck proposed that enduring phenotypic modifications and gene mutations could have similar adaptive effects, and he postulated that their molecular bases would be different. Mutations occurred in genes, while enduring modifications were based on something he called theMatrix. He suggested that this matrix (i) was associated with the chromosomes, (ii) that it was heritable, (iii) it changed during development of the organisms, and (iv) that changes of the matrix could be simple chemical substitutions of an unknown, but probably polymeric molecule. We reasoned that the chromatin has all postulated features of this matrix and revisited Woltereck’s classical experiments withdaphnia. We developed a robust and rapid ATAC-seq technique that allows for analyzing chromatin of individual daphnia and show here (i) that this technique can be used with minimal expertise in molecular biology, and (ii) we used it to identify open chromatin structure in daphnia exposed to different environmental cues. Our result indicates that chromatin structure changes consistently in daphnia upon this exposure confirming Woltereck’s classical postulate.
A rationally designed oral vaccine induces Immunoglobulin A in the murine gut that directs the evolution of attenuatedSalmonellavariants
Authors: Diard Médéric , Bakkeren Erik , Lentsch Verena , Rocker Andrea , Bekele Nahimi Amare , Hoces Daniel , Aslani Selma , Arnoldini Markus , Böhi Flurina , Schumann-Moor Kathrin , Adamcik Jozef , Piccoli Luca , Lanzavecchia Antonio , Stadtmueller Beth M. , Donohue Nicholas , van der Woude Marjan W. , Hockenberry Alyson , Viollier Patrick H. , Falquet Laurent , Wüthrich Daniel , Bonfiglio Ferdinando , Loverdo Claude , Egli Adrian , Zandomeneghi Giorgia , Mezzenga Raffaele , Holst Otto , Meier Beat H. , Hardt Wolf-Dietrich , Slack Emma
Published: October 2019

Introductory paragraph

The ability of gut bacterial pathogens to escape immunity by antigenic variation, particularly via changes to surface-exposed antigens, is a major barrier to immune clearance1. However, not all variants are equally fit in all environments2, 3. It should therefore be possible to exploit such immune escape mechanisms to direct an evolutionary trade-off. Here we demonstrated this phenomenon usingSalmonella entericasubspeciesentericaserovar Typhimurium (S.Tm). A dominant surface antigen ofS.Tm is its O-antigen: A long, repetitive glycan that can be rapidly varied by mutations in biosynthetic pathways or by phase-variation4, 5. We quantified the selective advantage of O-antigen variants in the presence and absence of O-antigen specific IgA and identified a set of evolutionary trajectories allowing immune escape without an associated fitness cost in naïve mice. Through the use of oral vaccines, we rationally induced IgA responses blocking all of these trajectories, which selected forSalmonellamutants carrying deletions of the O-antigen polymerasewzyB.Due to their short O-antigen, these evolved mutants were more susceptible to environmental stressors (detergents, complement), predation (bacteriophages), and were impaired in gut colonization and virulence in mice. Therefore, a rationally induced cocktail of intestinal antibodies can direct an evolutionary trade-off inS.Tm. This lays the foundations for the exploration of mucosal vaccines capable of setting evolutionary traps as a prophylactic strategy.
Shared neural representations of cognitive conflict and negative affect in the medial frontal cortex
Authors: Vermeylen Luc , Wisniewski David , González-García Carlos , Hoofs Vincent , Notebaert Wim , Braem Senne
Published: October 2019

Influential theories of medial frontal cortex (MFC) function suggest that the MFC registers cognitive conflict as an aversive signal, but no study directly tested this idea. Instead, recent studies suggested that non-overlapping regions in the MFC process conflict and affect. In this pre-registered human fMRI study, we used multivariate pattern analyses to identify which regions respond similarly to conflict and aversive signals. The results reveal that, of all conflict- and value-related regions, the ventral pre-supplementary motor area (or dorsal anterior cingulate cortex) showed a shared neural pattern response to different conflict and affect tasks. These findings challenge recent conclusions that conflict and affect are processed independently, and provide support for integrative views of MFC function.
Structure of the space of taboo-free sequences
Authors: Manuel Cassius , von Haeseler Arndt
Published: October 2019

Models of sequence evolution typically assume that all sequences are possible. However, restriction enzymes that cut DNA at specific recognition sites provide an example where carrying a recognition sequence can be lethal. Motivated by this observation, we studied the set of strings over a finite alphabet withtaboos, that is, with prohibited substrings. The taboo-set is referred to asand any allowed string as a taboo-free string. We consider the graphwhose vertices are taboo-free strings of lengthnand whose edges connect two taboo-free strings if their Hamming distance equals 1. Any (random) walk on this graph describes the evolution of a DNA sequence that avoids deleterious taboos. We describe the construction of the vertex set of. Then we state conditions under whichand its suffix subgraphs are connected. Moreover, we provide a simple algorithm that can determine, for an arbitrary, if all these graphs are connected. We concluded that bacterial taboo-free Hamming graphs are nearly always connected, although 4 properly chosen taboos are enough to disconnect one of its suffix subgraphs.
SLAMF6 deficiency augments tumor killing and skews towards an effector phenotype revealing it as a novel T cell checkpoint
Authors: Hajaj Emma , Eisenberg Galit , Klein Shiri , Frankenburg Shoshana , Merims Sharon , Ben-David Inna , Eisenhaure Thomas , Henrickson Sarah E. , Villani Alexandra-Chloé , Hacohen Nir , Abudi Nathalie , Abramovich Rinat , Cohen Jonathan , Peretz Tamar , Veillette André , Lotem Michal
Published: October 2019

SLAMF6 is a homotypic receptor of the Ig-superfamily whose exact role in immune modulation has remained elusive. Its constitutive expression on resting and activated T cells precludes it from being abona fideexhaustion marker. By breeding Pmel-1 mice with SLAMF6 KO mice, we generated donors for T cells lacking SLAMF6 and expressing a transgenic TCR for gp100-melanoma antigen. Activated Pmel-1xSLAMF6 KO CD8 T cells displayed improved polyfunctionality and strong tumor cytolysis. T-bet was the dominant transcription factor in Pmel-1xSLAMF6 KO cells, and upon activation, they acquired an effector-memory phenotype. Blocking LAG-3 improved the function of SLAMF6 deficient T cells even further. Finally, adoptive transfer of Pmel-1xSLAMF6 KO T cells into melanoma-bearing mice resulted in lasting tumor regression in contrast to temporary responses achieved with Pmel-1 T cells. These results support the notion that SLAMF6 is an inhibitory immune receptor whose absence enables powerful CD8 T cells to eradicate tumors.
Metagenomic analysis of a blood stain from the French revolutionary Jean-Paul Marat (1743-1793)
Authors: de-Dios Toni , van Dorp Lucy , Charlier Philippe , Morfopoulou Sofia , Lizano Esther , Bon Celine , Le Bitouzé Corinne , Alvarez-Estape Marina , Marquès-Bonet Tomas , Balloux François , Lalueza-Fox Carles
Published: October 2019

The French revolutionary Jean-Paul Marat (1743-1793) was assassinated in 1793 in his bathtub, where he was trying to find relief from the debilitating skin disease he was suffering from. At the time of his death, Marat was annotating newspapers, which got stained with his blood and were subsequently preserved by his sister. We extracted and sequenced DNA from the blood stain and also from another section of the newspaper, which we used for comparison. Results from the human DNA sequence analyses were compatible with a heterogeneous ancestry of Marat, with his mother being of French origin and his father born in Sardinia. Metagenomic analyses of the non-human reads uncovered the presence of fungal, bacterial and low levels of viral DNA. Relying on the presence/absence of microbial species in the samples, we could cast doubt on several putative infectious agents that have been previously hypothesised as the cause of his condition but for which we detect not a single sequencing read. Conversely, some of the species we detect are uncommon as environmental contaminants and may represent plausible infective agents. Based on all the available evidence, we hypothesize that Marat may have suffered from a fungal infection (seborrheic dermatitis), possibly superinfected with bacterial opportunistic pathogens.
Hippocampal-like network dynamics underlie avian sharp wave-ripples
Authors: Yeganegi Hamed , Luksch Harald , Ondracek Janie M.
Published: October 2019

Sharp wave ripples (SWR) represent one of the most synchronous population patterns in the mammalian brain. Although SWRs are highly conserved throughout mammalian evolution, the existence of SWRs in non-mammalian species remains controversial. We reexamined the existence of avian SWRs by recording the brain activity during sleep and under anesthesia in two species of birds, the zebra finch and the chicken. Electrophysiological recordings using silicon probes implanted in the avian telencephalon revealed highly dynamic switching between high and low delta phases during sleep. High delta phases were composed of large-amplitude, negative deflections (sharp waves) that coincided with a high frequency oscillation (ripple). Correlation analysis revealed that these events were highly synchronous and spanned a large anatomical range of the avian telencephalon. Finally, detailed spike analysis revealed that an increase in the population spiking activity coincided with the occurrence of SWRs, that this spiking activity occurred in specific sequences of spike patterns locked to the SWRs, and that the mean population spiking activity peaked prior to the trough of the negative deflection. These results provide the first evidence of avian SWRs during natural sleep and under anesthesia, and suggest that the evolutionary origin of SWR activity may precede the mammalian-sauropsid bifurcation.
Accumulation of storage proteins in plant seeds is mediated by amyloid formation
Authors: Antonets Kirill S. , Belousov Mikhail V. , Sulatskaya Anna I. , Belousova Maria E. , Kosolapova Anastasiia O. , Sulatsky Maksim I. , Andreeva Elena A. , Zykin Pavel A. , Malovichko Yury V. , Shtark Oksana Y. , Lykholay Anna N. , Volkov Kirill V. , Kuznetsova Irina M. , Turoverov Konstantin K. , Kochetkova Elena Y. , Demidov Oleg. N. , Tikhonovich Igor A. , Nizhnikov Anton A.
Published: October 2019

Amyloids are protein aggregates with a highly ordered spatial structure giving them unique physicochemical properties. Different amyloids not only participate in the development of numerous incurable diseases but control vital functions in Archaea, Bacteria and Eukarya. Plants are a poorly studied systematic group in the field of amyloid biology. Amyloid properties have not yet been demonstrated for plant proteins under native conditionsin vivo.Here we show that seeds of garden peaPisum sativumL. contain amyloid-like aggregates of storage proteins, the most abundant one, 7S globulin Vicilin, formsbona fideamyloidsin vivoandin vitro. The Vicilin amyloid accumulation increases during seed maturation and wanes at germination. Amyloids of Vicilin resist digestion by gastrointestinal enzymes, persist in canned peas and exhibit toxicity for yeast and mammalian cells. Our finding for the first time reveals involvement of amyloid formation in the accumulation of storage proteins in plant seeds.
The short-term high fat diet-induced increase in %5-methylcytosine expression in peripheral blood T lymphocytes, is attenuated by low-dose aspirin
Authors: Mutize Tinashe , Dludla Phiwayinkosi V. , Mkandla Zibusiso , Nkambule Bongani B.
Published: October 2019

Objective

To assess peripheral lymphocyte DNA methylation profiles in prediabetes using a high fat-diet-fed C57BL/6 animal model. We further evaluated whether low dose-aspirin, or low-dose aspirin in combination with metformin, could modulate global DNA methylation levels in peripheral blood lymphocytes.

Methods

Twenty-eight (28) male C57BL/6 mice were used in two experimental phases. The first experiment involved animals (n=16) which were randomised to receive a low-fat diet (LFD) or high-fat diet (HFD) (n = 8/group) for 10 weeks. Whereas in the second experiment, HFD-fed mice (n=15) were randomised into 3 treatment groups, a low-dose aspirin (LDA), LDA and metformin group, and a clopidogrel group. DNA methylation profiles of were determined using flow cytometry.

Results

The HFD group showed moderate weight gain and elevated postprandial blood glucose levels when compared to the LFD group after 2 weeks of HFD-feeding (p < 0.05). Interestingly, the HFD group had elevated levels of T cells expressing high levels %5-methylcytosine (p<0, 05). Notably, these elevated levels were lowered by short-term low-dose aspirin treatment.

Discussion

T cells are involved in the propagation of the inflammatory response. Persistent T cell activation promotes chronic inflammation and insulin resistance. Low-dose aspirin may be effective in modulating T cell-specific global methylation.
CRISPR/Cas9 mediated intersectional knockout of GSK3β in D2 receptor expressing mPFC neurons reveals contributions to emotional regulation
Authors: Khlghatyan Jivan , Beaulieu Jean-Martin
Published: October 2019

Background

Glycogen synthase kinase 3β (GSK3β) regulates neurodevelopment, synaptic plasticity as well as mood, cognition, social interaction, and depressive-like behaviors. Inhibition of GSK3β is a shared consequence of treatment by lithium, SSRIs, ketamine and antipsychotics. GSK3β activity is regulated by dopamine D2 receptor signaling and can be inhibited by psychoactive drugs in a D2 receptor dependent manner. Functions of GSK3β in striatal D2 neurons has been studied extensively. However, GSK3β is ubiquitously expressed in the brain and D2 receptor expressing cells are distributed as a mosaic in multiple cortical regions. This complicates the interrogation of GSK3β functions in cortical D2 cells in a circuit defined manner using conventional animal models.

Methods

We have used a CRISPR/Cas9 mediated intersectional approach to achieve targeted deletion of GSK3β in D2 expressing neurons of the adult medial prefrontal cortex (mPFC).

Results

Isolation and analysis of ribosome associated RNA specifically from mPFC D2 neurons lacking GSK3β demonstrated large scale translatome alterations. Deletion of GSK3β in mPFC D2 neurons revealed its contribution to anxiety-related, cognitive, and social behaviors.

Conclusions

Our results underscore the viability of intersectional knockout approach to study functions of a ubiquitous gene in a network defined fashion while uncovering a contribution of GSK3β expressed in mPFC D2 neurons in the regulation of behavioral dimensions related to mood and emotions. This advances our understanding of GSK3β action at a brain circuit level and can potentially lead to the development of circuit selective therapeutics.
Ubiquitin and SUMO conjugation as biomarkers of Acute Myeloid Leukemias response to chemotherapies
Authors: Gâtel Pierre , Brockly Frédérique , Reynes Christelle , Pastore Manuela , Hicheri Yosr , Cartron Guillaume , Piechaczyk Marc , Bossis Guillaume
Published: October 2019

Ubiquitin and the ubiquitin-like SUMO are covalently conjugated to thousands of proteins to modulate their function and fate. Many of the enzymes involved in their conjugation are dysregulated in cancers and involved in cancer cells response to therapies. We describe here the identification of biomarkers of the activity of these enzymes and their use to predict Acute Myeloid Leukemias (AML) response to standard chemotherapy (daunorubicine-DNR and cytarabine-Ara-C). We compared the ability of extracts from chemosensitive and chemoresistant AML cells to conjugate ubiquitin or SUMO-1 on 9000 proteins spotted on protein-arrays. We identified 122 proteins whose conjugation by these post-translational modifiers marks AML resistance to DNR and/or Ara-C. Based on this modifomic signature, we defined a statistical score able to predict AML patient response to standard chemotherapy. We finally developed a miniaturized assay to easily assess the modification level of the selected biomarkers and validated it in patient cell extracts. Thus, our work identifies a new type of ubiquitin-based biomarkers that could be used to predict cancer patients response to treatments.

Summary blurb

This study describes the identification of a new class of biomarkers of cancer response to therapies based on protein modification by Ubiquitin and SUMO and provides the tools to analyze them in Acute Myeloid Leukemia patient samples.
Short-wavelength violet light (420nm) stimulates melanopsin-dependent acute alertness responses in zebrafish
Authors: Contreras Jorge E. , Lisse Thomas S. , Bouzidi Chifaa , Cavanaugh Ann M. , Matynia Anna , Rieger Sandra
Published: October 2019

Sunlight throughout the day and seasons strongly influences our biological rhythms and activity. In recent years, it has become evident that night-time overexposure to bright light in urban environments can profoundly affect physiology and behaviour in humans and animals. In particular, the artificial emission of short-wavelength light has been shown to stimulate alertness in humans, but the mechanisms remain largely unknown. Utilising a diurnal larval zebrafish model, we identified instant, non-image-forming (NIF) responses to short-wavelength violet light (~420nm), which are activated only during light exposure, and are reminiscent of alertness, including increased heart rate, enhanced locomotor activity, and pectoral fin beating (for increased oxygen supply). We further determined that these responses are driven by sympathetic neuronal circuits and depend on the zebrafish melanopsin homologue Opn4a. We also found that these responses can be modulated by the sleep-regulatory hormone melatonin, but that melatonin is not essential. Our findings reveal a previously unknown mechanism for violet light-dependent acute alertness.
Cockroaches show individuality in learning and memory during classical and operant conditioning
Authors: Arican Cansu , Bulk Janice , Deisig Nina , Nawrot Martin Paul
Published: October 2019

Animal personality and individuality are intensively researched in vertebrates and both concepts are increasingly applied to behavioral science in insects. However, only few studies have looked into individuality with respect to performance in learning and memory tasks. In vertebrates individual learning capabilities vary considerably with respect to learning speed and learning rate. Likewise, honeybees express individual learning abilities in a wide range of classical conditioning protocols. Here, we study individuality in the learning and memory performance of cockroaches, both in classical and operant conditioning tasks. We implemented a novel classical (olfactory) conditioning paradigm where the conditioned response is established in the maxilla-labia response (MLR). Operant spatial learning was investigated in a forced two-choice task using a T-maze. Our results confirm individual learning abilities in classical conditioning of cockroaches that was reported for honeybees and vertebrates but contrast long-standing reports on stochastic learning behavior in fruit flies. In our experiments, most learners expressed a correct behavior after only a single learning trial showing a consistent high performance during training and test. We can further show that individual learning differences in insects are not limited to classical conditioning but equally appear in operant conditioning of the cockroach.
RNA Pol II Length and Disorder Enable Cooperative Scaling of Transcriptional Bursting
Authors: Quintero-Cadena Porfirio , Lenstra Tineke L. , Sternberg Paul W.
Published: October 2019

RNA Polymerase II contains a disordered C-terminal domain (CTD) whose length enigmatically correlates with genome size. The CTD is crucial to eukaryotic transcription, yet the functional and evolutionary relevance of this variation remains unclear. Here, we use smFISH, live imaging, and RNA-seq to investigate how CTD length and disorder influence transcription. We find that length modulates the size and frequency of transcriptional bursting. Disorder is highly conserved and mediates CTD-CTD interactions, an ability we show is separable from protein sequence and necessary for efficient transcription. We build a data-driven quantitative model, simulations of which recapitulate experiments and support CTD length promotes initial polymerase recruitment to the promoter but slows down its release from it, and that CTD-CTD interactions enable promoter recruitment of multiple polymerases. Our results reveal how these tunable parameters provide access to a range of transcriptional activity, offering a new perspective for the mechanistic significance of CTD length and disorder in transcription across eukaryotes.