bluuebunny/crossref_metadata_2025 huggingface dataset:
Biological Reinforcement Learning via Predictive Spacetime Encoding
Authors: Yang Minsu Abel , Lee Jee Hang , Lee Sang Wan
Published: August 2020

Recent advances in reinforcement learning (RL) have successfully addressed several challenges, such as performance, scalability, or sample efficiency associated with the use of this technology. Although RL algorithms bear relevance to psychology and neuroscience in a broader context, they lack biological plausibility. Motivated by recent neural findings demonstrating the capacity of the hippocampus and prefrontal cortex to gather space and time information from the environment, this study presents a novel RL model, called spacetime Q-Network (STQN), that exploits predictive spatiotemporal encoding to reliably learn highly uncertain environment. The proposed method consists of two primary components. The first component is the successor representation with theta phase precession implements hippocampal spacetime encoding, acting as a rollout prediction. The second component, called Q switch ensemble, implements prefrontal population coding for reliable reward prediction. We also implement a single learning rule to accommodate both hippocampal-prefrontal replay and synaptic homeostasis, which subserves confidence-based metacognitive learning. To demonstrate the capacity of our model, we design a task array simulating various levels of environmental uncertainty and complexity. Results show that our model significantly outperforms a few state-of-the-art RL models. In the subsequent ablation study, we showed unique contributions of each component to resolving task uncertainty and complexity. Our study has two important implications. First, it provides the theoretical groundwork for closely linking unique characteristics of the distinct brain regions in the context of RL. Second, our implementation is performed in a simple matrix form that accommodates expansion into biologically-plausible, highly-scalable, and generalizable neural architectures.
ENERGY OPTIMIZATION DURING WALKING CAN BE A PRIMARILY IMPLICIT PROCESS
Authors: McAllister Megan J. , Blair Rachel L. , Donelan J. Maxwell , Selinger Jessica C.
Published: August 2020

Gait adaptations, in response to novel environments, devices or changes to the body, can be driven by the continuous optimization of energy expenditure. However, whether energy optimization is primarily an implicit process—occurring automatically and with minimal cognitive attention—or an explicit process—occurring as a result of a conscious, attention-demanding, strategy—remains unclear. Here, we use a dual-task paradigm to test whether energy optimization during walking is primarily an implicit or explicit process. To create our primary energy optimization task, we used lower-limb exoskeletons to shift people’s energetically optimal step frequency to frequencies lower than normally preferred. Our secondary task, designed to draw explicit attention from the optimization task, was an auditory tone discrimination task. We found that adding this secondary task did not disrupt energy optimization during walking; participants in our dual-task experiment adapted their step frequency toward the optima by an amount similar to participants in our previous single-task experiment. We also found that performance on the tone discrimination task did not worsen when participants were optimizing for energetic cost; accuracy scores and reaction times remained unchanged when the exoskeleton altered the energy optimal gaits. Survey responses suggest that dual-task participants were largely unaware of the changes they made to their gait to optimize energy, whereas single-task participants were more aware of their gait changes yet did not leverage this explicit awareness to improve gait optimization. Collectively, our results suggest that energy optimization is primarily an implicit process, allowing attentional resources to be directed toward other cognitive and motor objectives during walking.

Summary statement

People can adapt to energy optimal walking patterns without being consciously aware they are doing so. This allows people to discover energetically efficient gaits while preserving attentional resources for other tasks.
Meta-analysis reveals that sexual signalling in animals is honest and resource-based
Authors: Dougherty Liam R.
Published: August 2020

Animals often need to signal to attract mates, and sexual signalling may impose significant energetic and fitness costs to signallers. Consequently, individuals should strategically adjust signalling effort in order to maximise the fitness payoffs of signalling. An important determinant of these payoffs is individual state, which can influence the resources available to signallers, the likelihood of mating, and the motivation to mate. However, empirical studies often find contradictory patterns of state-based signalling. For example, some studies find that individuals in poor condition signal less, in order to conserve resources (ability-based signalling). In other cases, individuals in poor condition signal more, in order to maximise short-term reproductive success (needs-based signalling). I used meta-analysis to examine animal sexual signalling behaviour in relation to six aspects of individual state: age, mated status, attractiveness, body size, condition, and parasite load. Across 228 studies and 147 species, individuals (who were overwhelmingly male) signalled significantly more when in good condition, and there was a strong positive trend for increased signalling for large, attractive individuals with a low parasite load. Overall, this suggests that animal sexual signalling behaviour is generally honest and ability-based. However, needs-based signalling (terminal investment) was found when considering age, with old virgins signalling more than young virgins. Sexual signalling was not significantly influenced by mated status. There was a large amount of heterogeneity across studies that remained unexplained, and therefore more work is needed to determine the ecological factors influencing the magnitude and direction of state-dependent sexual signalling.
Load-Dependent Relationships between Frontal fNIRS Activity and Performance: A Data-Driven PLS Approach
Authors: Meidenbauer Kimberly L. , Choe Kyoung Whan , Cardenas-Iniguez Carlos , Huppert Theodore J. , Berman Marc G.
Published: August 2020

Neuroimaging research frequently demonstrates load-dependent activation in the prefrontal cortex during working memory tasks such as the N-back. Most of this work has been conducted in fMRI, but functional near-infrared spectroscopy (fNIRS) is gaining traction as a less invasive and more flexible alternative to measuring cortical hemodynamics. Few fNIRS studies, however, have examined how working memory load-dependent changes in brain hemodynamics relate to performance. The current study employs a newly developed and robust statistical analysis of task-based fNIRS data in a large sample, and demonstrates the utility of data-driven, multivariate analyses to link brain activation and behavior in this modality. Seventy participants completed a standard N-back task with three N-back levels (N = 1, 2, 3) while fNIRS data were collected from frontal and parietal cortex. Overall, participants showed reliably greater fronto-parietal activation for the 2-back versus the 1-back task, suggesting fronto-parietal fNIRS measurements are sensitive to differences in cognitive load. The results for 3-back were much less consistent, potentially due to poor behavioral performance in the 3-back task. To address this, a multivariate analysis (behavioral partial least squares, PLS) was conducted to examine the interaction between fNIRS activation and performance at each N-back level. Results of the PLS analysis demonstrated differences in the relationship between accuracy and change in the deoxyhemoglobin fNIRS signal as a function of N-back level in four mid-frontal channels. Specifically, greater reductions in deoxyhemoglobin (i.e., more activation) were positively related to performance on the 3-back task, unrelated to accuracy in the 2-back task, and negatively associated with accuracy in the 1-back task. This pattern of results suggests that the metabolic demands correlated with neural activity required for high levels of accuracy vary as a consequence of task difficulty/cognitive load, whereby more automaticity during the 1-back task (less mid-frontal activity) predicted superior performance on this relatively easy task, and successful engagement of this mid-frontal region was required for high accuracy on a more difficult and cognitively demanding 3-back task. In summary, we show that fNIRS activity can track working memory load and can uncover significant associations between brain activity and performance, thus opening the door for this modality to be used in more wide-spread applications.
A closed-loop optogenetic screen for neurons controlling feeding inDrosophila
Authors: Lau Celia KS , Gordon Michael D
Published: August 2020

Feeding is an essential part of animal life that is impacted greatly by the sense of taste. Although the characterization of taste-detection at the periphery is extensive, higher-order taste and feeding circuits are still being elucidated. Here, we use an automated closed-loop optogenetic activation screen for novel taste and feeding neurons inDrosophila melanogaster. Out of 122 Janelia FlyLight Project GAL4 lines preselected based on expression pattern, we identify six lines that acutely promote feeding and 35 lines that inhibit it. As proof of principle, we follow up on theR70C07-GAL4neuron population, which strongly inhibits feeding. Using split-GAL4 lines to isolate subsets of theR70C07-GAL4population, we find both appetitive and aversive neurons. We also show thatR70C07-GAL4labels a population of putative second-order taste interneurons that contact both sweet and bitter sensory neurons. These results serve as a resource for further functional dissection of fly feeding circuits.
Predicting gene regulatory networks from cell atlases
Authors: Møller Andreas Fønss , Natarajan Kedar Nath
Published: August 2020

Recent single-cell RNA-sequencing atlases have surveyed and identified major cell-types across different mouse tissues. Here, we computationally reconstruct gene regulatory networks from 3 major mouse cell atlases to capture functional regulators critical for cell identity, while accounting for a variety of technical differences including sampled tissues, sequencing depth and author assigned cell-type labels. Extracting the regulatory crosstalk from mouse atlases, we identify and distinguish global regulons active in multiple cell-types from specialised cell-type specific regulons. We demonstrate that regulon activities accurately distinguish individual cell types, despite differences between individual atlases. We generate an integrated network that further uncovers regulon modules with coordinated activities critical for cell-types, and validate modules using available experimental data. Inferring regulatory networks during myeloid differentiation from wildtype and Irf8 KO cells, we uncover functional contribution of Irf8 regulon activity and composition towards monocyte lineage. Our analysis provides an avenue to further extract and integrate the regulatory crosstalk from single-cell expression data.

Integrated single-cell gene regulatory network from three mouse cell atlases captures global and cell-type specific regulatory modules and crosstalk, important for cellular identity.
Generation of thymidine auxotrophicAgrobacterium tumefaciensstrains for plant transformation
Authors: Aliu Ephraim , Azanu Mercy K. , Wang Kan , Lee Keunsub
Published: August 2020

Agrobacterium-mediated transformation is a widely used gene delivery method for fundamental researches and crop trait improvement projects. AuxotrophicAgrobacterium tumefaciensstrains are highly desirable for plant transformation because they can be easily removed from the explants after co-cultivation due to their dependence on essential nutrient supplementation. The thymidine auxotrophicA. tumefaciensstrain LBA4404Thy- has been successfully used for plant transformation, however, auxotrophic version of other commonly used strains are not available yet to public laboratories. Here we report the generation of EHA101, EHA105 and EHA105D thymidine auxotrophic strains. These strains exhibited thymidine-dependent growth in the bacterial medium, and the transient GUS expression assay using Arabidopsis seedling showed that they retain the equivalent T-DNA transfer capability as the original strains thus are suitable for plant transformation.
Differential effects of redox conditions on the decomposition of litter and soil organic matter
Authors: Lin Yang , Campbell Ashley N. , Bhattacharyya Amrita , DiDonato Nicole , Thompson Allison M. , Tfaily Malak M. , Nico Peter S. , Silver Whendee L. , Pett-Ridge Jennifer
Published: August 2020

Soil redox conditions exert substantial influence on biogeochemical processes in terrestrial ecosystems. Humid tropical forest soils are often characterized by fluctuating redox dynamics, yet how these dynamics affect patterns in soil versus litter decomposition and associated CO2fluxes is not well understood. We used a13C-labeled litter addition to explicitly follow the decomposition of litter-derived vs. native soil-derived organic matter in response to four different soil redox regimes—static oxic or anoxic, and two oscillating treatments—in soil from the Luquillo Experimental Forest, Puerto Rico. We coupled this incubation experiment with high-resolution mass spectrometry to characterize the preferential decomposition of specific classes of organic molecules. CO2production from litter and soil organic matter (SOM) showed distinctly different responses to redox manipulation. The cumulative production of SOM-derived CO2was positively correlated with the length of soil exposure to an oxic headspace (r= 0.89,n= 20), whereas cumulative13C-litter-derived CO2production was not linked to oxygen availability. The CO2production rate from litter was highest under static anoxic conditions in the first half of the incubation period, and later dropped to the lowest among all redox treatments. In the consistently anoxic soils, we observed the depletion of more oxidized water-extractable organic matter (especially amino sugars, carbohydrates, and proteins) over time, suggesting that under anaerobic conditions, microbes preferentially used more oxidized litter-derived compounds during the early stages of decomposition. Results from kinetic modeling showed that more frequent anoxic exposure limited the decomposition of a slow-cycling C pool, but not a fast-cycling pool. Overall, our results demonstrate that substrate source—freshly added litter vs. native organic matter—plays an important role in the redox sensitivity of organic matter decomposition. In soil environments that regularly experience redox fluctuations, anaerobic heterotrophs can be surprisingly effective in degrading fresh plant litter.
Evaluation of SARS-CoV-2 neutralizing antibodies using a vesicular stomatitis virus possessing SARS-CoV-2 spike protein
Authors: Tani Hideki , Tan Long , Kimura Miyuki , Yoshida Yoshihiro , Yamada Hiroshi , Fukushi Shuetsu , Saijo Masayuki , Kawasuji Hitoshi , Ueno Akitoshi , Miyajima Yuki , Fukui Yasutaka , Sakamaki Ippei , Yamamoto Yoshihiro , Morinaga Yoshitomo
Published: August 2020

SARS-CoV-2 is a novel coronavirus that emerged in 2019 and is now classified in the genus Coronavirus with closely related SARS-CoV. SARS-CoV-2 is highly pathogenic in humans and is classified as a biosafety level (BSL)-3 pathogen, which makes manipulating it relatively difficult due to its infectious nature. To circumvent the need for BSL-3 laboratories, an alternative assay was developed that avoids live virus and instead uses a recombinant VSV expressing luciferase and possesses the full length or truncated spike proteins of SARS-CoV-2. Furthermore, to measure SARS-CoV-2 neutralizing antibodies under BSL2 conditions, a chemiluminescence reduction neutralization test (CRNT) for SARS-CoV-2 was developed. The neutralization values of the serum samples collected from hospitalized patients with COVID-19 or SARS-CoV-2 PCR-negative donors against the pseudotyped virus infection evaluated by the CRNT were compared with antibody titers determined from an immunofluorescence assay (IFA). The CRNT, which used whole blood collected from hospitalized patients with COVID-19, was also examined. As a result, the inhibition of pseudotyped virus infection was specifically observed in both serum and whole blood and was also correlated with the results of the IFA. In conclusion, the CRNT for COVID-19 is a convenient assay system that can be performed in a BSL-2 laboratory with high specificity and sensitivity for evaluating the occurrence of neutralizing antibodies against SARS-CoV-2.
DNA extraction and host depletion methods significantly impact and potentially bias bacterial detection in a biological fluid
Authors: Ganda Erika , Beck Kristen L. , Haiminen Niina , Silverman Justin D. , Kawas Ban , Cronk Brittany , Anderson Renee R. , Goodman Laura B. , Wiedmann Martin
Published: August 2020

Untargeted sequencing of nucleic acids present in food can inform the detection of food safety and origin, as well as product tampering and mislabeling issues. The application of such technologies to food analysis could reveal valuable insights that are simply unobtainable by targeted testing, leading to the efforts of applying such technologies in the food industry. However, before these approaches can be applied, it is imperative to verify that the most appropriate methods are used at every step of the process: gathering primary material, laboratory methods, data analysis, and interpretation.

The focus of this study is in gathering the primary material, in this case, DNA. We used bovine milk as a model to 1) evaluate commercially available kits for their ability to extract nucleic acids from inoculated bovine milk; 2) evaluate host DNA depletion methods for use with milk, and 3) develop and evaluate a selective lysis-PMA based protocol for host DNA depletion in milk.

Our results suggest that magnetic-based nucleic acid extraction methods are best for nucleic acid isolation of bovine milk. Removal of host DNA remains a challenge for untargeted sequencing of milk, highlighting that the individual matrix characteristics should always be considered in food testing. Some reported methods introduce bias against specific types of microbes, which may be particularly problematic in food safety where the detection of Gram-negative pathogens and indicators is essential. Continuous efforts are needed to develop and validate new approaches for untargeted metagenomics in samples with large amounts of DNA from a single host.

Importance

Tracking the bacterial communities present in our food has the potential to inform food safety and product origin. To do so, the entire genetic material present in a sample is extracted using chemical methods or commercially available kits and sequenced using next-generation platforms to provide a snapshot of what the relative composition looks like. Because the genetic material of higher organisms present in food (e.g., cow in milk or beef, wheat in flour) is around one thousand times larger than the bacterial content, challenges exist in gathering the information of interest. Additionally, specific bacterial characteristics can make them easier or harder to detect, adding another layer of complexity to this issue. In this study, we demonstrate the impact of using different methods in the ability of detecting specific bacteria and highlight the need to ensure that the most appropriate methods are being used for each particular sample.
Control Strategies against COVID-19 in China: Significance of Effective Testing in the Long Run
Authors: Lin Yatang , Peng Fangyuan
Published: August 2020

The coronavirus disease 2019 (COVID-19) outbreak is reasonably contained in China. In this paper, we evaluated the effectiveness of different containment strategies in halting the pandemic spread in both short- and long-term. We combined a networked metapopulation SEIR model featuring undocumented infections, actual mobility data and Bayesian inference to simulate the counterfactual outbreak scenarios removing each one or a combination of the following three policies in place: i) city lockdowns, ii) intercity travel bans, and iii) testing, detection, and quarantine. Our estimates revealed that 11.4% [95% credible interval (CI): 9.7–13.0%] of the infected cases were unidentified before January 23, 2020. The rate grew to 92.5% [95% credible interval (CI): 85.9–94.5%] in early March, thanks to the boost in coronavirus testing capacity. We show that increasing the detection rate of infections from 11.4% to 92.5% alone would explain 75% of the reduction in infections from a no-policy baseline by March 15, 2020.

The most pronounced policy implication is that city lockdowns appeared to be the more effective intervention in the short-run but effective testing is essential in containing the COVID-19 spread in the long run. By March 15, restoring within-city personal contact to its 2019 level would lead to a 678% growth in infections with all the other interventions remaining unaffected. Removing intercity travel restrictions and effective detection measures would lead to 3% and 477% growth, respectively. Extending the time horizon to July 15, the counterfactual increase in infections would become 581%, 3% and 3.0 ∗ 105% had the three classes of interventions been lifted individually.

Significance

The COVID-19 pandemic has become a long-term crisis that calls for long-term solutions. We combined an augmented SEIR simulation model with real-time human mobility data to decompose the effects of lockdown, travel bans and effective testing measures in the curtailment of COVID-19 spread in China over different time horizons. Our analysis reveals that the significant growth in the detection rate of infectious cases, thanks to the expansion in testing effi-ciency, were as effective as city lockdowns in explaining the reduction in new infections up to mid-March. However, as we extended the analysis to July, increasing the detection rate to at least 50% is the only reliable way to bring the spread under control.
Zoonotic viruses in three species of voles (Microtusspp.) from Poland
Authors: Grzybek Maciej , Tołkacz Katarzyna , Sironen Tarja , Mäki Sanna , Alsarraf Mohammed , Behnke-Borowczyk Jolanta , Biernat Beata , Nowicka Joanna , Vaheri Antti , Henttonen Heikki , Behnke Jerzy M. , Bajer Anna
Published: August 2020

Rodents are known to be reservoir hosts for a plethora of zoonotic viruses and therefore play a significant role in the dissemination of these pathogens. We trapped three vole species (Microtus arvalis, M. oeconomusandM. agrestis) in N.E. Poland, all of which are widely distributed species in Europe, and, using immunofluorescence assays, we assessed serum samples for the presence of antibodies to hantaviruses, arenaviruses and cowpox viruses (CPXV). We detected antibodies against CPXV and Puumala virus (PUUV), overall seroprevalence of combined viral infections of 18.2% [10.5-29.3] and mostly attributed to CPXV. Antibodies to Tula hantavirus, typical forMicrotusvoles, are known to cross-react strongly with the PUUV antigen used in PUUV screening, but we detected only one PUUV/TULV cross-reaction inMicrotus arvalis(1.3% [0.1-7.9]). We found antibodies against CPXV in all threeMicrotusspp. Seroprevalence was similar in all vole species. There were no significant differences in seroprevalence between the sexes and among host age categories. Our results contribute to the increasing understanding of CPXV abundance in voles in Europe, and confirm that CPXV circulates also inMicrotusspp. voles in NE Poland.
Lipid droplets fuel SARS-CoV-2 replication and production of inflammatory mediators
Authors: da Silva Gomes Dias Suelen , Soares Vinicius Cardoso , Ferreira André C. , Sacramento Carolina Q. , Fintelman-Rodrigues Natalia , Temerozo Jairo R. , Teixeira Lívia , Barreto Ester , Mattos Mayara , de Freitas Caroline S. , Azevedo-Quintanilha Isaclaudia G. , Manso Pedro Paulo A. , Hottz Eugenio D. , Pão Camila R. R. , Bou-Habib Dumith C. , Bozza Fernando A. , Souza Thiago M. L. , Bozza Patrícia T.
Published: August 2020

Viruses are obligate intracellular parasites that make use of the host metabolic machineries to meet their biosynthetic needs, identifying the host pathways essential for the virus replication may lead to potential targets for therapeutic intervention. The mechanisms and pathways explored by SARS-CoV-2 to support its replication within host cells are not fully known. Lipid droplets (LD) are organelles with major functions in lipid metabolism and energy homeostasis, and have multiple roles in infections and inflammation. Here we described that monocytes from COVID-19 patients have an increased LD accumulation compared to SARS-CoV-2 negative donors.In vitro, SARS-CoV-2 infection modulates pathways of lipid synthesis and uptake, including CD36, SREBP-1, PPARγ and DGAT-1 in monocytes and triggered LD formation in different human cells. LDs were found in close apposition with SARS-CoV-2 proteins and double-stranded (ds)-RNA in infected cells. Pharmacological modulation of LD formation by inhibition of DGAT-1 with A922500 significantly inhibited SARS-CoV-2 replication as well as reduced production of pro-inflammatory mediators. Taken together, we demonstrate the essential role of lipid metabolic reprograming and LD formation in SARS-CoV-2 replication and pathogenesis, opening new opportunities for therapeutic strategies to COVID-19.
Phenotypic plasticity and evolution of thermal tolerance in two lineages of bacteria from temperate and hot environments
Authors: Hurtado-Bautista Enrique , Pérez-Sánchez Laura F. , Islas-Robles África , Santoyo Gustavo , Olmedo-Álvarez Gabriela
Published: August 2020

Despite the crucial role of microorganisms to sustain life on Earth, there is little research on the evolution of thermal tolerance of bacteria in the face of the challenge that global warming poses. Phenotypic adaptation to a new environment requires plasticity to allow individuals to respond to selective forces, followed by adaptive evolution. We do not know to what extent phenotypic plasticity allows thermal tolerance evolution in bacteria at the border of their physiological limits. We analyzed growth and thermal reaction norms to temperature of strains of two bacterial lineages,Bacillus cereus sensu latoandBacillus subtilis sensu lato, that evolved in two contrasting environments, a temperate lagoon (T) and a hot spring (H). Our results showed that despite co-occurrence of members of both lineages in the two contrasting environments, norms of reactions to temperature exhibited a similar pattern only within the lineages, suggesting fixed phenotypic plasticity. Additionally, within theB. cereuslineage, strains from the H environment showed only two to three °C more heat tolerance than strains from the T environment. The limited evolutionary changes towards an increase in heat tolerance in bacteria should alert us of the negative impact that climate change can have on all biological cycles in the planet.
EmpiReS: Differential Analysis of Gene Expression and Alternative Splicing
Authors: Csaba Gergely , Berchtold Evi , Hadziahmetovic Armin , Gruber Markus , Ammar Constantin , Zimmer Ralf
Published: August 2020

While absolute quantification is challenging in high-throughput measurements, changes of features between conditions can often be determined with high precision. Therefore, analysis of fold changes is the standard method, but often, a doubly differential analysis of changes of changes is required. Differential alternative splicing is an example of a doubly differential analysis, i.e. fold changes between conditions for different isoforms of a gene. EmpiRe is a quantitative approach for various kinds of omics data based on fold changes for appropriate features of biological objects. Empirical error distributions for these fold changes are estimated from Replicate measurements and used to quantify feature fold changes and their directions. We assess the performance of EmpiRe to detect differentially expressed genes applied to RNA-Seq using simulated data. It achieved higher precision than established tools at nearly the same recall level. Furthermore, we assess the detection of alternatively Spliced genes via changes of isoform fold changes (EmpiReS) on distribution-free simulations and experimentally validated splicing events. EmpiReS achieves the best precision-recall values for simulations based on different biological datasets. We propose EmpiRe(S) as a general, quantitative and fast approach with high reliability and an excellent trade-off between sensitivity and precision in (doubly) differential analyses.
Hyperpolyploidization of hepatocyte initiates preneoplastic lesion formation in the liver
Authors: Lin Heng , Huang Yen-Sung , Fustin Jean-Michel , Doi Masao , Chen Huatao , Lai Hui-Huang , Lin Shu-Hui , Lee Yen-Lurk , King Pei-Chih , Hou Hsien-San , Chen Hao-Wen , Young Pei-Yun , Chao Hsu-Wen
Published: August 2020

Hepatocellular carcinoma (HCC) is the most predominant primary malignancy in the liver. Genotoxic and genetic models have revealed that HCC cells are derived from hepatocytes, but where the critical region for tumor foci emergence is and how this transformation occurs are still unclear. Here, hyperpolyploidization of hepatocytes around the centrilobular (CL) region was demonstrated to be closely linked with the development of HCC cells after diethylnitrosamine treatment. We identified the CL region as a dominant lobule for accumulation of hyperpolyploid hepatocytes and preneoplastic tumor foci formation. We also demonstrated that upregulation ofAurkbplays a critical role in promoting hyperpolyploidization. Increase of AURKB phosphorylation was detected on the midbody during cytokinesis, causing abscission failure and hyperpolyploidization. Pharmacological inhibition of AURKB dramatically reduced nucleus size and tumor foci number surrounding the CL region in diethylnitrosamine-treated liver. Our work reveals an intimate molecular link between pathological hyperpolyploidy of CL hepatocytes and transformation into HCC cells.
RUNX1 haploinsufficiency causes a marked deficiency of megakaryocyte-biased hematopoietic progenitor cells: Mechanistic studies and drug correction
Authors: Estevez Brian , Borst Sara , Jarocha Danuta , Sudunagunta Varun , Gonzalez Michael , Garifallou James , Hakonarson Hakon , Gao Peng , Tan Kai , Liu Paul , Bagga Sumedha , Holdreith Nicholas , Tong Wei , Speck Nancy , French Deborah L. , Gadue Paul , Poncz Mortimer
Published: August 2020

Patients with familial platelet disorder with a predisposition to myeloid malignancy (FPDMM) harbor germline monoallelic mutations in a key hematopoietic transcription factor RUNX1. Previous studies of FPDMM have focused on megakaryocyte (Mk) differentiation, and platelet production and signaling. However, the effects of RUNX1 haploinsufficiency on hematopoietic progenitor cells (HPCs) and subsequent megakaryopoiesis remains incomplete. To address this issue, we studied induced-pluripotent stem cell (iPSC)-derived HPCs (iHPCs) and Mks (iMks) from both patient-derived lines and a wildtype line modified to be RUNX1 haploinsufficient (RUNX1+/−), each compared to their isogenic wildtype control. All RUNX1+/−lines showed decreased iMk yield and depletion of a Mk-biased iHPC subpopulation. To investigate global and local gene expression changes underlying this iHPC shift, single-cell RNA sequencing was performed on sorted FPDMM and control iHPCs. We defined several cell subpopulations in FPDMM Mk-biased iHPCs. Analyses of gene sets upregulated in FPDMM iHPCs indicated enrichment for response to stress, regulation of signal transduction and response to cytokine gene sets. Immunoblotting studies in FPDMM iMks were consistent with these findings, but also identified augmented baseline c-Jun N-terminal kinase (JNK) phosphorylation, known to be activated by transforming growth factor β1 and cellular stressors. J-IN8 and RepSox, small drugs targeting these pathways, corrected quantitative defects in FPDMM iHPC production. These findings were confirmed in adult human CD34+-derived stem and progenitor cells transduced with lentiviralRUNX1short-hairpin (sh) RNA to mimic RUNX1+/−. These mechanistic studies of the defect in megakaryopoiesis in FPDMM suggest druggable pathways for clinical management of thrombocytopenia in affected patients.

Key points

RUNX1 haploinsufficiency results in a deficiency of megakaryocyte-biased hematopoietic progenitor cells (HPCs).

RUNX1 haploinsufficiency elevates druggable proinflammatory and TGFβR1-related pathways in HPCs.
High Cysteinyl Leukotriene Receptor 1 Expression Correlates with Poor Survival of Uveal Melanoma Patients and Cognate Antagonist Drugs Modulate the Growth, Cancer Secretome, and Metabolism of Uveal Melanoma Cells
Authors: Slater Kayleigh , Heeran Aisling B. , Sanz-Pamplona Rebeca , Kalirai Helen , Rahman Arman , Helmi Mays , Garcia-Mulero Sandra , O’Connell Fiona , Bosch Rosa , Portela Anna , Villanueva Alberto , Piulats Josep M. , Gallagher William M. , Jensen Lasse D. , Coupland Sarah E. , O’Sullivan Jacintha , Kennedy Breandán N.
Published: August 2020

Uveal melanoma (UM) is a rare, but often lethal, form of ocular cancer arising from melanocytes within the uveal tract. UM has a high propensity to spread hematogenously to the liver, with up to 50% of patients developing liver metastases. Unfortunately, once liver metastasis occurs, patient prognosis is extremely poor with as few as 8% of patients surviving beyond two years. There are nostandard-of-caretherapies available for the treatment of metastatic uveal melanoma, hence it is a clinical area of urgent unmet need. Here, the clinical relevance and therapeutic potential of cysteinyl leukotriene receptors (CysLT1and CysLT2) in UM was evaluated. High expression ofCYSLTR1orCYSLTR2transcripts is significantly associated with poor disease-free survival and poor overall survival in UM patients. Digital pathology analysis identified high expression of CysLT1in primary UM is associated with reduced disease-specific survival (p = 0.012) and overall survival (p = 0.011). High CysLT1expression shows a statistically significant (p = 0.041) correlation with ciliary body involvement, a poor prognostic indicator in UM. Small molecule drugs targeting CysLT1were vastly superior at exerting anti-cancer phenotypes in UM cell lines and zebrafish xenografts than drugs targeting CysLT2. Quininib, a selective CysLT1antagonist, significantly inhibits survival (p < 0.0001), long-term proliferation (p < 0.0001), and oxidative phosphorylation (p < 0.001), but not glycolysis, in primary and metastatic UM cell lines. Quininib exerts opposing effects on the secretion of inflammatory markers in primary versus metastatic UM cell lines. Quininib significantly downregulated IL-2 and IL-6 in Mel285 cells (p < 0.05), but significantly upregulated IL-10, IL-1β, IL-2 (p < 0.0001), IL-13, IL-8 (p < 0.001), IL-12p70 and IL-6 (p < 0.05) in OMM2.5 cells. Finally, quininib significantly inhibits tumour growth in orthotopic zebrafish xenograft models of UM. These preclinical data suggest that antagonism of CysLT1, but not CysLT2, may be of therapeutic interest in the treatment of UM.
In-situ observation of mitochondrial biogenesis as the early event of apoptosis
Authors: Shao Chang-Sheng , Zhou Xiu-Hong , Miao Yu-Hui , Wang Peng , Zhang Qian-Qian , Huang Qing
Published: August 2020

Mitochondrial biogenesis is a cell response to external stimuli which is generally believed to suppress apoptosis. However, during the process of apoptosis, whether mitochondrial biogenesis occurs in the early stage of the apoptotic cells remains unclear. To address this question, we constructed the COX8-EGFP-ACTIN-mCherry HeLa cells with recombinant fluorescent proteins respectively tagged on the nucleus and mitochondria, and monitored the mitochondrial changes in living cells exposed to gamma-ray radiation. Besides in situ detection of mitochondrial fluorescence changes, we also examined the cell viability, nuclear DNA damage, reactive oxygen species (ROS), Mitochondrial superoxide, citrate synthase activity, ATP, cytoplasmic and mitochondrial calcium, mitochondrial DNA copy number and expression of transcription genes related to mitochondrial biogenesis as well as the apoptosis biomarkers. As a result, we confirmed that significant mitochondrial biogenesis took place preceding the radiation-induced apoptosis, and the change of mitochondrial biogenesis at early time was closely correlated with the apoptotic cells at late stage. The involved mechanism was also discussed.

Highlights

A dual fluorescence reporter system was successfully constructed for in-situ observation of mitochondrial biogenesis in living cells.

The whole process of radiation-induced mitochondrial biogenesis and apoptosis was scrutinized.

The conception of the relationship between mitochondrial biogenesis and apoptosis was revised.

Assessment of the early event of mitochondrial biogenesis is critical for prediction of the late fate of cells.

Graphical abstract
Modeling Genetic Epileptic Encephalopathies using Brain Organoids
Authors: Steinberg Daniel J. , Saleem Afifa , Repudi Srinivasa Rao , Banne Ehud , Mahajnah Muhammad , Hanna Jacob H. , Carlen Peter L. , Aqeilan Rami I.
Published: August 2020

Epileptic encephalopathies (EEs) are a group of disorders associated with intractable seizures, brain development and functional abnormalities, and in some cases, premature death. Pathogenic human germline biallelic mutations in tumor suppressor WW domain-containing oxidoreductase (WWOX) are associated with a relatively mild autosomal-recessive spinocerebellar ataxia-12 (SCAR12) and a more severe early infantile WWOX-related epileptic encephalopathy (WOREE). In this study, we generated anin-vitromodel for EEs, using the devastating WOREE syndrome as a prototype, by establishing brain organoids from CRISPR-engineered human ES cells and from patient-derived iPSCs. Using these models, we discovered dramatic cellular and molecular CNS abnormalities, including neural population changes, cortical differentiation malfunctions, and Wnt-pathway and DNA-damage response impairment. Furthermore, we provide a proof-of-concept that ectopic WWOX expression could potentially rescue these phenotypes. Our findings underscore the utility of modeling childhood epileptic encephalopathies using brain organoids and their use as a unique platform to test possible therapeutic intervention strategies.
Crowding Effects in an Empirical Predator-Prey System
Authors: Subbey Sam , Frank Anna S. , Kobras Melanie
Published: August 2020

Abstract

This paper uses a Lotka-Volterra (predator-prey) modeling framework to investigate the dynamical link between the biomass of an empirical predator, and that of its prey. We use a system of ordinary (ODE) differential equations to describe the system dynamics, and derive theoretical conditions for stability, in terms of system parameters. We derive the empirical system parameters by fitting the ODE system to empirical data, using non-constrained optimization.

We present results to show that the predator biomass is regulated by that of the prey. Furthermore, that the system dynamics is subject to Hopf bifurcation, conditioned on independent second-order terms in the ODE system. In ecological terms, the findings translate into evidence for existence of population crowding (density) effects.
Conditioned place preference reveals tonic pain in Octopus
Authors: Crook Robyn J
Published: August 2020

Tonic pain is an ongoing, negative affective state arising from tissue damage or inflammation (1). Because pain is aversive and its relief is innately rewarding, mammals learn to avoid a context in which pain is experienced, and prefer one where pain relief occurs(2, 3). It is generally accepted that vertebrate animals experience pain(4), however, there is currently no compelling evidence that pain occurs in any invertebrate(5). Here we show that octopuses exhibit tonic pain behavior after subcutaneous injection of dilute acetic acid. In conditioned place preference assays, octopuses avoid contexts in which pain was experienced, prefer a location in which they experienced tonic pain relief, and show no conditioned preference in pain’s absence. Octopuses are thus the first invertebrate shown to experience pain.

One sentence summary

A cognitive test demonstrating the emotional component of pain in mammals reveals the first example of pain in any invertebrate.
A simple high efficiency and low costin vitrogrowth system for phenotypic characterization and seed propagation ofArabidopsis thaliana
Authors: Pasternak Taras , Ruperti Benedetto , Palme Klaus
Published: August 2020

Background

Arabidopsis research relies extensively on the use ofin vitrogrowth for phenotypic analysis of the seedlings and characterization of plant responses to intrinsic and extrinsic cues. For this purpose, stress-free optimal growth conditions should be set up and used as a reference especially in studies aimed at characterizing the plant responses to abiotic and biotic stresses. Currently used standardin vitroprotocols for growth and characterization ofArabidopsis thalianaplants often suffer from sub-optimal composition due to an excessively high nutritional content which represents a stress per se and an experimental bias.

Results

We describe a simple protocol forin vitrogrowth of Arabidopsis plants in which the phenotypic analysis is based on an optimized and nutritionally balanced culture medium. We show that the protocol is robustly applicable for growth of several Arabidopsis mutants, including mutants lacking the root system. This protocol enables rapid high scale seed productionin vitroavoiding soil usage while saving space and time. The optimizedin vitroprotocol aims at: 1) makingin vitrogrowth as close as possible to natural soil conditions by optimizing nutrient balance in the medium; 2) simplifying phenotypic and molecular investigation of individual plants by standardizing all steps of plant growth; 3) enabling seeds formation also in genotypes with severe defect in the root system; 4) minimizing the amount of waste and space for plant growth by avoiding soil usage.

Conclusions

Here we report an optimized protocol for optimal growth ofArabidopsis thalianaplants to avoid biases in phenotypic observation of abiotic/biotic stress experiments. The protocol also enables the completion of the whole life cyclein vitrowithin 40-45 days and a satisfactory seed set for further propagation with no need for facilities for plant growth in soil and seed sterilisation.
Focal Electrical Stimulation of Human Retinal Ganglion Cells for Vision Restoration
Authors: Madugula Sasidhar S. , Gogliettino Alex R. , Zaidi Moosa , Aggarwal Gorish , Kling Alexandra , Shah Nishal P. , Vilkhu Ramandeep , Hays Madeline R. , Nguyen Huy , Fan Victoria , Wu Eric G. , Hottowy Pawel , Sher Alexander , Litke Alan M. , Silva Ruwan A. , Chichilnisky E.J.
Published: August 2020

Vision restoration with retinal implants that electrically stimulate retinal ganglion cells (RGCs), which transmit visual information to the brain, is limited by indiscriminate activation of many cells and cell types. Recent work in isolated macaque retina has demonstrated that direct electrical stimulation of RGCs can be performed with single-cell, single-spike resolution. However, the fidelity of epiretinal stimulation has not been examined in the human retina. Here, electrical activation of the major RGC types was examined using large-scale, multi-electrode recording and stimulation in the human retinaex vivoand compared directly to results from macaque. Targeted activation with single-cell, single-spike resolution was often possible without activating overlying axon bundles, at low stimulation current levels similar to those in macaque. Distinct cell types could be identified and targeted based on their distinct electrical signatures. Simulation based on these measurements revealed that a novel, dynamic stimulation approach would produce a nearly optimal evoked visual signal. These results indicate that high-fidelity control of spiking in human RGCs is achievable with extracellular stimulation and that the macaque retina is an accurate model for vision restoration with epiretinal implants.
pMAT: An Open-Source, Modular Software Suite for the Analysis of Fiber Photometry Calcium Imaging
Authors: Bruno Carissa A. , O’Brien Chris , Bryant Svetlana , Mejaes Jennifer , Pizzano Carina , Estrin David J. , Barker David J.
Published: August 2020

The combined development of new technologies for neuronal recordings and the development of novel sensors for recording both cellular activity and neurotransmitter binding has ushered in a new era for the field of neuroscience. Among these new technologies is fiber photometry, a technique wherein an implanted fiber optic is used to record signals from genetically encoded fluorescent sensors in bulk tissue. Fiber photometry has been widely adapted due to its cost-effectiveness, ability to examine the activity of neurons with specific anatomical or genetic identities, and the ability to use these highly modular systems to record from one or more sensors or brain sites in both superficial and deep-brain structures. Despite these many benefits, one major hurdle for laboratories adopting this technique is the steep learning curve associated with the analysis of fiber photometry data. This has been further complicated by a lack of standardization in analysis pipelines. In the present communication, we present pMAT, a ‘photometry modular analysis tool’ that allows users to accomplish common analysis routines through the use of a graphical user interface. This tool can be deployed in MATLAB and edited by more advanced users, but is also available as an independently deployable, open-source application.
Neuron-class specific responses govern adaptive remodeling of myelination in the neocortex
Authors: Yang Sung Min , Michel Katrin , Jokhi Vahbiz , Nedivi Elly , Arlotta Paola
Published: August 2020

Myelination plasticity plays a critical role in neurological function, including learning and memory. However, it is unknown whether this plasticity is enacted through uniform changes across all neuronal subtypes, or whether myelin dynamics vary between neuronal classes to enable fine-tuning of adaptive circuit responses. We performedin vivotwo-photon imaging to investigate the dynamics of myelin sheaths along single axons of both excitatory callosal projection neurons and inhibitory parvalbumin+interneurons in layer 2/3 of adult mouse visual cortex. We find that both neuron types show dynamic, homeostatic myelin remodeling under normal vision. However, monocular deprivation results in experience-dependent adaptive myelin remodeling only in parvalbumin+interneurons, but not in callosal projection neurons. Monocular deprivation induces an initial increase in elongation events in myelin segments of parvalbumin+interneurons, followed by a contraction phase affecting a separate cohort of segments. Sensory experience does not alter the generation rate of new myelinating oligodendrocytes, but can recruit pre-existing oligodendrocytes to generate new myelin sheaths. Parvalbumin+interneurons also show a concomitant increase in axonal branch tip dynamics independent from myelination events. These findings suggest that adaptive myelination is part of a coordinated suite of circuit reconfiguration processes, and demonstrate that distinct classes of neocortical neurons individualize adaptive remodeling of their myelination profiles to diversify circuit tuning in response to sensory experience.