bluuebunny/crossref_metadata_2025 huggingface dataset:
Intrinsic neuronal activity during migration controls the recruitment of specific interneuron subtypes in the postnatal mouse olfactory bulb
Authors: Stéphane Bugeon , Clara Haubold , Alexandre Ryzynski , Harold Cremer , Jean-Claude Platel
Published: July 2020

Neuronal activity has been identified as a key regulator of neuronal network development, but the impact of activity on migration and terminal positioning of interneuron subtypes is poorly understood. The absence of early subpopulation markers and the presence of intermingled migratory and post-migratory neurons makes the developing cerebral cortex a difficult model to answer these questions. Postnatal neurogenesis in the subventricular zone offers a more accessible and compartmentalized model. Neural stem cells regionalized along the border of the lateral ventricle produce two main subtypes of neural progenitors, granule cells and periglomerular neurons that migrate tangentially in the rostral migratory stream before migrating radially in the OB layers. Here we take advantage of targeted postnatal electroporation to compare the migration of these two population. We do not observe any obvious differences regarding the mode of tangential or radial migration between these two subtypes. However, we find a very striking increase of intrinsic calcium activity only in granule cell precursors when they switch from tangential to radial migration. By decreasing neuronal excitability in granule cell precursors, we find that neuronal activity is critical for normal migratory speed at the end of tangential migration. Importantly, we also find that activity is required for normal positioning and survival of granule cell precursors in the OB layers. Strikingly, decreasing activity of periglomerular neuron precursors did not impact their positioning or survival. Altogether these findings suggest that neuronal excitability plays a subtype specific role during the late stage of migration of postnatally born olfactory bulb interneurons.

Significance Statement

While neuronal activity is a critical factor regulating different aspects of neurogenesis, it has been challenging to study its role during the migration of different neuronal subpopulations. Here, we use postnatal targeted electroporation to label and manipulate the two main olfactory bulb interneuron subpopulations during their migration: granule cell and periglomerular neuron precursors. We find a very striking increase of calcium activity only in granule cell precursors when they switch from tangential to radial migration. Interestingly, blocking activity in granule cell precursors affected their migration, positioning and survival while periglomerular neuron precursors are not affected. These results suggest that neuronal activity is required specifically for the recruitment of granule cell precursors in the olfactory bulb layers.
Three-dimensional random walk models of individual animal movement and their application to trap counts modelling
Authors: Ahmed DA , Benhamou S , Bonsall MB , Petrovskii SV
Published: July 2020

Background

Random walks (RWs) have proved to be a powerful modelling tool in ecology, particularly in the study of animal movement. An application of RW concerns trapping which is the predominant sampling method to date in insect ecology, invasive species, and agricultural pest management. A lot of research effort has been directed towards modelling ground-dwelling insects by simulating their movement in 2D, and computing pitfall trap counts, but comparatively very little for flying insects with 3D elevated traps.

Methods

We introduce the mathematics behind 3D RWs and present key metrics such as the mean squared displacement (MSD) and path sinuosity, which are already well known in 2D. We develop the mathematical theory behind the 3D correlated random walk (CRW) which involves short-term directional persistence and the 3D Biased random walk (BRW) which introduces a long-term directional bias in the movement so that there is an overall preferred movement direction. In this study, we consider three types of shape of 3D traps, which are commonly used in ecological field studies; a spheroidal trap, a cylindrical trap and a rectangular cuboidal trap. By simulating movement in 3D space, we investigated the effect of 3D trap shapes and sizes and of movement diffusion on trapping efficiency.

Results

We found that there is a non-linear dependence of trap counts on the trap surface area or volume, but the effect of volume appeared to be a simple consequence of changes in area. Nevertheless, there is a slight but clear hierarchy of trap shapes in terms of capture efficiency, with the spheroidal trap retaining more counts than a cylinder, followed by the cuboidal type for a given area. We also showed that there is no effect of short-term persistence when diffusion is kept constant, but trap counts significantly decrease with increasing diffusion.

Conclusion

Our results provide a better understanding of the interplay between the movement pattern, trap geometry and impacts on trapping efficiency, which leads to improved trap count interpretations, and more broadly, has implications for spatial ecology and population dynamics.
Selecting Student-Authored Questions for Summative Assessments
Authors: Huang Alice , Hancock Dale , Clemson Matthew , Yeo Giselle , Harney Dylan J , Denny Paul , Denyer Gareth
Published: July 2020

Production of high-quality multiple-choice questions (MCQs) for both formative and summative assessment is a time-consuming task requiring great skill, creativity, and insight. The transition to online examinations, with the concomitant exposure of previously tried-and-tested MCQs, exacerbates the challenges of question production, and highlights the need for innovative solutions.

Several groups have shown that it is practical to leverage the student cohort to produce a very large number of syllabus-aligned MCQs for study banks. Although student-generated questions are well suited for formative feedback and practice activities, they are generally not thought to be suitable for high-stakes assessments. In this study, we aimed to demonstrate that training can be provided to students in a scalable fashion to generate questions of similar quality to those produced by experts, and that identification of suitable questions can be achieved with minimal academic review and editing.

Biochemistry and Molecular Biology students were assigned a series of activities designed to coach them in the art of writing and critiquing MCQs. This training resulted in the production of over one thousand MCQs that were then gauged for potential by either expert academic judgement, or via a data-driven approach in which the questions were trialled objectively in a low-stakes test. Questions selected by either method were then deployed in a high-stakes in-semester assessment alongside questions from two academically authored sources: textbook-derived MCQs, and past paper questions.

A total of 120 MCQs from these four sources were deployed in assessments attempted by over 600 students. Each question was subjected to rigorous performance analysis, including the calculation of standard metrics from classical test theory and more sophisticated Item Response Theory (IRT) measures. The results showed that MCQs authored by students and selected at low cost performed as well as questions authored by academics, illustrating the potential of this strategy for the efficient creation of large numbers of high quality MCQs for summative assessment.
Rapid detection of SARS-CoV-2 by pulse-controlled amplification (PCA)
Authors: Katrin Zwirglmaier , Maria Weyh , Christian Krüger , Rosina Ehmann , Katharina Müller , Roman Wölfel , Kilian Stoecker
Published: July 2020

In the current pandemic of SARS-CoV-2, rapid identification of infected individuals is crucial for management and control of the outbreak. However, transport of samples, sample processing and RT-qPCR analysis in laboratories are time-consuming. Here we present a nucleic acid-based test format – pulse controlled amplification – that allows detection of SARS-CoV-2 directly from up to eight swab samples simultaneously without the need for RNA extraction within 20 min in a point-of-care setting.
A blueprint for academic labs to produce SARS-CoV-2 RT-qPCR test kits
Authors: Mascuch Samantha J. , Fakhretaha-Aval Sara , Bowman Jessica C. , Ma Minh Thu H. , Thomas Gwendell , Bommarius Bettina , Ito Chieri , Zhao Liangjun , Newnam Gary P. , Matange Kavita R. , Thapa Hem R. , Barlow Brett , Donegan Rebecca K. , Nguyen Nguyet A. , Saccuzzo Emily G. , Obianyor Chiamaka T. , Karunakaran Suneesh C. , Pollet Pamela , Rothschild-Mancinelli Brooke , Mestre-Fos Santi , Guth-Metzler Rebecca , Bryksin Anton V. , Petrov Anton S. , Hazell Mallory , Ibberson Carolyn B. , Penev Petar I. , Mannino Robert G. , Lam Wilbur A. , Garcia Andrés J. , Kubanek Julia M. , Agarwal Vinayak , Hud Nicholas V. , Glass Jennifer B. , Williams Loren Dean , Lieberman Raquel L.
Published: July 2020

Widespread testing for the presence of the novel coronavirus SARS-CoV-2 in individuals remains vital for controlling the COVID-19 pandemic prior to the advent of an effective treatment. Challenges in testing can be traced to an initial shortage of supplies, expertise and/or instrumentation necessary to detect the virus by quantitative reverse transcription polymerase chain reaction (RT-qPCR), the most robust, sensitive, and specific assay currently available. Here we show that academic biochemistry and molecular biology laboratories equipped with appropriate expertise and infrastructure can replicate commercially available SARS-CoV-2 RT-qPCR test kits and backfill pipeline shortages. The Georgia Tech COVID-19 Test Kit Support Group, composed of faculty, staff, and trainees across the biotechnology quad at Georgia Institute of Technology, synthesized multiplexed primers and probes and formulated a master mix composed of enzymes and proteins produced in-house. Our in-house kit compares favorably to a commercial product used for diagnostic testing. We also developed an environmental testing protocol to readily monitor surfaces across various campus laboratories for the presence of SARS-CoV-2. Our blueprint should be readily reproducible by research teams at other institutions, and our protocols may be modified and adapted to enable SARS-CoV-2 detection in more resource-limited settings.
Tocilizumab shortens time on mechanical ventilation and length of hospital stay in patients with severe COVID-19: a retrospective cohort study
Authors: Eimer Johannes , Vesterbacka Jan , Svensson Anna-Karin , Stojanovic Bertil , Wagrell Charlotta , Sönnerborg Anders , Nowak Piotr
Published: July 2020

Background

Hyperinflammation is a key feature of the pathogenesis of COVID-19 with a central role of the interleukin-6 pathway. We aimed to study the impact of the IL-6 receptor antagonist tocilizumab on the outcome of patients admitted to the intensive care unit (ICU) with acute respiratory distress syndrome (ARDS) related to COVID-19.

Methods

Eighty-seven patients with confirmed SARS-CoV-2 infection and moderate to severe ARDS were included (n tocilizumab = 29, n controls = 58). A matched cohort was created using a propensity score. The primary endpoint was 30-day all-cause mortality, secondary endpoints included ventilation-free days and length of stay.

Results

No difference was found in 30-day all-cause mortality in patients treated with tocilizumab compared to controls (17.2% vs. 32.8%, p = 0.2; HR = 0.52 [0.19 - 1.39], p = 0.19). Ventilator-free days were 19.0 (IQR 12.5 - 20.0) versus 9 (IQR 0.0 - 18.5; p = 0.04), respectively. A higher rate of freedom from mechanical ventilation at 30 days was achieved in patients receiving tocilizumab (HR 2.83 [1.48 - 5.40], p < 0.002). Median length of stay in ICU and total length of stay were reduced by 8 and 9.5 days in patients treated with tocilizumab. Similar results were obtained in the analysis of the propensity score matched cohort.

Conclusions

Treatment of critically ill patients with ARDS due to COVID-19 with tocilizumab was not associated with reduced 30-day all-cause mortality, but shorter duration on ventilatory support as well as shorter overall length of stay in hospital and in ICU.
Disease severity dictates SARS-CoV-2-specific neutralizing antibody responses in COVID-19
Authors: Chen Xiangyu , Pan Zhiwei , Yue Shuai , Yu Fei , Zhang Junsong , Yang Yang , Li Ren , Liu Bingfeng , Yang Xiaofan , Gao Leiqiong , Li Zhirong , Lin Yao , Huang Qizhao , Xu Lifan , Tang Jianfang , Hu Li , Zhao Jing , Liu Pinghuang , Zhang Guozhong , Chen Yaokai , Deng Kai , Ye Lilin
Published: July 2020

COVID-19 patients exhibit differential disease severity after SARS-CoV-2 infection. It is currently unknown as to the correlation between the magnitude of neutralizing antibody (NAb) responses and the disease severity in COVID-19 patients. In a cohort of 59 recovered patients with disease severity including severe, moderate, mild and asymptomatic, we observed the positive correlation between serum neutralizing capacity and disease severity, in particular, the highest NAb capacity in sera from the patients with severe disease, while a lack of ability of asymptomatic patients to mount competent NAbs. Furthermore, the compositions of NAb subtypes were also different between recovered patients with severe symptoms and with mild-to-moderate symptoms. These results reveal the tremendous heterogeneity of SARS-CoV-2-specific NAb responses and their correlations to disease severity, highlighting the needs of future vaccination in COVID-19 patients recovered from asymptomatic or mild illness.
On the Digital Psychopharmacology of Valproic Acid in Mice
Authors: Bass John Samuel , Tuo Anney , Ton Linh , Jankovic Miranda J. , Kapadia Paarth K. , Schirmer Catharina , Krishnan Vaishnav
Published: July 2020

Objective

Antiepileptic drugs (AEDs) require daily ingestion for maximal seizure prophylaxis. Adverse psychiatric consequences of AEDs present as: (i) reversible changes in mood, anger, anxiety and/or irritability that often necessitate drug discontinuation, and (ii) autism and/or cognitive/psychomotor developmental delays following fetal exposure. Technical advances in quantifying naturalistic rodent behaviors may provide sensitive preclinical estimates of AED psychiatric tolerability and neuropsychiatric teratogenicity.

Methods

Using instrumented home-cage monitoring, we assessed how valproic acid (VPA, dissolved in sweetened drinking water) alters home-cage behavior in adult C57BL/6J mice and in the adult offspring of VPA-exposed breeder pairs. By utilizing a pup open field assay, we also examined how prenatal VPA exposure impacts early spontaneous exploratory behavior.

Results

At 500-600mg/kg/d, chronic VPA produced hyperphagia and increased wheel-running without impacting sleep, activity and measures of risk aversion. When applied chronically to breeder pairs of mice, VPA prolonged the latency to viable litters without affecting litter size. Two-week old VPA-exposed pups displayed open field hypoactivity without alterations in thigmotaxis. As adults, prenatal VPA-exposed mice displayed active state fragmentation, hypophagia and increased wheel running, together with subtle alterations in home-cage dyadic behavior.

Interpretation

Through automated home-cage assessments of C57BL/6J mice, we capture an ethologically centered psychopharmacological profile of enterally administered VPA that is aligned with human clinical experience. By characterizing the effects of pangestational VPA exposure, we discover novel murine expressions of pervasive neurodevelopment. Incorporating rigorous comprehensive assessments of neuropsychiatric tolerability may inform the design of future AEDs with improved neuropsychiatric safety profiles, both for patients and their offspring.
The malaria metabolite HMBPP does not trigger erythrocyte terpene production
Authors: Miller Justin J. , Odom John Audrey R.
Published: July 2020

Infection with malarial parasites renders hosts more mosquito attractive than their uninfected, healthy, counterparts. One volatile organic compound, α-pinene, is associated withPlasmodiumspp. infection in multiple studies and is a known mosquito attractant. However, how malarial infection results in elevated levels of host-associated α-pinene remains unclear. One study suggests that erythrocyte exposure to the malarial metabolite, (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), results in increased levels of α-pinene. Here, we establish that endogenous levels of α-pinene are present in human erythrocytes, that these levels vary widely by erythrocyte donor, and that α-pinene levels are not altered by HMBPP treatment.
Generation of nonhuman primate retinitis pigmentosa model byin situknockout ofRHOin rhesus macaque retina
Authors: Li Shouzhen , Hu Yingzhou , Li Yunqin , Hu Min , Wang Wenchao , Ma Yuqian , Cai Yuan , Wei Min , Yao Yichuan , Wang Yun , Dong Kai , Gu Yonghao , Zhao Huan , Bao Jin , Qiu Zilong , Zhang Mei , Hu Xintian , Xue Tian
Published: July 2020

Retinitis pigmentosa (RP) is a form of inherited retinal degenerative disease that ultimately involves the macula, which is present in primates but not in the rodents. Therefore, creating nonhuman primate (NHP) models of RP is of critical importance to study its mechanism of pathogenesis and to evaluate potential therapeutic options in the future. Here we applied adeno-associated virus (AAV)-delivered CRISPR/SaCas9 technology to knockout theRHOgene in the retinae of the adult rhesus macaque (Macaca mulatta) to investigate the hypothesis whether non-germline mutation of theRHOgene is sufficient to recapitulate RP. Through a series of studies, we were able to demonstrate successful somatic editing of theRHOgene and reduced RHO protein expression. More importantly, the mutant macaque retinae displayed clinical RP phenotypes, including photoreceptor degeneration, retinal thinning, abnormal rod subcellular structures, and reduced photoresponse. Therefore, we suggest somatic editing of theRHOgene is able to phenocopy RP, and the reduced time span in generating NHP mutant accelerates RP research and expands the utility of NHP model for human disease study.
E-cigarettes compromise the gut barrier and trigger gut inflammation
Authors: Sharma Aditi , Lee Jasper , Fonseca Ayden G. , Moshensky Alex , Kothari Taha , Sayed Ibrahim M. , Ibeawuchi Stella-Rita , Pranadinata Rama F. , Ear Jason , Sahoo Debashis , Crotty-Alexander Laura E. , Ghosh Pradipta , Das Soumita
Published: July 2020

E-cigarette and vaping device use continue to rise, particularly in adolescents and young adults, but the safety of inhaling the multitude of chemicals within e-cigarette aerosols has been questioned. While several studies have evaluated vaping effects on the lungs and heart; effects on the gastrointestinal tract remain unknown. Using established murine models of acute (1 week) and chronic (3 month) daily e-cigarette aerosol inhalation, both with nicotine-containing and vehicle control e-liquids, murine colon transcriptomics and organoid co-culture models, we assessed the effects of e-cigarette use on the gut barrier and mucosal health. Histologic analyses revealed that chronic exposure to nicotine-free e-cigarette aerosols induced mucosal inflammation. Transcriptome analyses revealed that chronic, but not acute, nicotine-free e-cigarette use significantly reduced expression of tight junction markers, including occluding, and drove expression of pro-inflammatory cytokines. Exposure of murine and human enteroid-derived monolayers (EDMs) to nicotine-free e-cigarette aerosols alone, or in co-culture with invasiveE. coli,confirmed that repetitive exposure was sufficient to recapitulate the key findings observedin vivo, i.e., barrier-disruption, downregulation of occludin, inflammation, and an accentuated risk of and response to bacterial infection. These data highlight an unexpected harmful effect of e-cigarette use on the gut barrier and pinpoint non-nicotine chemical components common across >90% of e-cigarette e-liquids as the source of harm. Given the ever-expanding importance of the integrity of the gut barrier for host fitness, and impact of gut mucosal inflammation on a multitude of chronic diseases, these findings are broadly relevant to medicine and public health.

SIGNIFICANCE

The safety of electronic cigarettes has been questioned amidst emerging evidence that they may derail our immune system and increase our susceptibility to infections. Despite these insights, their impact on the most critical entity that separates trillions of microbes from the largest immune system in our body, i.e., the gut barrier, remains unexplored. Using a combination of mouse models, gut transcriptomics, and murine and human gut-derived organoids, here we show that chronic exposure to aerosols of electronic-cigarette disrupts the gut barrier, increases its susceptibility to bacterial infections and triggers inflammation. Given the importance of the gut barrier in the maintenance of immune homeostasis, these findings provide valuable insights into the potential long-term harmful effects of electronic cigarettes on health.
Signatures of neutral evolution in exponentially growing tumors: a theoretical perspective
Authors: Tung Hwai-Ray , Durrett Rick
Published: July 2020

We investigate the site frequency spectrum in the two-type model of clonal evolution. If the fitnesses of the two types are λ0< λ1then the site frequency spectrum isc/fαwhereα= λ0/λ1. This is due to the advantageous mutations that produce the founders of the type 1 population. Mutations within the growing type 0 and type 1 populations follow the 1/flaw. Our results show that neutral evolution can be distinguished from the two-type model using the site frequency spectrum.
SARS-CoV-2 Spike Protein Interacts with Multiple Innate Immune Receptors
Authors: Gao Chao , Zeng Junwei , Jia Nan , Stavenhagen Kathrin , Matsumoto Yasuyuki , Zhang Hua , Li Jiang , Hume Adam J. , Mühlberger Elke , van Die Irma , Kwan Julian , Tantisira Kelan , Emili Andrew , Cummings Richard D.
Published: July 2020

The spike (S) glycoprotein in the envelope of SARS-CoV-2 is densely glycosylated but the functions of its glycosylation are unknown. Here we demonstrate that S is recognized in a glycan-dependent manner by multiple innate immune receptors including the mannose receptor MR/CD206, DC-SIGN/CD209, L-SIGN/CD209L, and MGL/CLEC10A/CD301. Single-cell RNA sequencing analyses indicate that such receptors are highly expressed in innate immune cells in tissues susceptible to SARS-CoV-2 infection. Binding of the above receptors to S is characterized by affinities in the picomolar range and consistent with S glycosylation analysis demonstrating a variety of N- and O-glycans as receptor ligands. These results indicate multiple routes for SARS-CoV-2 to interact with human cells and suggest alternative strategies for therapeutic intervention.
Noise regularization removes correlation artifacts in single-cell RNA-seq data preprocessing
Authors: Zhang Ruoyu , Atwal Gurinder S. , Lim Wei Keat
Published: July 2020

With the rapid advancement of single-cell RNA-seq (scRNA-seq) technology, many data preprocessing methods have been proposed to address numerous systematic errors and technical variabilities inherent in this technology. While these methods have been demonstrated to be effective in recovering individual gene expression, the suitability to the inference of gene-gene associations and subsequent gene networks reconstruction have not been systemically investigated. In this study, we benchmarked five representative scRNA-seq normalization/imputation methods on human cell atlas bone marrow data with respect to their impact on inferred gene-gene associations. Our results suggested that a considerable amount of spurious correlations was introduced during the data preprocessing steps due to over-smoothing of the raw data. We proposed a model-agnostic noise regularization method that can effectively eliminate the correlation artifacts. The noise regularized gene-gene correlations were further used to reconstruct gene co-expression network and successfully revealed several known immune cell modules.
A Next Generation Bivalent Human Ad5 COVID-19 Vaccine Delivering Both Spike and Nucleocapsid Antigens Elicits Th1 Dominant CD4+, CD8+ T-cell and Neutralizing Antibody Responses
Authors: Rice Adrian , Verma Mohit , Shin Annie , Zakin Lise , Sieling Peter , Tanaka Shiho , Adisetiyo Helty , Taft Justin , Patel Rosheel , Buta Sofija , Martin-Fernandez Marta , Morimoto Brett , Gabitzsch Elizabeth , Safrit Jeffrey T. , Balint Joseph , Dinkins Kyle , Spilman Patricia , Bogunovic Dusan , Rabizadeh Shahrooz , Niazi Kayvan , Soon-Shiong Patrick
Published: July 2020

In response to the health crisis presented by the COVID-19 pandemic, rapid development of safe and effective vaccines that elicit durable immune responses is imperative. Recent reports have raised the concern that antibodies in COVID-19 convalescent patients may not be long lasting and thus even these individuals may require vaccination. Vaccine candidates currently in clinical testing have focused on the SARS-CoV-2 wild type spike (S) protein (S-WT) as the major antigen of choice and while pre-clinical and early clinical testing have shown that S elicits an antibody response, we believe the optimal vaccine candidate should be capable of inducing robust, durable T-cell responses as well as humoral responses. We report here on a next generation bivalent human adenovirus serotype 5 (hAd5) vaccine capable of inducing immunity in patients with pre-existing adenovirus immunity, comprisingbothan S sequence optimized for cell surface expression (S-Fusion) and a conserved nucleocapsid (N) antigen designed to be transported to the endosomal subcellular compartment, with the potential to generate durable immune protection. Our studies suggest that this bivalent vaccine is optimized for immunogenicity as evidenced by the following findings: (i) The optimized S-Fusion displayed improved S receptor binding domain (RBD) cell surface expression compared to S-WT where little surface expression was detected; (ii) the expressed RBD from S-Fusion retained conformational integrity and recognition by ACE2-Fc; (iii) the viral N protein modified with an enhanced T-cell stimulation domain (ETSD) localized to endosomal/lysosomal subcellular compartments for MHC I/II presentation; and (iv) these optimizations to S and N (S-Fusion and N-ETSD) generated enhancedde novoantigen-specific B cell and CD4+ and CD8+ T-cell responses in antigen-naive pre-clinical models. Both the T-cell and antibody immune responses to S and N demonstrated a T-helper 1 (Th1) bias. The antibody responses were neutralizing as demonstrated by two independent SARS-CoV-2 neutralization assays. Based on these findings, we are advancing this next generation bivalent hAd5 S-Fusion + N-ETSD vaccine as our lead clinical candidate to test for its ability to provide robust, durable cell-mediated and humoral immunity against SARS-CoV-2 infection. Further studies are ongoing to explore utilizing this vaccine construct in oral, intranasal, and sublingual formulations to induce mucosal immunity in addition to cell-mediated and humoral immunity. The ultimate goal of an ideal COVID-19 vaccine is to generate long-term T and B cell memory.
Cullin3 promotes stem cell progeny differentiation by facilitating aPKC-directed asymmetric Numb localization
Authors: Komori Hideyuki , Rives-Quinto Noemi , Han Xu , Anhezini Lucas , Esrig Ari J. , Skeath James B. , Lee Cheng-Yu
Published: July 2020

Asymmetric segregation of Numb is a conserved mechanism for regulating Notch-mediated binary cell fate decisions; however, the mechanisms controlling Numb segregation remain unclear. Previous studies have proposed an “exclusion” model, suggesting that atypical protein kinase C (aPKC) negatively regulates Numb cortical localization. Here, we report that aPKC kinase activity positively promotes basal cortical Numb localization during asymmetric division ofDrosophilaneural stem cells (neuroblasts) and that Cullin 3 (Cul3) is required for aPKC-directed basal Numb localization. Innumb-orcul3-mutant brains, decreased levels of Numb segregated into neuroblast progeny failed to downregulate Notch, leading to supernumerary neuroblast formation. Increased aPKC kinase activity suppressed supernumerary neuroblast formation by concentrating residual Numb protein at the basal cortex and in neuroblast progeny, whereas decreased aPKC function enhanced the supernumerary neuroblast phenotype by reducing basal Numb levels. We propose that aPKC and Cul3 promote basal Numb localization, which is required to downregulate Notch signaling and promote differentiation in neuroblast progeny.
Reversible fronto-occipitotemporal signaling complements task encoding and switching under ambiguous cues
Authors: Tsumura Kaho , Kosugi Keita , Hattori Yoshiki , Aoki Ryuta , Takeda Masaki , Chikazoe Junichi , Nakahara Kiyoshi , Jimura Koji
Published: July 2020

Adaptation to changing environments involves the appropriate extraction of environmental information to achieve a behavioral goal. It remains unclear how behavioral flexibility is guided under situations where the relevant behavior is ambiguous. Using functional brain mapping of machine-learning decoders and directional functional connectivity, we show that brain-wide reversible neural signaling underpins task encoding and behavioral flexibility in ambiguously changing environments. When relevant behavior is cued ambiguously during behavioral shifting, neural coding is attenuated in distributed cortical regions, but top-down signals from the prefrontal cortex complement the coding. When behavioral shifting is cued more explicitly, modality-specialized occipitotemporal regions implement distinct neural coding about relevant behavior, and bottom-up signals from the occipitotemporal region to the prefrontal cortex supplement the behavioral shift. These results suggest that our adaptation to an ever-changing world is orchestrated by the alternation of top-down and bottom-up signaling in the fronto-occipitotemporal circuit depending on the availability of environmental information.
Cone-shaped HIV-1 capsids are transported through intact nuclear pores
Authors: Zila Vojtech , Margiotta Erica , Turonova Beata , Müller Thorsten G. , Zimmerli Christian E. , Mattei Simone , Allegretti Matteo , Börner Kathleen , Rada Jona , Müller Barbara , Lusic Marina , Kräusslich Hans-Georg , Beck Martin
Published: July 2020

Human immunodeficiency virus (HIV-1) remains a major health threat. Viral capsid uncoating and nuclear import of the viral genome are critical for productive infection. The size of the HIV-1 capsid is generally believed to exceed the diameter of the nuclear pore complex (NPC), indicating that capsid uncoating has to occur prior to nuclear import. Here, we combined correlative light and electron microscopy with subtomogram averaging to capture the structural status of reverse transcription-competent HIV-1 complexes in infected T cells. We demonstrate that the diameter of the NPCin cellulois sufficient for the import of apparently intact, coneshaped capsids. Subsequent to nuclear import, we detected disrupted and empty capsid fragments, indicating that uncoating of the replication complex occurs by breaking the capsid open, and not by disassembly into individual subunits. Our data directly visualize a key step in HIV-1 replication and enhance our mechanistic understanding of the viral life cycle.
In-vivoevaluation of the anti-diarrheal effect ofLactococcus lactis subspecies lactisandLactococcus pisciumisolated from yogurt
Authors: Mahmud Abu Sayeed Mohammad , Chowdhury Mobarak , Akter Rasheda , Islam Saiful , Mazumdar Santosh , Taznin Tarannum , Chowdhury Rocky , Talukder Hridika , Bhuiyan Habibur Rahman
Published: July 2020

Lactobacillus and Lactococcus species found in the yogurt of different sources are most widely assayed and used all over the world as a probiotic agent. This study aimed to isolate and identify novel probiotic agents with therapeutic value against diarrhea. Initially, the probiotic properties of the isolated lactic acid bacteria from the yogurt samples of the Chittagong division, Bangladesh, were evaluated. All probiotic candidates inhibited the growth of selected pathogens, includingEscheriachia coli, Serratia sp.Salmonella paratyphi, Streptococcus Group-B,Staphylococcus aureus, Haemophillus influenzae, Bacillus subtillis, andKlebsiella pneumoniae. Lactococcus lactissubsp lactis were found most useful in inhibiting all the selected pathogens. When the probiotics were applied against castor oil-induced diarrhea in the rat model,Lactococcus lactissubspecieslactisandLactococcus pisciumwere found significantly effective relative to the controls indicating their potentiality as an alternative therapeutic against diarrhea.

Highlights

Lactococcus lactissubspecies lactis andLactococcus pisciumhas shown potentiality to be a therapeutic agent against castor-oil induced diarrhea in an animal model.

Lactococcus lactissubspecies lactis andLactococcus pisciuminhibited the growth of specified pathogens.
Young Infants Process Prediction Errors at the Theta Rhythm
Authors: Köster Moritz , Langeloh Miriam , Michel Christine , Hoehl Stefanie
Published: July 2020

Examining how young infants respond to unexpected events is key to our understanding of their emerging concepts about the world around them. From a predictive processing perspective, it is intriguing to investigate how the infant brain responds to unexpected events (i.e., prediction errors), because they require infants to refine their predictions about the environment. Here, to better understand prediction error processes in the infant brain, we presented 9-month-olds (N= 36) a variety of physical and social events with unexpected versus expected outcomes, while recording their electroencephalogram (EEG). We found a pronounced response in the ongoing 4 – 5 Hz theta rhythm for the processing of unexpected (in contrast to expected) events, for a prolonged time window (2 s) and across all scalp-recorded electrodes. The condition difference in the theta rhythm was not related to the condition difference in infants’ event-related activity to unexpected (versus expected) events in the negative central (Nc) component (.4 – .6 s), a component, which is commonly analyzed in infant violation of expectation studies using EEG. These findings constitute critical evidence that the theta rhythm is involved in the processing of prediction errors from very early in human brain development. We discuss how the theta rhythm may support infants’ refinement of basic concepts about the physical and social environment.
Structural Insights into Photoactivation of Plant Cryptochrome-2
Authors: Palayam Malathy , Ganapathy Jagadeesan , Guercio Angelica M. , Tal Lior , Deck Samuel L. , Shabek Nitzan
Published: July 2020

Cryptochromes (CRYs) are evolutionarily conserved photoreceptors that mediate various light-induced responses in bacteria, plants, and animals. Plant cryptochromes govern a variety of critical growth and developmental processes including seed germination, flowering time and entrainment of the circadian clock. CRY’s photocycle involves reduction of their flavin adenine dinucleotide (FAD)-bound chromophore, which is completely oxidized in the dark and semi to fully reduced in the light signaling-active state. Despite the significant progress in characterizing cryptochromes, important aspects of their photochemistry, regulation, and light-induced structural changes remain to be addressed. In this study, we determine the crystal structure of the photosensory domain of Arabidopsis CRY2 in a tetrameric active state. Systematic structure-based analyses of photo-activated and inactive plant CRYs elucidate new structural elements and critical residues that dynamically partake in photo-induced oligomerization. Our study offers an updated model of CRYs photoactivation mechanism as well as the mode of its regulation by interacting proteins.
Riluzole suppresses growth and enhances response to endocrine therapy in ER+ breast cancer
Authors: Olukoya Ayodeji O. , Stires Hillary , Bahnassy Shaymaa , Persaud Sonali , Guerra Yanira , Ranjit Suman , Ma Shihong , Cruz M. Idalia , Benitez Carlos , Rozeboom Aaron M. , Ceuleers Hannah , Berry Deborah L. , Jacobsen Britta M. , Raj Ganesh V. , Riggins Rebecca B.
Published: July 2020

Background

Resistance to endocrine therapy in estrogen receptor-positive (ER+) breast cancer remains a significant clinical problem. Riluzole is FDA-approved for the treatment of amyotrophic lateral sclerosis. A benzothiazole-based glutamate release inhibitor with several context-dependent mechanism(s) of action, Riluzole has shown anti-tumor activity in multiple malignancies, including melanoma, glioblastoma, and breast cancer. We previously reported that the acquisition of Tamoxifen resistance in a cellular model of invasive lobular breast cancer is accompanied by the upregulation of GRM mRNA expression and growth inhibition by Riluzole.

Methods

We tested the ability of Riluzole to reduce cell growth, alone and in combination with endocrine therapy, in a diverse set of ER+ invasive ductal and lobular breast cancer-derived cell lines, primary breast tumor explant cultures, and the estrogen-independent,ESR1-mutated invasive lobular breast cancer patient-derived xenograft model HCI-013EI.

Results

Single-agent Riluzole suppressed the growth of ER+ invasive ductal and lobular breast cancer cell linesin vitro, inducing a histologic subtype-associated cell cycle arrest (G0-G1 for ductal, G2-M for lobular). Riluzole induced apoptosis and ferroptosis and reduced phosphorylation of multiple pro-survival signaling molecules, including Akt/mTOR, CREB, and Src/Fak family kinases. Riluzole, in combination with either Fulvestrant or 4-hydroxytamoxifen, additively suppressed ER+ breast cancer cell growthin vitro. Single-agent Riluzole significantly inhibited HCI-013EI patient-derived xenograft growthin vivo, and the combination of Riluzole plus Fulvestrant significantly reduced proliferation in primary breast tumor explant cultures.

Conclusions

Riluzole, alone or combined with endocrine therapy, may offer therapeutic benefits in diverse ER+ breast cancers, including lobular breast cancer.
Dynamics of nonlinguistic statistical learning: From neural entrainment to the emergence of explicit knowledge
Authors: Moser Julia , Batterink Laura , Hegner Yiwen Li , Schleger Franziska , Braun Christoph , Paller Ken A. , Preissl Hubert
Published: July 2020

Humans are highly attuned to patterns in the environment. This ability to detect environmental patterns, referred to as statistical learning, plays a key role in many diverse aspects of cognition. However, the spatiotemporal neural mechanisms underlying implicit statistical learning, and how these mechanisms may relate or give rise to explicit learning, remain poorly understood. In the present study, we investigated these different aspects of statistical learning by using an auditory nonlinguistic statistical learning paradigm combined with magnetoencephalography. Twenty-four healthy volunteers were exposed to structured and random tone sequences, and statistical learning was quantified by neural entrainment. Already early during exposure, participants showed strong entrainment to the embedded tone patterns. A significant increase in entrainment over exposure was detected only in the structured condition, reflecting the trajectory of learning. While source reconstruction revealed a wide range of brain areas involved in this process, entrainment in areas around the left pre-central gyrus as well as right temporo-frontal areas significantly predicted behavioral performance. Sensor level results confirmed this relationship between neural entrainment and subsequent explicit knowledge. These results give insights into the dynamic relation between neural entrainment and explicit learning of triplet structures, suggesting that these two aspects are systematically related yet dissociable. Neural entrainment reflects robust, implicit learning of underlying patterns, whereas the emergence of explicit knowledge, likely built on the implicit encoding of structure, varies across individuals and may depend on factors such as sufficient exposure time and attention.
A persistent giant algal virus, with a unique morphology, encodes an unprecedented number of genes involved in energy metabolism
Authors: Blanc-Mathieu Romain , Dahle Håkon , Hofgaard Antje , Brandt David , Ban Hiroki , Kalinowski Jörn , Ogata Hiroyuki , Sandaa Ruth-Anne
Published: July 2020

Viruses have long been viewed as entities possessing extremely limited metabolic capacities. Over the last decade, however, this view has been challenged, as metabolic genes have been identified in viruses possessing large genomes and virions—the synthesis of which is energetically demanding. Here, we unveil peculiar phenotypic and genomic features ofPrymnesium kappavirus RF01 (PkV RF01), a giant virus of theMimiviridaefamily. We found that this virus encodes an unprecedented number of proteins involved in energy metabolism, such as all four succinate dehydrogenase (SDH) subunits (A–D) as well as key enzymes in theβ-oxidation pathway. TheSDHAgene was transcribed upon infection, indicating that the viral SDH is actively used by the virus— potentially to modulate its host’s energy metabolism. We detected orthologousSDHAandSDHBgenes in numerous genome fragments from uncultivated marineMimiviridaeviruses, which suggests that the viral SDH is widespread in oceans. PkV RF01 was less virulent compared with other cultured prymnesioviruses, a phenomenon possibly linked to the metabolic capacity of this virus and suggestive of relatively long co-evolution with its hosts. It also has a unique morphology, compared to other characterized viruses in theMimiviridaefamily. Finally, we found that PkV RF01 is the only alga-infectingMimiviridaevirus encoding two aminoacyl-tRNA synthetases and enzymes corresponding to an entire base-excision repair pathway, as seen in heterotroph-infectingMimiviridae. TheseMimiviridaeencoded-enzymes were found to be monophyletic and branching at the root of the eukaryotic tree of life. This placement suggests that the last common ancestor ofMimiviridaewas endowed with a large, complex genome prior to the divergence of known extant eukaryotes.

Importance

Viruses on Earth are tremendously diverse in terms of morphology, functionality, and genomic composition. Over the last decade, the conceptual gap separating viruses and cellular life has tightened because of the detection of metabolic genes in viral genomes that express complex virus phenotypes upon infection. Here, we describePrymnesium kappavirus RF01, a large alga-infecting virus with a unique morphology, an atypical infection profile, and an unprecedented number of genes involved in energy metabolism (such as the tricarboxylic (TCA) cycle and theβ-oxidation pathway). Moreover, we show that the gene corresponding to one of these enzymes (the succinate dehydrogenase subunit A) is transcribed during infection and is widespread among marine viruses. This discovery provides evidence that a virus has the potential to actively regulate energy metabolism with its own gene.
Distinct dopamine circuits transmit the reinforcing and anxiogenic effects of nicotine
Authors: Nguyen C , Mondoloni S , Centeno I , Durand-de Cuttoli R , Tolu S , Valverde S , Le Borgne T , Hannesse B , Pons S , Maskos U , Dalkara D , Hardelin JP , Mourot A , Marti F , Faure P
Published: July 2020

Nicotine, the addictive component of tobacco, stimulates dopamine (DA) neurons of the ventral tegmental area (VTA) to establish and maintain reinforcement. Nicotine also induces negative emotional states such as anxiety, yet through an unknown circuitry. Here we show that nicotine at reinforcing doses drives opposite functional responses on two distinct populations of VTA DA neurons with anatomically segregated projections: it activates those that project to the nucleus accumbens (NAc) while it inhibits those that project to the amygdala nuclei (Amg). We further show that nicotine, by acting on β2 subunit-containing nicotinic acetylcholine receptors of the VTA, mediates both reinforcement and anxiety. Finally, using optogenetic experiments we dissociate the roles of the VTA-NAc excitation and VTA-Amg inhibition in reinforcement and anxiety-like behavior, respectively. We thus propose that the positive and negative behavioral outcomes of nicotine consumption involve distinct subpopulations of VTA DA neurons with opposite responses to nicotine.
Immuno-informatics Design of a Multimeric Epitope Peptide Based Vaccine Targeting SARS-CoV-2 Spike Glycoprotein
Authors: Chukwudozie Onyeka S. , Gray Clive M. , Fagbayi Tawakalt A. , Chukwuanukwu Rebecca C. , Oyebanji Victor O. , Bankole Taiwo T. , Adewole A. Richard , Daniel Eze M.
Published: July 2020

Developing an efficacious vaccine to SARS-CoV-2 infection is critical to stem COVID-19 fatalities and providing the global community with immune protection. We have used a bioinformatic approach to aid in the design of an epitope peptide-based vaccine against the spike protein of the virus. Five antigenic B cell epitopes with viable antigenicity and a total of 27 discontinuous B cell epitopes were mapped out structurally in the spike protein for antibody recognition. We identified eight CD8+T cell 9-mers along with 12 CD4+T cell 14-15-mer as promising candidate epitopes putatively restricted by a large number of MHC-I and II alleles respectively. We used this information to construct anin silicochimeric peptide vaccine whose translational rate was highly expressed when cloned in pET28a (+) vector. The vaccine construct was predicted to elicit high antigenicity and cell-mediated immunity when given as a homologous prime-boost, with triggering of toll-like receptor 5 by the adjuvant linker. The vaccine was characterized by an increase in IgM and IgG and an array of Th1 and Th2 cytokines. Uponin silicochallenge with SARS-CoV-2, there was a decrease in antigen levels using our immune simulations. We therefore propose that potential vaccine designs consider this approach.
Biomaterial encapsulation of human mesenchymal stromal cells modulates paracrine signaling response and enhances efficacy for treatment of established osteoarthritis
Authors: McKinney Jay M. , Pucha Krishna A. , Doan Thanh N. , Wang Lanfang , Weinstock Laura D. , Tignor Benjamin T. , Fowle Kelsey L. , Levit Rebecca D. , Wood Levi B. , Willett Nick J.
Published: July 2020

Mesenchymal stromal cells (MSCs) have shown promise as a treatment for osteoarthritis (OA); however, effective translation has been limited by numerous factors ranging from high variability and heterogeneity of hMSCs, to suboptimal delivery strategies, to poor understanding of critical quality and potency attributes. The objective of the current study was to assess the effects of biomaterial encapsulation in alginate microcapsules on human MSC (hMSC) secretion of immunomodulatory cytokines in an OA microenvironment and therapeutic efficacy in treating established OA. Lewis rats underwent Medial Meniscal Transection (MMT) surgery to induce OA. Three weeks post-surgery, after OA was established, rats received intra-articular injections of either encapsulated hMSCs or controls (saline, empty capsules, or non-encapsulated hMSCs). Six weeks post-surgery, microstructural changes in the knee joint were quantified using contrast enhanced microCT. Encapsulated hMSCs attenuated progression of OA including articular cartilage degeneration (swelling and cartilage loss) and subchondral bone remodeling (thickening and hardening). A multiplexed immunoassay panel (41 cytokines) was used to profile thein vitrosecretome of encapsulated and non-encapsulated hMSCs in response to IL-1□, a key cytokine involved in OA. Non-encapsulated hMSCs showed an indiscriminate increase in all cytokines in response to IL-1□ while encapsulated hMSCs showed a highly targeted secretory response with increased expression of some pro-inflammatory (IL-1β, IL-6, IL-7, IL-8), anti-inflammatory (IL-1RA), and chemotactic (G-CSF, MDC, IP10) cytokines. These data show that biomaterial encapsulation using alginate microcapsules can modulate hMSC paracrine signaling in response to OA cytokines and enhance the therapeutic efficacy of the hMSCs in treating established OA.