bluuebunny/crossref_metadata_2025 huggingface dataset:
Understanding paraxial mesoderm development and sclerotome specification for skeletal repair
Authors: Tani Shoichiro , Chung Ung-il , Ohba Shinsuke , Hojo Hironori
Published: August 2020

Pluripotent stem cells (PSCs) are attractive regenerative therapy tools for skeletal tissues. However, a deep understanding of skeletal development is required in order to model this development with PSCs, and for the application of PSCs in clinical settings. Skeletal tissues originate from three types of cell populations: the paraxial mesoderm, lateral plate mesoderm, and neural crest. The paraxial mesoderm gives rise to the sclerotome mainly through somitogenesis. In this process, key developmental processes, including initiation of the segmentation clock, formation of the determination front, and the mesenchymal–epithelial transition, are sequentially coordinated. The sclerotome further forms vertebral columns and contributes to various other tissues, such as tendons, vessels (including the dorsal aorta), and even meninges. To understand the molecular mechanisms underlying these developmental processes, extensive studies have been conducted. These studies have demonstrated that a gradient of activities involving multiple signaling pathways specify the embryonic axis and induce cell-type-specific master transcription factors in a spatiotemporal manner. Moreover, applying the knowledge of mesoderm development, researchers have attempted to recapitulate the in vivo development processes in in vitro settings, using mouse and human PSCs. In this review, we summarize the state-of-the-art understanding of mesoderm development and in vitro modeling of mesoderm development using PSCs. We also discuss future perspectives on the use of PSCs to generate skeletal tissues for basic research and clinical applications.
Angelman syndrome genotypes manifest varying degrees of clinical severity and developmental impairment
Authors: Keute Marius , Miller Meghan T. , Krishnan Michelle L. , Sadhwani Anjali , Chamberlain Stormy , Thibert Ronald L. , Tan Wen-Hann , Bird Lynne M. , Hipp Joerg F.
Published: August 2020

Angelman Syndrome (AS) is a severe neurodevelopmental disorder due to impaired expression of UBE3A in neurons. There are several genetic mechanisms that impair UBE3A expression, but they differ in how neighboring genes on chromosome 15 at 15q11–q13 are affected. There is evidence that different genetic subtypes present with different clinical severity, but a systematic quantitative investigation is lacking. Here we analyze natural history data on a large sample of individuals with AS (n = 250, 848 assessments), including clinical scales that quantify development of motor, cognitive, and language skills (Bayley Scales of Infant Development, Third Edition; Preschool Language Scale, Fourth Edition), adaptive behavior (Vineland Adaptive Behavioral Scales, Second Edition), and AS-specific symptoms (AS Clinical Severity Scale). We found that clinical severity, as captured by these scales, differs between genetic subtypes: individuals with UBE3A pathogenic variants and imprinting defects (IPD) are less affected than individuals with uniparental paternal disomy (UPD); of those with UBE3A pathogenic variants, individuals with truncating mutations are more impaired than those with missense mutations. Individuals with a deletion that encompasses UBE3A and other genes are most impaired, but in contrast to previous work, we found little evidence for an influence of deletion length (class I vs. II) on severity of manifestations. The results of this systematic analysis highlight the relevance of genomic regions beyond UBE3A as contributing factors in the AS phenotype, and provide important information for the development of new therapies for AS. More generally, this work exemplifies how increasing genetic irregularities are reflected in clinical severity.
Interpretation of psychiatric genome-wide association studies with multispecies heterogeneous functional genomic data integration
Authors: Reynolds Timothy , Johnson Emma C. , Huggett Spencer B. , Bubier Jason A. , Palmer Rohan H. C. , Agrawal Arpana , Baker Erich J. , Chesler Elissa J.
Published: August 2020

Genome-wide association studies and other discovery genetics methods provide a means to identify previously unknown biological mechanisms underlying behavioral disorders that may point to new therapeutic avenues, augment diagnostic tools, and yield a deeper understanding of the biology of psychiatric conditions. Recent advances in psychiatric genetics have been made possible through large-scale collaborative efforts. These studies have begun to unearth many novel genetic variants associated with psychiatric disorders and behavioral traits in human populations. Significant challenges remain in characterizing the resulting disease-associated genetic variants and prioritizing functional follow-up to make them useful for mechanistic understanding and development of therapeutics. Model organism research has generated extensive genomic data that can provide insight into the neurobiological mechanisms of variant action, but a cohesive effort must be made to establish which aspects of the biological modulation of behavioral traits are evolutionarily conserved across species. Scalable computing, new data integration strategies, and advanced analysis methods outlined in this review provide a framework to efficiently harness model organism data in support of clinically relevant psychiatric phenotypes.
Empirical validation of a touchscreen probabilistic reward task in rats
Authors: Kangas Brian D. , Wooldridge Lisa M. , Luc Oanh T. , Bergman Jack , Pizzagalli Diego A.
Published: August 2020

Anhedonia, the loss of pleasure from previously rewarding activities, is implicated in several neuropsychiatric conditions, including major depressive disorder (MDD). In order to accelerate drug development for mood disorders, quantitative approaches are needed to objectively measure responsiveness to reward as a means to identify deficits. One such approach, the probabilistic reward task (PRT), uses visual discrimination methodology to quantify reward learning. In this computerized task, humans make visual discriminations, and probabilistic contingencies are arranged such that correct responses to one alternative are rewarded more often (rich) than correct responses to the other (lean). Healthy participants consistently develop a response bias in favor of the rich alternative. However, participants with MDD typically exhibit lower response biases, and this blunting correlates with current and future anhedonia. The present studies validated a touchscreen-based PRT in rodents with formal and functional similarity to the human task. First, rats were trained to discriminate between two lines that differed in length. Next, parametric manipulations of probabilistic contingencies, line-length stimuli, and drug treatment (amphetamine, 0.32–3.2 mg/kg; scopolamine, 0.1–1.0 mg/kg; oxycodone, 0.1–1.0 mg/kg) on response bias were evaluated. Results demonstrated orderly shifts in bias and discriminability that varied as a function of, respectively, the asymmetry of rich/lean probabilities and disparity in line lengths. Drugs that enhance reward responsiveness (amphetamine and scopolamine, but not oxycodone) increased bias, verifying pharmacological task sensitivity. Finally, performance outcomes under optimized conditions were replicated in female rats. Collectively, the touchscreen-based rodent PRT appears to have high preclinical value as a quantitative assay of reward learning.
Mex3a interacts with LAMA2 to promote lung adenocarcinoma metastasis via PI3K/AKT pathway
Authors: Liang Jinghui , Li Haixia , Han Jingyi , Jiang Jin , Wang Jiang , Li Yongmeng , Feng Zitong , Zhao Renchang , Sun Zhenguo , Lv Bin , Tian Hui
Published: August 2020

Lung adenocarcinoma (LUAD) is the main subtype of lung cancer. In this study, we found that RBP Mex3a was significantly upregulated in LUAD tissues and elevated Mex3a expression was associated with poor LUAD prognosis and metastasis. Furthermore, we demonstrated that Mex3a knockdown significantly inhibited LUAD cell migration and invasion in vitro and metastasis in nude mice. Transcriptome sequencing indicated that Mex3a affected gene expression linked to ECM-receptor interactions, including laminin subunit alpha 2(LAMA2). RNA immunoprecipitation (RIP) assay revealed Mex3a directly bound to LAMA2 mRNA and Mex3a increased the instability of LAMA2 mRNA in LUAD cells. Furthermore, we discovered that LAMA2 was surprisingly downregulated in LUAD and inhibited LUAD metastasis. LAMA2 knockdown partially reverse the decrease of cell migration and invasion caused by Mex3a knockdown. In addition, we found that both Mex3a and LAMA2 could influence PI3K-AKT pathway, which are downstream effectors of the ECM-receptor pathway. Moreover, the reduced activation of PI3K-AKT pathway in caused by Mex3a depletion was rescued by LAMA2 knockdown. In conclusion, we demonstrated that Mex3a downregulates LAMA2 expression to exert a prometastatic role in LUAD. Our study revealed the prognostic and prometastatic effects of Mex3a in LUAD, suggesting that Mex3a can serve as a prognostic biomarker and a target for metastatic therapy.
Isoform specific FBXW7 mediates NOTCH1 Abruptex mutation C1133Y deregulation in oral squamous cell carcinoma
Authors: Zheng Yang , Song An , Wang Chundi , Zhang Wei , Liang Dong , Ding Xu , Li Gang , Zhang Hongchuang , Zhang Wei , Du Yifei , Zhou Junbo , Wu Heming , Wu Yunong , Song Xiaomeng
Published: August 2020

Our group previously identified that the NOTCH1 Abruptex domain contains the most mutations in Chinese OSCC patients, including a hotspot mutation (C1133Y). FBXW7 is an E3 ubiquitin ligase that regulates a network of proteins, including NOTCH1, via degradation. In this study, we first described the co-localization of isoform specific FBXW7-FBXW7β and NOTCH1C1133Y mutation in the same cytoplasmic sites. Gain- and loss-of-function assays were performed to examine the tumor suppressor role of FBXW7β in the proliferation and invasion of OSCC cells. The co-expression of NOTCH1C1133Y and FBXW7β significantly attenuated tumor growth. Meanwhile, FBXW7β reversed the oncogenic phenotype and the activation of the AKT/ERK/NFκB pathway induced by NOTCH1C1133Y mutation. FBXW7β downregulated the stability of NOTCH1C1133Y protein and promoted protein ubiquitination. This was the first time that we selected a NOTCH1 hotspot mutation detected in clinical samples and identified the function of FBXW7β that mediated NOTCH1 mutation degradation in OSCC. The newly identified interaction between FBXW7β and NOTCH1C1133Y protein provides new insights into the progression of OSCC, especially regarding Abruptex domain mutations, and represents a valuable target for OSCC therapy.
PLK1 inhibition exhibits strong anti-tumoral activity in CCND1-driven breast cancer metastases with acquired palbociclib resistance
Authors: Montaudon Elodie , Nikitorowicz-Buniak Joanna , Sourd Laura , Morisset Ludivine , El Botty Rania , Huguet Léa , Dahmani Ahmed , Painsec Pierre , Nemati Fariba , Vacher Sophie , Chemlali Walid , Masliah-Planchon Julien , Château-Joubert Sophie , Rega Camilla , Leal Mariana Ferreira , Simigdala Nikiana , Pancholi Sunil , Ribas Ricardo , Nicolas André , Meseure Didier , Vincent-Salomon Anne , Reyes Cécile , Rapinat Audrey , Gentien David , Larcher Thibaut , Bohec Mylène , Baulande Sylvain , Bernard Virginie , Decaudin Didier , Coussy Florence , Le Romancer Muriel , Dutertre Guillaume , Tariq Zakia , Cottu Paul , Driouch Keltouma , Bièche Ivan , Martin Lesley-Ann , Marangoni Elisabetta
Published: August 2020

A significant proportion of patients with oestrogen receptor (ER) positive breast cancers (BC) develop resistance to endocrine treatments (ET) and relapse with metastatic disease. Here we perform whole exome sequencing and gene expression analysis of matched primary breast tumours and bone metastasis-derived patient-derived xenografts (PDX). Transcriptomic analyses reveal enrichment of the G2/M checkpoint and up-regulation of Polo-like kinase 1 (PLK1) in PDX. PLK1 inhibition results in tumour shrinkage in highly proliferating CCND1-driven PDX, including different RB-positive PDX with acquired palbociclib resistance. Mechanistic studies in endocrine resistant cell lines, suggest an ER-independent function of PLK1 in regulating cell proliferation. Finally, in two independent clinical cohorts of ER positive BC, we find a strong association between high expression of PLK1 and a shorter metastases-free survival and poor response to anastrozole. In conclusion, our findings support clinical development of PLK1 inhibitors in patients with advanced CCND1-driven BC, including patients progressing on palbociclib treatment.
Engineering regulatory networks for complex phenotypes in E. coli
Authors: Liu Rongming , Liang Liya , Freed Emily F. , Choudhury Alaksh , Eckert Carrie A. , Gill Ryan T.
Published: August 2020

Regulatory networks describe the hierarchical relationship between transcription factors, associated proteins, and their target genes. Regulatory networks respond to environmental and genetic perturbations by reprogramming cellular metabolism. Here we design, construct, and map a comprehensive regulatory network library containing 110,120 specific mutations in 82 regulators expected to perturb metabolism. We screen the library for different targeted phenotypes, and identify mutants that confer strong resistance to various inhibitors, and/or enhanced production of target compounds. These improvements are identified in a single round of selection, showing that the regulatory network library is universally applicable and is convenient and effective for engineering targeted phenotypes. The facile construction and mapping of the regulatory network library provides a path for developing a more detailed understanding of global regulation in E. coli, with potential for adaptation and use in less-understood organisms, expanding toolkits for future strain engineering, synthetic biology, and broader efforts.
Engineering designer beta cells with a CRISPR-Cas9 conjugation platform
Authors: Lim Donghyun , Sreekanth Vedagopuram , Cox Kurt J. , Law Benjamin K. , Wagner Bridget K. , Karp Jeffrey M. , Choudhary Amit
Published: August 2020

Genetically fusing protein domains to Cas9 has yielded several transformative technologies; however, the genetic modifications are limited to natural polypeptide chains at the Cas9 termini, which excludes a diverse array of molecules useful for gene editing. Here, we report chemical modifications that allow site-specific and multiple-site conjugation of a wide assortment of molecules on both the termini and internal sites of Cas9, creating a platform for endowing Cas9 with diverse functions. Using this platform, Cas9 can be modified to more precisely incorporate exogenously supplied single-stranded oligonucleotide donor (ssODN) at the DNA break site. We demonstrate that the multiple-site conjugation of ssODN to Cas9 significantly increases the efficiency of precision genome editing, and such a platform is compatible with ssODNs of diverse lengths. By leveraging the conjugation platform, we successfully engineer INS-1E, a β-cell line, to repurpose the insulin secretion machinery, which enables the glucose-dependent secretion of protective immunomodulatory factor interleukin-10.
Clearance of HIV infection by selective elimination of host cells capable of producing HIV
Authors: Li Min , Liu Wei , Bauch Tonya , Graviss Edward A. , Arduino Roberto C. , Kimata Jason T. , Chen Min , Wang Jin
Published: August 2020

The RNA genome of the human immunodeficiency virus (HIV) is reverse-transcribed into DNA and integrated into the host genome, resulting in latent infections that are difficult to clear. Here we show an approach to eradicate HIV infections by selective elimination of host cells harboring replication-competent HIV (SECH), which includes viral reactivation, induction of cell death, inhibition of autophagy and the blocking of new infections. Viral reactivation triggers cell death specifically in HIV-1-infected T cells, which is promoted by agents that induce apoptosis and inhibit autophagy. SECH treatments can clear HIV-1 in >50% mice reconstituted with a human immune system, as demonstrated by the lack of viral rebound after withdrawal of treatments, and by adoptive transfer of treated lymphocytes into uninfected humanized mice. Moreover, SECH clears HIV-1 in blood samples from HIV-1-infected patients. Our results suggest a strategy to eradicate HIV infections by selectively eliminating host cells capable of producing HIV.
Optogenetic control of protein binding using light-switchable nanobodies
Authors: Gil Agnieszka A. , Carrasco-López César , Zhu Liyuan , Zhao Evan M. , Ravindran Pavithran T. , Wilson Maxwell Z. , Goglia Alexander G. , Avalos José L. , Toettcher Jared E.
Published: August 2020

A growing number of optogenetic tools have been developed to reversibly control binding between two engineered protein domains. In contrast, relatively few tools confer light-switchable binding to a generic target protein of interest. Such a capability would offer substantial advantages, enabling photoswitchable binding to endogenous target proteins in cells or light-based protein purification in vitro. Here, we report the development of opto-nanobodies (OptoNBs), a versatile class of chimeric photoswitchable proteins whose binding to proteins of interest can be enhanced or inhibited upon blue light illumination. We find that OptoNBs are suitable for a range of applications including reversibly binding to endogenous intracellular targets, modulating signaling pathway activity, and controlling binding to purified protein targets in vitro. This work represents a step towards programmable photoswitchable regulation of a wide variety of target proteins.
Brain-inspired replay for continual learning with artificial neural networks
Authors: van de Ven Gido M. , Siegelmann Hava T. , Tolias Andreas S.
Published: August 2020

Artificial neural networks suffer from catastrophic forgetting. Unlike humans, when these networks are trained on something new, they rapidly forget what was learned before. In the brain, a mechanism thought to be important for protecting memories is the reactivation of neuronal activity patterns representing those memories. In artificial neural networks, such memory replay can be implemented as ‘generative replay’, which can successfully – and surprisingly efficiently – prevent catastrophic forgetting on toy examples even in a class-incremental learning scenario. However, scaling up generative replay to complicated problems with many tasks or complex inputs is challenging. We propose a new, brain-inspired variant of replay in which internal or hidden representations are replayed that are generated by the network’s own, context-modulated feedback connections. Our method achieves state-of-the-art performance on challenging continual learning benchmarks (e.g., class-incremental learning on CIFAR-100) without storing data, and it provides a novel model for replay in the brain.
Autophagy regulates fatty acid availability for oxidative phosphorylation through mitochondria-endoplasmic reticulum contact sites
Authors: Bosc Claudie , Broin Nicolas , Fanjul Marjorie , Saland Estelle , Farge Thomas , Courdy Charly , Batut Aurélie , Masoud Rawand , Larrue Clément , Skuli Sarah , Espagnolle Nicolas , Pagès Jean-Christophe , Carrier Alice , Bost Frédéric , Bertrand-Michel Justine , Tamburini Jérôme , Récher Christian , Bertoli Sarah , Mansat-De Mas Véronique , Manenti Stéphane , Sarry Jean-Emmanuel , Joffre Carine
Published: August 2020

Autophagy has been associated with oncogenesis with one of its emerging key functions being its contribution to the metabolism of tumors. Therefore, deciphering the mechanisms of how autophagy supports tumor cell metabolism is essential. Here, we demonstrate that the inhibition of autophagy induces an accumulation of lipid droplets (LD) due to a decrease in fatty acid β-oxidation, that leads to a reduction of oxidative phosphorylation (OxPHOS) in acute myeloid leukemia (AML), but not in normal cells. Thus, the autophagic process participates in lipid catabolism that supports OxPHOS in AML cells. Interestingly, the inhibition of OxPHOS leads to LD accumulation with the concomitant inhibition of autophagy. Mechanistically, we show that the disruption of mitochondria–endoplasmic reticulum (ER) contact sites (MERCs) phenocopies OxPHOS inhibition. Altogether, our data establish that mitochondria, through the regulation of MERCs, controls autophagy that, in turn finely tunes lipid degradation to fuel OxPHOS supporting proliferation and growth in leukemia.
Genome-wide specificity of dCpf1 cytidine base editors
Authors: Kim Daesik , Lim Kayeong , Kim Da-eun , Kim Jin-Soo
Published: August 2020

Cpf1-linked base editors broaden the targeting scope of programmable cytidine deaminases by recognizing thymidine-rich protospacer-adjacent motifs (PAM) without inducing DNA double-strand breaks (DSBs). Here we present an unbiased in vitro method for identifying genome-wide off-target sites of Cpf1 base editors via whole genome sequencing. First, we treat human genomic DNA with dLbCpf1-BE ribonucleoprotein (RNP) complexes, which convert C-to-U at on-target and off-target sites and, then, with a mixture of E. coli uracil DNA glycosylase (UDG) and DNA glycosylase-lyase Endonuclease VIII, which removes uracil and produces single-strand breaks (SSBs) in vitro. Whole-genome sequencing of the resulting digested genome (Digenome-seq) reveals that, on average, dLbCpf1-BE induces 12 SSBs in vitro per crRNA in the human genome. Off-target sites with an editing frequency as low as 0.1% are successfully identified by this modified Digenome-seq method, demonstrating its high sensitivity. dLbCpf1-BEs and LbCpf1 nucleases often recognize different off-target sites, calling for independent analysis of each tool.
Single-trial cross-area neural population dynamics during long-term skill learning
Authors: Veuthey T. L. , Derosier K. , Kondapavulur S. , Ganguly K.
Published: August 2020

Mammalian cortex has both local and cross-area connections, suggesting vital roles for both local and cross-area neural population dynamics in cortically-dependent tasks, like movement learning. Prior studies of movement learning have focused on how single-area population dynamics change during short-term adaptation. It is unclear how cross-area dynamics contribute to movement learning, particularly long-term learning and skill acquisition. Using simultaneous recordings of rodent motor (M1) and premotor (M2) cortex and computational methods, we show how cross-area activity patterns evolve during reach-to-grasp learning in rats. The emergence of reach-related modulation in cross-area activity correlates with skill acquisition, and single-trial modulation in cross-area activity predicts reaction time and reach duration. Local M2 neural activity precedes local M1 activity, supporting top–down hierarchy between the regions. M2 inactivation preferentially affects cross-area dynamics and behavior, with minimal disruption of local M1 dynamics. Together, these results indicate that cross-area population dynamics are necessary for learned motor skills.
A hidden gene in astroviruses encodes a viroporin
Authors: Lulla Valeria , Firth Andrew E.
Published: August 2020

Human astroviruses are small non-enveloped viruses with positive-sense single-stranded RNA genomes. Astroviruses cause acute gastroenteritis in children worldwide and have been associated with encephalitis and meningitis in immunocompromised individuals. It is still unknown how astrovirus particles exit infected cells following replication. Through comparative genomic analysis and ribosome profiling we here identify and confirm the expression of a conserved alternative-frame ORF, encoding the protein XP. XP-knockout astroviruses are attenuated and pseudo-revert on passaging. Further investigation into the function of XP revealed plasma and trans Golgi network membrane-associated roles in virus assembly and/or release through a viroporin-like activity. XP-knockout replicons have only a minor replication defect, demonstrating the role of XP at late stages of infection. The discovery of XP advances our knowledge of these important human viruses and opens an additional direction of research into their life cycle and pathogenesis.
FGF2 alters macrophage polarization, tumour immunity and growth and can be targeted during radiotherapy
Authors: Im Jae Hong , Buzzelli Jon N. , Jones Keaton , Franchini Fanny , Gordon-Weeks Alex , Markelc Bostjan , Chen Jianzhou , Kim Jin , Cao Yunhong , Muschel Ruth J.
Published: August 2020

Regulation of the programming of tumour-associated macrophages (TAMs) controls tumour growth and anti-tumour immunity. We examined the role of FGF2 in that regulation. Tumours in mice genetically deficient in low-molecular weight FGF2 (FGF2LMW) regress dependent on T cells. Yet, TAMS not T cells express FGF receptors. Bone marrow derived-macrophages from Fgf2LMW−/− mice co-injected with cancer cells reduce tumour growth and express more inflammatory cytokines. FGF2 is induced in the tumour microenvironment following fractionated radiation in murine tumours consistent with clinical reports. Combination treatment of in vivo tumours with fractionated radiation and a blocking antibody to FGF2 prolongs tumour growth delay, increases long-term survival and leads to a higher iNOS+/CD206+ TAM ratio compared to irradiation alone. These studies show for the first time that FGF2 affects macrophage programming and is a critical regulator of immunity in the tumour microenvironment.
Identification of modified peptides using localization-aware open search
Authors: Yu Fengchao , Teo Guo Ci , Kong Andy T. , Haynes Sarah E. , Avtonomov Dmitry M. , Geiszler Daniel J. , Nesvizhskii Alexey I.
Published: August 2020

Identification of post-translationally or chemically modified peptides in mass spectrometry-based proteomics experiments is a crucial yet challenging task. We have recently introduced a fragment ion indexing method and the MSFragger search engine to empower an open search strategy for comprehensive analysis of modified peptides. However, this strategy does not consider fragment ions shifted by unknown modifications, preventing modification localization and limiting the sensitivity of the search. Here we present a localization-aware open search method, in which both modification-containing (shifted) and regular fragment ions are indexed and used in scoring. We also implement a fast mass calibration and optimization method, allowing optimization of the mass tolerances and other key search parameters. We demonstrate that MSFragger with mass calibration and localization-aware open search identifies modified peptides with significantly higher sensitivity and accuracy. Comparing MSFragger to other modification-focused tools (pFind3, MetaMorpheus, and TagGraph) shows that MSFragger remains an excellent option for fast, comprehensive, and sensitive searches for modified peptides in shotgun proteomics data.
Face mask use in the general population and optimal resource allocation during the COVID-19 pandemic
Authors: Worby Colin J. , Chang Hsiao-Han
Published: August 2020

The ongoing novel coronavirus disease (COVID-19) pandemic has already infected millions worldwide and, with no vaccine available, interventions to mitigate transmission are urgently needed. While there is broad agreement that travel restrictions and social distancing are beneficial in limiting spread, recommendations around face mask use are inconsistent. Here, we use mathematical modeling to examine the epidemiological impact of face masks, considering resource limitations and a range of supply and demand dynamics. Even with a limited protective effect, face masks can reduce total infections and deaths, and can delay the peak time of the epidemic. However, random distribution of masks is generally suboptimal; prioritized coverage of the elderly improves outcomes, while retaining resources for detected cases provides further mitigation under a range of scenarios. Face mask use, particularly for a pathogen with relatively common asymptomatic carriage, is an effective intervention strategy, while optimized distribution is important when resources are limited.
Dscam1 establishes the columnar units through lineage-dependent repulsion between sister neurons in the fly brain
Authors: Liu Chuyan , Trush Olena , Han Xujun , Wang Miaoxing , Takayama Rie , Yasugi Tetsuo , Hayashi Takashi , Sato Makoto
Published: August 2020

The brain is organized morphologically and functionally into a columnar structure. According to the radial unit hypothesis, neurons from the same lineage form a radial unit that contributes to column formation. However, the molecular mechanisms that link neuronal lineage and column formation remain elusive. Here, we show that neurons from the same lineage project to different columns under control of Down syndrome cell adhesion molecule (Dscam) in the fly brain. Dscam1 is temporally expressed in newly born neuroblasts and is inherited by their daughter neurons. The transient transcription of Dscam1 in neuroblasts enables the expression of the same Dscam1 splice isoform within cells of the same lineage, causing lineage-dependent repulsion. In the absence of Dscam1 function, neurons from the same lineage project to the same column. When the splice diversity of Dscam1 is reduced, column formation is significantly compromised. Thus, Dscam1 controls column formation through lineage-dependent repulsion.
ACDC, a global database of amphibian cytochrome-b sequences using reproducible curation for GenBank records
Authors: van den Burg Matthijs P. , Herrando-Pérez Salvador , Vieites David R.
Published: August 2020

Genetic data are a crucial and exponentially growing resource across all biological sciences, yet curated databases are scarce. The widespread occurrence of sequence and (meta)data errors in public repositories calls for comprehensive improvements of curation protocols leading to robust research and downstream analyses. We collated and curated all available GenBank cytochrome-b sequences for amphibians, a benchmark marker in this globally declining vertebrate clade. The Amphibia’s Curated Database of Cytochrome-b (ACDC) consists of 36,514 sequences representing 2,309 species from 398 genera (median = 2 with 50% interquartile ranges of 1–7 species/genus). We updated the taxonomic identity of >4,800 sequences (ca. 13%) and found 2,359 (6%) conflicting sequences with 84% of the errors originating from taxonomic misidentifications. The database (accessible athttps://doi.org/10.6084/m9.figshare.9944759) also includes anRscript to replicate our study for other loci and taxonomic groups. We provide recommendations to improve genetic-data quality in public repositories and flag species for which there is a need for taxonomic refinement in the face of increased rate of amphibian extinctions in the Anthropocene.
Impact of low-intensity pulsed ultrasound on transcription and metabolite compositions in proliferation and functionalization of human adipose-derived mesenchymal stromal cells
Authors: Huang Denggao , Gao Yuanhui , Wang Shunlan , Zhang Wei , Cao Hui , Zheng Linlin , Chen Yang , Zhang Shufang , Chen Jie
Published: August 2020

To investigate the effect of low-intensity pulsed ultrasound (LIPUS) on the proliferation of human adipose-derived mesenchymal stromal cells (hASCs) and uncovered its stimulation mechanism. LIPUS at 30 mW/cm2 was applied for 5 min/day to promote the proliferation of hASCs. Flow cytometry was used to study the cell surface markers, cell cycle, and apoptosis of hASCs. The proliferation of hASCs was detected by cell counting kit-8, cell cycle assay, and RT-PCR. The expression of hASCs cytokines was determined by ELISA. The differences between transcriptional genes and metabolites were analyzed by transcript analysis and metabolomic profiling experiments. The number of cells increased after LIPUS stimulation, but there was no significant difference in cell surface markers. The results of flow cytometry, RT-PCR, and ELISA after LIPUS was administered showed that the G1 and S phases of the cell cycle were prolonged. The expression of cell proliferation related genes (CyclinD1 and c-myc) and the paracrine function related gene (SDF-1α) were up-regulated. The expression of cytokines was increased, while the apoptosis rate was decreased. The results of transcriptome experiments showed that there were significant differences in 27 genes;15 genes were up-regulated, while 12 genes were down-regulated. The results of metabolomics experiments showed significant differences in 30 metabolites; 7 metabolites were up-regulated, and 23 metabolites were down-regulated. LIPUS at 30 mW/cm2 intensity can promote the proliferation of hASCs cells in an undifferentiating state, and the stem-cell property of hASCs was maintained. CyclinD1 gene, c-myc gene, and various genes of transcription and products of metabolism play an essential role in cell proliferation. This study provides an important experimental and theoretical basis for the clinical application of LIPUS in promoting the proliferation of hASCs cells.
Time-dependent branching processes: a model of oscillating neuronal avalanches
Authors: Pausch Johannes , Garcia-Millan Rosalba , Pruessner Gunnar
Published: August 2020

Recently, neuronal avalanches have been observed to display oscillations, a phenomenon regarded as the co-existence of a scale-free behaviour (the avalanches close to criticality) and scale-dependent dynamics (the oscillations). Ordinary continuous-time branching processes with constant extinction and branching rates are commonly used as models of neuronal activity, yet they lack any such time-dependence. In the present work, we extend a basic branching process by allowing the extinction rate to oscillate in time as a new model to describe cortical dynamics. By means of a perturbative field theory, we derive relevant observables in closed form. We support our findings by quantitative comparison to numerics and qualitative comparison to available experimental results.
Autophagy is a pro-survival adaptive response to heat shock in bovine cumulus-oocyte complexes
Authors: Latorraca Lais B. , Feitosa Weber B. , Mariano Camila , Moura Marcelo T. , Fontes Patrícia K. , Nogueira Marcelo F. G. , Paula-Lopes Fabíola F.
Published: August 2020

Autophagy is a physiological mechanism that can be activated under stress conditions. However, the role of autophagy during oocyte maturation has been poorly investigated. Therefore, this study characterized the role of autophagy on developmental competence and gene expression of bovine oocytes exposed to heat shock (HS). Cumulus-oocyte-complexes (COCs) were matured at Control (38.5 °C) and HS (41 °C) temperatures in the presence of 0 and 10 mM 3-methyladenine (3MA; autophagy inhibitor). Western blotting analysis revealed that HS increased autophagy marker LC3-II/LC3-I ratio in oocytes. However, there was no effect of temperature for oocytes matured with 3MA. On cumulus cells, 3MA reduced LC3-II/LC3-I ratio regardless of temperature. Inhibition of autophagy during IVM of heat-shocked oocytes (3MA-41 °C) reduced cleavage and blastocyst rates compared to standard in vitro matured heat-shocked oocytes (IVM-41 °C). Therefore, the magnitude of HS detrimental effects was greater in the presence of autophagy inhibitor. Oocyte maturation under 3MA-41 °C reduced mRNA abundance for genes related to energy metabolism (MTIF3), heat shock response (HSF1), and oocyte maturation (HAS2 and GREM1). In conclusion, autophagy is a stress response induced on heat shocked oocytes. Inhibition of autophagy modulated key functional processes rendering the oocyte more susceptible to the deleterious effects of heat shock.
Mycoplasma hyopneumoniae J elicits an antioxidant response and decreases the expression of ciliary genes in infected swine epithelial cells
Authors: Mucha Scheila G. , Ferrarini Mariana G. , Moraga Carol , Di Genova Alex , Guyon Laurent , Tardy Florence , Rome Sophie , Sagot Marie-France , Zaha Arnaldo
Published: August 2020

Mycoplasma hyopneumoniaeis the most costly pathogen for swine production. Although several studies have focused on the host-bacterium association, little is known about the changes in gene expression of swine cells upon infection. To improve our understanding of this interaction, we infected swine epithelial NPTr cells withM. hyopneumoniaestrain J to identify differentially expressed mRNAs and miRNAs. The levels of 1,268 genes and 170 miRNAs were significantly modified post-infection. Up-regulated mRNAs were enriched in genes related to redox homeostasis and antioxidant defense, known to be regulated by the transcription factor NRF2 in related species. Down-regulated mRNAs were enriched in genes associated with cytoskeleton and ciliary functions. Bioinformatic analyses suggested a correlation between changes in miRNA and mRNA levels, since we detected down-regulation of miRNAs predicted to target antioxidant genes and up-regulation of miRNAs targeting ciliary and cytoskeleton genes. Interestingly, most down-regulated miRNAs were detected in exosome-like vesicles suggesting thatM. hyopneumoniaeinfection induced a modification of the composition of NPTr-released vesicles. Taken together, our data indicate thatM. hyopneumoniaeelicits an antioxidant response induced by NRF2 in infected cells. In addition, we propose that ciliostasis caused by this pathogen is partially explained by the down-regulation of ciliary genes.
Comprehensive retinal vascular measurements: a novel association with renal function in type 2 diabetic patients in China
Authors: Xu Xiayu , Sun Fei , Wang Qiong , Zhang Maiye , Ding Wenxiang , Yang Aili , Gao Bin
Published: August 2020

To examine the association between various retinal vascular measurements and microalbuminuria in patients with type 2 diabetes in a northwestern China study. Data from 911 patients with type 2 diabetes were analyzed. Novel retinal vascular measurements from the whole vascular tree were extracted using a validated fully automatic computer program. Retinal vascular measurements were analyzed continuously and categorically for associations with microalbuminuria using multiple logistic regressions, adjusted for related variables. In logistic regression adjusting for multiple variables, microalbuminuria was associated with smaller peripheral arteriolar caliber, larger peripheral venular caliber, larger arteriolar tortuosity, and smaller arteriolar fractal dimension (p = 0.028, p < 0.001, p = 0.038, p = 0.035, respectively). In further categorical analyses, microalbuminuria was related to smaller peripheral arteriolar caliber [T1 vs. T3: odds ratio (OR) 2.029; 95% confidence interval (CI) 1.186–3.473], larger peripheral venular caliber (T1 vs. T3: OR 0.609; 95% CI 0.362–1.024), and smaller arteriolar fractal dimension (T1 vs. T3: OR 1.659; 95% CI 1.028–2.675). Microalbuminuria in type 2 diabetes is associated with both retinal vascular caliber and geometry. These noninvasive vascular measurements serve as potential preclinical markers to identify populations at high risk of early kidney disease in the course of diabetes.
Effect of cereal fermentation and carbohydrase supplementation on growth, nutrient digestibility and intestinal microbiota in liquid-fed grow-finishing pigs
Authors: Torres-Pitarch Alberto , Gardiner Gillian E. , Cormican Paul , Rea Mary , Crispie Fiona , O’Doherty John V. , Cozannet Pierre , Ryan Tomas , Cullen James , Lawlor Peadar G.
Published: August 2020

This study aimed to determine the impact of fermenting the cereal fraction of the diet (Cferm) and enzyme supplementation (ENZ) on the bacterial composition of the feed, nutrient digestibility, pig growth, feed efficiency (FE), intestinal volatile fatty acid (VFA) concentrations and intestinal microbiota composition. A total of 252 grow-finisher pigs (~ 40.4 kg; 7 pigs/pen) were randomly allocated to 4 diets in a 2 × 2 factorial arrangement for 55d. The diets were: (1) fresh liquid feed (Fresh); (2) Cferm liquid feed (Ferm); (3) Fresh + ENZ and (4) Ferm + ENZ. Cferm increased total tract nutrient digestibility, reduced caecal butyrate and propionate concentrations, and increased average daily gain (ADG). ENZ increased ileal and total tract nutrient digestibility, reduced caecal isobutyrate and propionate concentrations, and improved FE. Bacterial taxa positively correlated with pig growth (Lactobacillus kisonensis in the ileum and Roseburia faecis in the caecum) were more abundant in pigs fed ENZ diets, whereas most of the ileal bacterial taxa negatively correlated with growth (Megasphaera, Bifidobacterium and Streptococcus) had lower abundance in pigs fed Cferm diets. In conclusion, Cferm increased ADG and ENZ improved FE, with these improvements possibly mediated by increased nutrient digestibility, and beneficial modulation of the intestinal microbiota.
Electrical antimicrobial susceptibility testing based on aptamer-functionalized capacitance sensor array for clinical isolates
Authors: Lee Kyo-Seok , Lee Sun-Mi , Oh Jeseung , Park In Ho , Song Jun Ho , Han Myeonggil , Yong Dongeun , Lim Kook Jin , Shin Jeon-Soo , Yoo Kyung-Hwa
Published: August 2020

To prescribe effective antibiotics to patients with bacterial infections in a timely manner and to avoid the misuse of antibiotics, a rapid antimicrobial susceptibility test (AST) is essential. However, conventional AST methods require more than 16 h to provide results; thus, we developed an electrical AST (e-AST) system, which provides results within 6 h. The proposed e-AST is based on an array of 60 aptamer-functionalized capacitance sensors that are comparable to currently available AST panels and a pattern-matching algorithm. The performance of the e-AST was evaluated in comparison with that of broth microdilution as the reference test for clinical strains isolated from septic patients. A total of 4,554 tests using e-AST showed a categorical agreement of 97% with a minor error of 2.2%, major error of 0.38%, and very major error of 0.38%. We expect that the proposed e-AST could potentially aid antimicrobial stewardship efforts and lead to improved patient outcomes.
Deletion of DJ-1 in rats affects protein abundance and mitochondrial function at the synapse
Authors: Almikhlafi Mohannad A. , Stauch Kelly L. , Villeneuve Lance M. , Purnell Phillip R. , Lamberty Benjamin G. , Fox Howard S.
Published: August 2020

DJ-1 is a multifunctional protein affecting different biological and cellular processes. In addition, DJ-1 has roles in regulating mitochondrial function. Loss-of-function mutations in DJ-1 were found to cause an autosomal recessive form of Parkinson’s disease. One of the main pathological features of PD is loss of dopamine neurons in the nigrostriatal pathway. DJ-1 knockout (KO) rats exhibit progressive nigral neurodegeneration with about 50% dopaminergic cell loss at 8 months of age. In order to assess the effects of DJ-1 deficiency on neuronal mitochondria prior to neuron loss, we performed proteomic analysis of synaptic mitochondria isolated from the striatum, the location of nigrostriatal pathway nerve terminals, of 3-month-old DJ-1 KO rats. In total, 371 mitochondrial proteins were quantified, and of these 76 were differentially expressed in DJ-1 KO rats. Proteins perturbed by the loss of DJ-1 were involved in several mitochondrial functional pathways, including the tricarboxylic acid cycle and electron transport chain. Thus, synaptic mitochondrial respiration was measured and showed a significant change due to DJ-1 deficiency. The dataset generated here highlights the role of synaptic mitochondria in PD associated with DJ-1. This study improves our understanding of DJ-1 effects in a complex tissue environment and the synaptic mitochondrial changes that accompany its loss.
New AMS 14C dates track the arrival and spread of broomcorn millet cultivation and agricultural change in prehistoric Europe
Authors: Filipović Dragana , Meadows John , Corso Marta Dal , Kirleis Wiebke , Alsleben Almuth , Akeret Örni , Bittmann Felix , Bosi Giovanna , Ciută Beatrice , Dreslerová Dagmar , Effenberger Henrike , Gyulai Ferenc , Heiss Andreas G. , Hellmund Monika , Jahns Susanne , Jakobitsch Thorsten , Kapcia Magda , Klooß Stefanie , Kohler-Schneider Marianne , Kroll Helmut , Makarowicz Przemysław , Marinova Elena , Märkle Tanja , Medović Aleksandar , Mercuri Anna Maria , Mueller-Bieniek Aldona , Nisbet Renato , Pashkevich Galina , Perego Renata , Pokorný Petr , Pospieszny Łukasz , Przybyła Marcin , Reed Kelly , Rennwanz Joanna , Stika Hans-Peter , Stobbe Astrid , Tolar Tjaša , Wasylikowa Krystyna , Wiethold Julian , Zerl Tanja
Published: August 2020

Broomcorn millet (Panicum miliaceum L.) is not one of the founder crops domesticated in Southwest Asia in the early Holocene, but was domesticated in northeast China by 6000 bc. In Europe, millet was reported in Early Neolithic contexts formed by 6000 bc, but recent radiocarbon dating of a dozen 'early' grains cast doubt on these claims. Archaeobotanical evidence reveals that millet was common in Europe from the 2nd millennium bc, when major societal and economic transformations took place in the Bronze Age. We conducted an extensive programme of AMS-dating of charred broomcorn millet grains from 75 prehistoric sites in Europe. Our Bayesian model reveals that millet cultivation began in Europe at the earliest during the sixteenth century bc, and spread rapidly during the fifteenth/fourteenth centuries bc. Broomcorn millet succeeds in exceptionally wide range of growing conditions and completes its lifecycle in less than three summer months. Offering an additional harvest and thus surplus food/fodder, it likely was a transformative innovation in European prehistoric agriculture previously based mainly on (winter) cropping of wheat and barley. We provide a new, high-resolution chronological framework for this key agricultural development that likely contributed to far-reaching changes in lifestyle in late 2nd millennium bc Europe.
Permalloy nanowires/graphene oxide composite with enhanced conductive properties
Authors: Arciniegas Jaimes Diana M. , Márquez Paulina , Ovalle Alexandra , Escrig Juan , Linarez Pérez Omar , Bajales Noelia
Published: August 2020

Carbon–metal-based composites arise as advanced materials in the frontiers with nanotechnology, since the properties inherent to each component are multiplexed into a new material with potential applications. In this work, a novel composite consisting of randomly oriented permalloy nanowires (Py NWs) intercalated among the sheets of multi-layered graphene oxide (GO) was performed. Py NWs were synthesized by electrodeposition inside mesoporous alumina templates, while GO sheets were separated by means of sonication. Sequential deposition steps of Py NWs and GO flakes allowed to reach a reproducible and stable graphene oxide-based magnetic assembly. Microscopic and spectroscopic results indicate that Py NWs are anchored on the surface as well as around the edges of the multi-layered GO, promoted by the presence of chemical groups, while magnetic characterization affords additional support to our hypothesis regarding the parallel orientation of the Py NWs with respect to the GO film, and also hints the parallel stacking of GO sheets with respect to the substrate. The most striking result remains on the electrochemical performance achieved by the composite that evidences an enhanced conductive behaviour compared to a standard electrode. Such effect provides an approach to the development of permalloy nanowires/graphene oxide-based electrodes as attractive candidates for molecular sensing devices.