bluuebunny/crossref_metadata_2025 huggingface dataset:
Myonuclear content regulates cell size with similar scaling properties in mice and humans
Authors: Hansson Kenth-Arne , Eftestøl Einar , Bruusgaard Jo C. , Juvkam Inga , Cramer Alyssa W. , Malthe-Sørenssen Anders , Millay Douglas P. , Gundersen Kristian
Published: December 2020

Muscle fibers are the largest cells in the body, and one of its few syncytia. Individual cell sizes are variable and adaptable, but what governs cell size has been unclear. We find that muscle fibers are DNA scarce compared to other cells, and that the nuclear number (N) adheres to the relationship N = aVb where V is the cytoplasmic volume. N invariably scales sublinearly to V (b < 1), making larger cells even more DNA scarce. N scales linearly to cell surface in adult humans, in adult and developing mice, and in mice with genetically reduced N, but in the latter the relationship eventually fails when they reach adulthood with extremely large myonuclear domains. Another exception is denervation-atrophy where nuclei are not eliminated. In conclusion, scaling exponents are remarkably similar across species, developmental stages and experimental conditions, suggesting an underlying scaling law where DNA-content functions as a limiter of muscle cell size.
A dual-labeling probe to track functional mitochondria–lysosome interactions in live cells
Authors: Chen Qixin , Fang Hongbao , Shao Xintian , Tian Zhiqi , Geng Shanshan , Zhang Yuming , Fan Huaxun , Xiang Pan , Zhang Jie , Tian Xiaohe , Zhang Kai , He Weijiang , Guo Zijian , Diao Jiajie
Published: December 2020

Mitochondria–lysosome interactions are essential for maintaining intracellular homeostasis. Although various fluorescent probes have been developed to visualize such interactions, they remain unable to label mitochondria and lysosomes simultaneously and dynamically track their interaction. Here, we introduce a cell-permeable, biocompatible, viscosity-responsive, small organic molecular probe, Coupa, to monitor the interaction of mitochondria and lysosomes in living cells. Through a functional fluorescence conversion, Coupa can simultaneously label mitochondria with blue fluorescence and lysosomes with red fluorescence, and the correlation between the red–blue fluorescence intensity indicates the progress of mitochondria–lysosome interplay during mitophagy. Moreover, because its fluorescence is sensitive to viscosity, Coupa allowed us to precisely localize sites of mitochondria–lysosome contact and reveal increases in local viscosity on mitochondria associated with mitochondria–lysosome contact. Thus, our probe represents an attractive tool for the localization and dynamic tracking of functional mitochondria–lysosome interactions in living cells.
Pontin arginine methylation by CARM1 is crucial for epigenetic regulation of autophagy
Authors: Yu Young Suk , Shin Hijai R. , Kim Dongha , Baek Seon Ah , Choi Seon Ah , Ahn Hyejin , Shamim Amen , Kim Jeonghwan , Kim Ik Soo , Kim Kyeong Kyu , Won Kyoung-Jae , Baek Sung Hee
Published: December 2020

Autophagy is a catabolic process through which cytoplasmic components are degraded and recycled in response to various stresses including starvation. Recently, transcriptional and epigenetic regulations of autophagy have emerged as essential mechanisms for maintaining homeostasis. Here, we identify that coactivator-associated arginine methyltransferase 1 (CARM1) methylates Pontin chromatin-remodeling factor under glucose starvation, and methylated Pontin binds Forkhead Box O 3a (FOXO3a). Genome-wide analyses and biochemical studies reveal that methylated Pontin functions as a platform for recruiting Tip60 histone acetyltransferase with increased H4 acetylation and subsequent activation of autophagy genes regulated by FOXO3a. Surprisingly, CARM1-Pontin-FOXO3a signaling axis can work in the distal regions and activate autophagy genes through enhancer activation. Together, our findings provide a signaling axis of CARM1-Pontin-FOXO3a and further expand the role of CARM1 in nuclear regulation of autophagy.
Cloning of wheat keto-acyl thiolase 2B reveals a role of jasmonic acid in grain weight determination
Authors: Chen Yun , Yan Yan , Wu Tian-Tian , Zhang Guo-Liang , Yin Huanran , Chen Wei , Wang Shuangshuang , Chang Fang , Gou Jin-Ying
Published: December 2020

Grain weight (GW) is one of the component traits of wheat yield. Existing reports have shown that multiple phytohormones are involved in the regulation of GW in different crops. However, the potential role of jasmonic acid (JA) remains unclear. Here, we report that triticale grain weight 1 (tgw1) mutant, with marked reductions in both GW and JA content, is caused by a premature stop mutation in keto-acyl thiolase 2B (KAT-2B) involved in β-oxidation during JA synthesis. KAT-2B overexpression increases GW in wild type and boosts yield. Additionally, KAT-2B compliments the grain defect in tgw1 and rescues the lethal phenotype of the Arabidopsis kat2 mutant in a sucrose-free medium. Despite the suppression of JA synthesis in tgw1 mutant, ABA synthesis is upregulated, which is accompanied by enhanced expression of SAG3 and reduction of chlorophyll content in leaves. Together, these results demonstrate a role of the JA synthetic gene KAT-2B in controlling GW and its potential application value for wheat improvement.
The bacterial multidrug resistance regulator BmrR distorts promoter DNA to activate transcription
Authors: Fang Chengli , Li Linyu , Zhao Yihan , Wu Xiaoxian , Philips Steven J. , You Linlin , Zhong Mingkang , Shi Xiaojin , O’Halloran Thomas V. , Li Qunyi , Zhang Yu
Published: December 2020

The MerR-family proteins represent a unique family of bacteria transcription factors (TFs), which activate transcription in a manner distinct from canonical ones. Here, we report a cryo-EM structure of a B. subtilis transcription activation complex comprising B. subtilis six-subunit (2αββ‘ωε) RNA Polymerase (RNAP) core enzyme, σA, a promoter DNA, and the ligand-bound B. subtilis BmrR, a prototype of MerR-family TFs. The structure reveals that RNAP and BmrR recognize the upstream promoter DNA from opposite faces and induce four significant kinks from the −35 element to the −10 element of the promoter DNA in a cooperative manner, which restores otherwise inactive promoter activity by shortening the length of promoter non-optimal −35/−10 spacer. Our structure supports a DNA-distortion and RNAP-non-contact paradigm of transcriptional activation by MerR TFs.
Optogenetic stimulation of the liver-projecting melanocortinergic pathway promotes hepatic glucose production
Authors: Kwon Eunjin , Joung Hye-Young , Liu Shun-Mei , Chua Streamson C. , Schwartz Gary J. , Jo Young-Hwan
Published: December 2020

The central melanocortin system plays a fundamental role in the control of feeding and body weight. Proopiomelanocortin (POMC) neurons in the arcuate nucleus of the hypothalamus (ARC) also regulate overall glucose homeostasis via insulin-dependent and -independent pathways. Here, we report that a subset of ARC POMC neurons innervate the liver via preganglionic parasympathetic acetylcholine (ACh) neurons in the dorsal motor nucleus of the vagus (DMV). Optogenetic stimulation of this liver-projecting melanocortinergic pathway elevates blood glucose levels that is associated with increased expression of hepatic gluconeogenic enzymes in female and male mice. Pharmacological blockade and knockdown of the melanocortin-4 receptor gene in the DMV abolish this stimulation-induced effect. Activation of melanocortin-4 receptors inhibits DMV cholinergic neurons and optogenetic inhibition of liver-projecting parasympathetic cholinergic fibers increases blood glucose levels. This elevated blood glucose is not due to altered pancreatic hormone release. Interestingly, insulin-induced hypoglycemia increases ARC POMC neuron activity. Hence, this liver-projecting melanocortinergic circuit that we identified may play a critical role in the counterregulatory response to hypoglycemia.
A computational model for classification of BRCA2 variants using mouse embryonic stem cell-based functional assays
Authors: Biswas Kajal , Lipton Gary B. , Stauffer Stacey , Sullivan Teresa , Cleveland Linda , Southon Eileen , Reid Susan , Magidson Valentin , Iversen Edwin S. , Sharan Shyam K.
Published: December 2020

Sequencing-based genetic tests to identify individuals at increased risk of hereditary breast and ovarian cancers have resulted in the identification of more than 40,000 sequence variants of BRCA1 and BRCA2. A majority of these variants are considered to be variants of uncertain significance (VUS) because their impact on disease risk remains unknown, largely due to lack of sufficient familial linkage and epidemiological data. Several assays have been developed to examine the effect of VUS on protein function, which can be used to assess their impact on cancer susceptibility. In this study, we report the functional characterization of 88 BRCA2 variants, including several previously uncharacterized variants, using a well-established mouse embryonic stem cell (mESC)-based assay. We have examined their ability to rescue the lethality of Brca2 null mESC as well as sensitivity to six DNA damaging agents including ionizing radiation and a PARP inhibitor. We have also examined the impact of BRCA2 variants on splicing. In addition, we have developed a computational model to determine the probability of impact on function of the variants that can be used for risk assessment. In contrast to the previous VarCall models that are based on a single functional assay, we have developed a new platform to analyze the data from multiple functional assays separately and in combination. We have validated our VarCall models using 12 known pathogenic and 10 neutral variants and demonstrated their usefulness in determining the pathogenicity of BRCA2 variants that are listed as VUS or as variants with conflicting functional interpretation.
A behavioural dataset for studying individual differences in language skills
Authors: Hintz Florian , Dijkhuis Marjolijn , van ‘t Hoff Vera , McQueen James M. , Meyer Antje S.
Published: December 2020

This resource contains data from 112 Dutch adults (18–29 years of age) who completed the Individual Differences in Language Skills test battery that included 33 behavioural tests assessing language skills and domain-general cognitive skills likely involved in language tasks. The battery included tests measuring linguistic experience (e.g. vocabulary size, prescriptive grammar knowledge), general cognitive skills (e.g. working memory, non-verbal intelligence) and linguistic processing skills (word production/comprehension, sentence production/comprehension). Testing was done in a lab-based setting resulting in high quality data due to tight monitoring of the experimental protocol and to the use of software and hardware that were optimized for behavioural testing. Each participant completed the battery twice (i.e., two test days of four hours each). We provide the raw data from all tests on both days as well as pre-processed data that were used to calculate various reliability measures (including internal consistency and test-retest reliability). We encourage other researchers to use this resource for conducting exploratory and/or targeted analyses of individual differences in language and general cognitive skills.
Expanded dataset of mechanical properties and observed phases of multi-principal element alloys
Authors: Borg Christopher K. H. , Frey Carolina , Moh Jasper , Pollock Tresa M. , Gorsse Stéphane , Miracle Daniel B. , Senkov Oleg N. , Meredig Bryce , Saal James E.
Published: December 2020

This data article presents a compilation of mechanical properties of 630 multi-principal element alloys (MPEAs). Built upon recently published MPEA databases, this article includes updated records from previous reviews (with minor error corrections) along with new data from articles that were published since 2019. The extracted properties include reported composition, processing method, microstructure, density, hardness, yield strength, ultimate tensile strength (or maximum compression strength), elongation (or maximum compression strain), and Young’s modulus. Additionally, descriptors (e.g. grain size) not included in previous reviews were also extracted for articles that reported them. The database is hosted and continually updated on an open data platform, Citrination. To promote interpretation, some data are graphically presented.
3-D ocean particle tracking modeling reveals extensive vertical movement and downstream interdependence of closed areas in the northwest Atlantic
Authors: Wang S. , Kenchington E. L. , Wang Z. , Yashayaev I. , Davies A. J.
Published: December 2020

Novel 3-D passive particle tracking experiments were performed in the northwest Atlantic to elucidate connectivity among areas closed to protect vulnerable marine ecosystems. We examined (1) the degree of vertical movement of particles released at different depths and locations; (2) the location of potential source populations for the deep-sea taxa protected by the closures; and (3) the degree of functional connectivity. A long-term oceanographic dataset (EN4) was queried to characterize the temperature and salinity regimes in each of the closed areas as a basis for interpreting recently published climate change projections. Using the Parcels Lagrangian particle tracking framework and the BNAM hydrodynamic model, we found enhanced connectivity over previously developed 2-D models and unexpected, current-driven, strong (to a maximum of about 1340 m) downward displacement at depth (450, 1000 and 2250 m), with weaker upward displacement except for the release depth of 2250 m which showed upward movement of 955 m with a drift duration of 3 months. The current velocities create down-stream interdependence among closed areas and allow redundancy to develop in some of the areas of the network, with some of the larger areas also showing retention. Source populations for sponges in the upstream closure are likely in adjacent waters of the Canadian continental shelf. Collectively this information can be used to inform management decisions related to the size and placement of these closed areas, and vertical velocity surfaces have potential for use in species distribution modeling of benthic species and habitats.
Differently expressed microRNA in response to the first Ig replacement therapy in common variable immunodeficiency patients
Authors: De Felice Bruna , Nigro Ersilia , Polito Rita , Rossi Francesca Wanda , Pecoraro Antonio , Spadaro Giuseppe , Daniele Aurora
Published: December 2020

Common variable immunodeficiency (CVID) is a complex primary immunodeficiency disorder characterized by a high clinical and genetic heterogeneity. The molecular underlying causes of CVID are not still now clear and the delays in diagnosis and treatment worsen the prognosis of the patients. MicroRNAs are non-coding, endogenous small RNAs often deregulated in human diseases, such as autoimmune and other immune-based disorders. In the present study, we aimed to evaluate miRNAs associated with the CVID and, in particular, with the response to the first Ig replacement therapy. To this aim, we compared miRNA profile obtained by serum samples of treatment-naïve CVID patients before and 24 h after the first Ig replacement therapy. For the first time, using a microarray assay followed by an integrated bioinformatics/biostatistics analysis, we identified five microRNAs (hsa-miR-6742, hsa-miR-1825, hsa-miR-4769-3p, hsa-miR-1228-3p, hsa-miR-1972) differently modulated in CVID patients by Ig infusion. All of them were down-regulated, excepted miR-6742 which was up-regulated. The latter may be of particular interest, since its functions are related to pathways involving Class I MHC mediated antigen processing and adaptive as well as innate Immune System. In conclusion, this study shows for the first time the modulation of miRNAs involved in CVID patients after the first Ig replacement therapy. Further studies are needed to assess whether such miRNAs could represent novel potential biomarkers in management and therapy of CVID patients.
Novel statistical approach for assessing the persistence of the circadian rhythms of social activity from telephone call detail records in older adults
Authors: Aubourg Timothée , Demongeot Jacques , Vuillerme Nicolas
Published: December 2020

How circadian rhythms of activity manifest themselves in social life of humans remains one of the most intriguing questions in chronobiology and a major issue for personalized medicine. Over the past years, substantial advances have been made in understanding the personal nature and the robustness—i.e. the persistence—of the circadian rhythms of social activity by the analysis of phone use. At this stage however, the consistency of such advances as their statistical validity remains unclear. The present paper has been specifically designed to address this issue. To this end, we propose a novel statistical procedure for the measurement of the circadian rhythms of social activity which is particularly well-suited for the existing framework of persistence analysis. Furthermore, we illustrate how this procedure works concretely by assessing the persistence of the circadian rhythms of telephone call activity from a 12-month call detail records (CDRs) dataset of adults over than 65 years. The results show the ability of our approach for assessing persistence with a statistical significance. In the field of CDRs analysis, this novel statistical approach can be used for completing the existing methods used to analyze the persistence of the circadian rhythms of a social nature. More importantly, it provides an opportunity to open up the analysis of CDRs for various domains of application in personalized medicine requiring access to statistical significance such as health care monitoring.
Loss of miR-100 and miR-125b results in cancer stem cell properties through IGF2 upregulation in hepatocellular carcinoma
Authors: Seol Hyang Sook , Akiyama Yoshimitsu , Lee San-Eun , Shimada Shu , Jang Se Jin
Published: December 2020

Stemness factors control microRNA expression in cancer stem cells. Downregulation of miR-100 and miR-125b is associated with tumor progression and prognosis of various cancers. Comparing miRNA profiling of patient-derived tumorsphere (TS) and adherent (2D) hepatocellular carcinoma cells, miR-100 and miR-125b are identified to have association with stemness. In TS cells, miR-100 and miR-125b were downregulated comparing to 2D cells. The finding was reproduced in Hep3B cells. Overexpression of stemness factors NANOG, OCT4 and SOX2 by introduction of gene constructs in Hep3B cells suppressed these two miRNA expression levels. Treatment of chromeceptin, an IGF signaling pathway inhibitor, decreased numbers of TS and inhibited the AKT/mTOR pathway. Stable cell line of miR-100 and miR-125b overexpression decreased IGF2 expression and inhibited tumor growth in the xenograft model. In conclusion, miR-100 and miR-125b have tumor suppressor role in hepatocellular carcinoma through inhibiting IGF2 expression and activation of the AKT/mTOR pathway.
Multiscale 3D phenotyping of human cerebral organoids
Authors: Albanese Alexandre , Swaney Justin M. , Yun Dae Hee , Evans Nicholas B. , Antonucci Jenna M. , Velasco Silvia , Sohn Chang Ho , Arlotta Paola , Gehrke Lee , Chung Kwanghun
Published: December 2020

Brain organoids grown from human pluripotent stem cells self-organize into cytoarchitectures resembling the developing human brain. These three-dimensional models offer an unprecedented opportunity to study human brain development and dysfunction. Characterization currently sacrifices spatial information for single-cell or histological analysis leaving whole-tissue analysis mostly unexplored. Here, we present the SCOUT pipeline for automated multiscale comparative analysis of intact cerebral organoids. Our integrated technology platform can rapidly clear, label, and image intact organoids. Algorithmic- and convolutional neural network-based image analysis extract hundreds of features characterizing molecular, cellular, spatial, cytoarchitectural, and organoid-wide properties from fluorescence microscopy datasets. Comprehensive analysis of 46 intact organoids and ~ 100 million cells reveals quantitative multiscale “phenotypes" for organoid development, culture protocols and Zika virus infection. SCOUT provides a much-needed framework for comparative analysis of emerging 3D in vitro models using fluorescence microscopy.
Impact of the transverse direction on the many-body tunneling dynamics in a two-dimensional bosonic Josephson junction
Authors: Bhowmik Anal , Haldar Sudip Kumar , Alon Ofir E.
Published: December 2020

Tunneling in a many-body system appears as one of the novel implications of quantum physics, in which particles move in space under an otherwise classically-forbidden potential barrier. Here, we theoretically describe the quantum dynamics of the tunneling phenomenon of a few intricate bosonic clouds in a closed system of a two-dimensional symmetric double-well potential. We examine how the inclusion of the transverse direction, orthogonal to the junction of the double-well, can intervene in the tunneling dynamics of bosonic clouds. We use a well-known many-body numerical method, called the multiconfigurational time-dependent Hartree for bosons (MCTDHB) method. MCTDHB allows one to obtain accurately the time-dependent many-particle wavefunction of the bosons which in principle entails all the information of interest about the system under investigation. We analyze the tunneling dynamics by preparing the initial state of the bosonic clouds in the left well of the double-well either as the ground, longitudinally or transversely excited, or a vortex state. We unravel the detailed mechanism of the tunneling process by analyzing the evolution in time of the survival probability, depletion and fragmentation, and the many-particle position, momentum, and angular-momentum expectation values and their variances. As a general rule, all objects lose coherence while tunneling through the barrier and the states which include transverse excitations do so faster. In particular for the later states, we show that even when the transverse direction is seemingly frozen, prominent many-body dynamics in a two-dimensional bosonic Josephson junction occurs. Implications are briefly discussed.
Rapid development of strong, persistent, spatiotemporally extensive cortical synchrony and underlying oscillations following acute MCA focal ischemia
Authors: Wann Ellen G. , Wodeyar Anirudh , Srinivasan Ramesh , Frostig Ron D.
Published: December 2020

Stroke is a leading cause of death and the leading cause of long-term disability, but its electrophysiological basis is poorly understood. Characterizing acute ischemic neuronal activity dynamics is important for understanding the temporal and spatial development of ischemic pathophysiology and determining neuronal activity signatures of ischemia. Using a 32-microelectrode array spanning the depth of cortex, electrophysiological recordings generated for the first time a continuous spatiotemporal profile of local field potentials (LFP) and multi-unit activity (MUA) before (baseline) and directly after (0–5 h) distal, permanent MCA occlusion (pMCAo) in a rat model. Although evoked activity persisted for hours after pMCAo with minor differences from baseline, spatiotemporal analyses of spontaneous activity revealed that LFP became spatially and temporally synchronized regardless of cortical depth within minutes after pMCAo and extended over large parts of cortex. Such enhanced post-ischemic synchrony was found to be driven by increased bursts of low multi-frequency oscillations and continued throughout the acute ischemic period whereas synchrony measures minimally changed over the same recording period in surgical sham controls. EEG recordings of a similar frequency range have been applied to successfully predict stroke damage and recovery, suggesting clear clinical relevance for our rat model.
AnOxPePred: using deep learning for the prediction of antioxidative properties of peptides
Authors: Olsen Tobias Hegelund , Yesiltas Betül , Marin Frederikke Isa , Pertseva Margarita , García-Moreno Pedro J. , Gregersen Simon , Overgaard Michael Toft , Jacobsen Charlotte , Lund Ole , Hansen Egon Bech , Marcatili Paolo
Published: December 2020

Dietary antioxidants are an important preservative in food and have been suggested to help in disease prevention. With consumer demands for less synthetic and safer additives in food products, the food industry is searching for antioxidants that can be marketed as natural. Peptides derived from natural proteins show promise, as they are generally regarded as safe and potentially contain other beneficial bioactivities. Antioxidative peptides are usually obtained by testing various peptides derived from hydrolysis of proteins by a selection of proteases. This slow and cumbersome trial-and-error approach to identify antioxidative peptides has increased interest in developing computational approaches for prediction of antioxidant activity and thereby reduce laboratory work. A few antioxidant predictors exist, however, no tool predicting the antioxidative properties of peptides is, to the best of our knowledge, currently available as a web-server. We here present the AnOxPePred tool and web-server (http://services.bioinformatics.dtu.dk/service.php?AnOxPePred-1.0) that uses deep learning to predict the antioxidant properties of peptides. Our model was trained on a curated dataset consisting of experimentally-tested antioxidant and non-antioxidant peptides. For a variety of metrics our method displays a prediction performance better than a k-NN sequence identity-based approach. Furthermore, the developed tool will be a good benchmark for future predictors of antioxidant peptides.
Indication and benefit of upfront hematopoietic stem cell transplantation for T-cell lymphoblastic lymphoma in the era of ALL-type induction therapies
Authors: Morita-Fujita Mari , Arai Yasuyuki , Yoshioka Satoshi , Ishikawa Takayuki , Kanda Junya , Kondo Tadakazu , Akasaka Takashi , Ueda Yasunori , Imada Kazunori , Moriguchi Toshinori , Yago Kazuhiro , Kitano Toshiyuki , Yonezawa Akihito , Nohgawa Masaharu , Takaori-Kondo Akifumi ,   Kyoto Stem Cell Transplantation Group (KSCTG)
Published: December 2020

Since the introduction of leukemia-type induction therapies for T-cell lymphoblastic lymphoma (T-LBL), improvements in the long-term outcomes of T-LBL have been reported. However, indications for and the appropriate timing of hematopoietic stem cell transplantation (HSCT) have not yet been established. Therefore, we performed a multicenter retrospective cohort study of patients with T-LBL treated using leukemia-type initial therapies to compare the outcomes after HSCT at different disease stages. We enrolled 21 patients with T-LBL from a total of 11 centers, and all patients received hyper-CVAD as a leukemia-type initial regimen. HSCT was performed during the CR1/PR1 (standard disease) stage in 11 patients, while it was completed at a later or non-remission (advanced disease) stage in 10 patients. Following HSCT, the overall survival rate was significantly greater in standard disease than in advanced-disease patients (79.5% vs. 30.0% at 5 years; hazard ratio (HR) 5.97; p = 0.03), with trend to the lower incidence of relapse in the former group (27.3% vs. 60.0% at 5 years; HR 2.29; p = 0.19). A prognostic difference was not detected between cases treated with allogeneic and autologous HSCTs. Our study suggests that frontline HSCT may be a feasible treatment option for T-LBL, even in the era of leukemia-type initial therapy.
Development of a human primary gut-on-a-chip to model inflammatory processes
Authors: Beaurivage Claudia , Kanapeckaite Auste , Loomans Cindy , Erdmann Kai S. , Stallen Jan , Janssen Richard A. J.
Published: December 2020

Inflammatory bowel disease (IBD) is a complex multi-factorial disease for which physiologically relevant in vitro models are lacking. Existing models are often a compromise between biological relevance and scalability. Here, we integrated intestinal epithelial cells (IEC) derived from human intestinal organoids with monocyte-derived macrophages, in a gut-on-a-chip platform to model the human intestine and key aspects of IBD. The microfluidic culture of IEC lead to an increased polarization and differentiation state that closely resembled the expression profile of human colon in vivo. Activation of the model resulted in the polarized secretion of CXCL10, IL-8 and CCL-20 by IEC and could efficiently be prevented by TPCA-1 exposure. Importantly, upregulated gene expression by the inflammatory trigger correlated with dysregulated pathways in IBD patients. Finally, integration of activated macrophages offers a first-step towards a multi-factorial amenable IBD platform that could be scaled up to assess compound efficacy at early stages of drug development or in personalized medicine.
The vascular targeted citrus FLOWERING LOCUS T3 gene promotes non-inductive early flowering in transgenic Carrizo rootstocks and grafted juvenile scions
Authors: Soares Juliana M. , Weber Kyle C. , Qiu Wenming , Stanton Daniel , Mahmoud Lamiaa M. , Wu Hao , Huyck Patrick , Zale Janice , Al Jasim Kawther , Grosser Jude W. , Dutt Manjul
Published: December 2020

Shortening the juvenile stage in citrus and inducing early flowering has been the focus of several citrus genetic improvement programs. FLOWERING LOCUS T (FT) is a small phloem-translocated protein that regulates precocious flowering. In this study, two populations of transgenic Carrizo citrange rootstocks expressing either Citrus clementina FT1 or FT3 genes under the control of the Arabidopsis thaliana phloem specific SUCROSE SYNTHASE 2 (AtSUC2) promoter were developed. The transgenic plants were morphologically similar to the non-transgenic controls (non-transgenic Carrizo citrange), however, only AtSUC2-CcFT3 was capable of inducing precocious flowers. The transgenic lines produced flowers 16 months after transformation and flower buds appeared 30–40 days on juvenile immature scions grafted onto transgenic rootstock. Gene expression analysis revealed that the expression of SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) and APETALA1 (AP1) were enhanced in the transgenics. Transcriptome profiling of a selected transgenic line showed the induction of genes in different groups including: genes from the flowering induction pathway, APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) family genes, and jasmonic acid (JA) pathway genes. Altogether, our results suggested that ectopic expression of CcFT3 in phloem tissues of Carrizo citrange triggered the expression of several genes to mediate early flowering.
Efficient viral delivery of Cas9 into human safe harbor
Authors: Hayashi Hideki , Kubo Yoshinao , Izumida Mai , Matsuyama Toshifumi
Published: December 2020

Gene editing using CRISPR/Cas9 is a promising method to cure many human genetic diseases. We have developed an efficient system to deliver Cas9 into the adeno-associated virus integration site 1 (AAVS1) locus, known as a safe harbor, using lentivirus and AAV viral vectors, as a step toward future in vivo transduction. First, we introduced Cas9v1 (derived from Streptococcus pyogenes) at random into the genome using a lentiviral vector. Cas9v1 activity was used when the N-terminal 1.9 kb, and C-terminal 2.3 kb fragments of another Cas9v2 (human codon-optimized) were employed sequentially with specific single-guide RNAs (sgRNAs) and homology donors carried by AAV vectors into the AAVS1 locus. Then, Cas9v1 was removed from the genome by another AAV vector containing sgRNA targeting the long terminal repeat of the lentivirus vector. The reconstituted Cas9v2 in the AAVS1 locus was functional and gene editing was efficient.
Simultaneous imaging of hard and soft biological tissues in a low-field dental MRI scanner
Authors: Algarín José M. , Díaz-Caballero Elena , Borreguero José , Galve Fernando , Grau-Ruiz Daniel , Rigla Juan P. , Bosch Rubén , González José M. , Pallás Eduardo , Corberán Miguel , Gramage Carlos , Aja-Fernández Santiago , Ríos Alfonso , Benlloch José M. , Alonso Joseba
Published: December 2020

Magnetic Resonance Imaging (MRI) of hard biological tissues is challenging due to the fleeting lifetime and low strength of their response to resonant stimuli, especially at low magnetic fields. Consequently, the impact of MRI on some medical applications, such as dentistry, continues to be limited. Here, we present three-dimensional reconstructions of ex-vivo human teeth, as well as a rabbit head and part of a cow femur, all obtained at a field strength of 260 mT. These images are the first featuring soft and hard tissues simultaneously at sub-Tesla fields, and they have been acquired in a home-made, special-purpose, pre-medical MRI scanner designed with the goal of demonstrating dental imaging at low field settings. We encode spatial information with two pulse sequences: Pointwise-Encoding Time reduction with Radial Acquisition and a new sequence we have called Double Radial Non-Stop Spin Echo, which we find to perform better than the former. For image reconstruction we employ Algebraic Reconstruction Techniques (ART) as well as standard Fourier methods. An analysis of the resulting images shows that ART reconstructions exhibit a higher signal-to-noise ratio with a more homogeneous noise distribution.
Deep-learned time-signal intensity pattern analysis using an autoencoder captures magnetic resonance perfusion heterogeneity for brain tumor differentiation
Authors: Park Ji Eun , Kim Ho Sung , Lee Junkyu , Cheong E.-Nae , Shin Ilah , Ahn Sung Soo , Shim Woo Hyun
Published: December 2020

Current image processing methods for dynamic susceptibility contrast (DSC) magnetic resonance imaging (MRI) do not capture complex dynamic information of time-signal intensity curves. We investigated whether an autoencoder-based pattern analysis of DSC MRI captured representative temporal features that improves tissue characterization and tumor diagnosis in a multicenter setting. The autoencoder was applied to the time-signal intensity curves to obtain representative temporal patterns, which were subsequently learned by a convolutional neural network. This network was trained with 216 preoperative DSC MRI acquisitions and validated using external data (n = 43) collected with different DSC acquisition protocols. The autoencoder applied to time-signal intensity curves and clustering obtained nine representative clusters of temporal patterns, which accurately identified tumor and non-tumoral tissues. The dominant clusters of temporal patterns distinguished primary central nervous system lymphoma (PCNSL) from glioblastoma (AUC 0.89) and metastasis from glioblastoma (AUC 0.95). The autoencoder captured DSC time-signal intensity patterns that improved identification of tumoral tissues and differentiation of tumor type and was generalizable across centers.
Diffusion kurtosis imaging of gray matter in young adults with autism spectrum disorder
Authors: McKenna Faye , Miles Laura , Donaldson Jeffrey , Castellanos F. Xavier , Lazar Mariana
Published: December 2020

Prior ex vivo histological postmortem studies of autism spectrum disorder (ASD) have shown gray matter microstructural abnormalities, however, in vivo examination of gray matter microstructure in ASD has remained scarce due to the relative lack of non-invasive methods to assess it. The aim of this work was to evaluate the feasibility of employing diffusional kurtosis imaging (DKI) to describe gray matter abnormalities in ASD in vivo. DKI data were examined for 16 male participants with a diagnosis of ASD and IQ>80 and 17 age- and IQ-matched male typically developing (TD) young adults 18–25 years old. Mean (MK), axial (AK), radial (RK) kurtosis and mean diffusivity (MD) metrics were calculated for lobar and sub-lobar regions of interest. Significantly decreased MK, RK, and MD were found in ASD compared to TD participants in the frontal and temporal lobes and several sub-lobar regions previously associated with ASD pathology. In ASD participants, decreased kurtosis in gray matter ROIs correlated with increased repetitive and restricted behaviors and poor social interaction symptoms. Decreased kurtosis in ASD may reflect a pathology associated with a less restrictive microstructural environment such as decreased neuronal density and size, atypically sized cortical columns, or limited dendritic arborizations.
Middle eastern genetic legacy in the paternal and maternal gene pools of Chuetas
Authors: Ferragut J. F. , Ramon C. , Castro J. A. , Amorim A. , Alvarez L. , Picornell A.
Published: December 2020

Chuetas are a group of descendants of Majorcan Crypto-Jews (Balearic Islands, Spain) who were socially stigmatized and segregated by their Majorcan neighbours until recently; generating a community that, although after the seventeenth century no longer contained Judaic religious elements, maintained strong group cohesion, Jewishness consciousness, and endogamy. Collective memory fixed 15 surnames as a most important defining element of Chueta families. Previous studies demonstrated Chuetas were a differentiated population, with a considerable proportion of their original genetic make-up. Genetic data of Y-chromosome polymorphism and mtDNA control region showed, in Chuetas’ paternal lineages, high prevalence of haplogroups J2-M172 (33%) and J1-M267 (18%). In maternal lineages, the Chuetas hallmark is the presence of a new sub-branching of the rare haplogroup R0a2m as their modal haplogroup (21%). Genetic diversity in both Y-chromosome and mtDNA indicates the Chueta community has managed to avoid the expected heterogeneity decrease in their gene pool after centuries of isolation and inbreeding. Moreover, the composition of their uniparentally transmitted lineages demonstrates a remarkable signature of Middle Eastern ancestry—despite some degree of host admixture—confirming Chuetas have retained over the centuries a considerable degree of ancestral genetic signature along with the cultural memory of their Jewish origin.
Mesoscopic cortical network reorganization during recovery of optic nerve injury in GCaMP6s mice
Authors: Groleau Marianne , Nazari-Ahangarkolaee Mojtaba , Vanni Matthieu P. , Higgins Jacqueline L. , Vézina Bédard Anne-Sophie , Sabel Bernhard A. , Mohajerani Majid H. , Vaucher Elvire
Published: December 2020

As the residual vision following a traumatic optic nerve injury can spontaneously recover over time, we explored the spontaneous plasticity of cortical networks during the early post-optic nerve crush (ONC) phase. Using in vivo wide-field calcium imaging on awake Thy1-GCaMP6s mice, we characterized resting state and evoked cortical activity before, during, and 31 days after ONC. The recovery of monocular visual acuity and depth perception was evaluated in parallel. Cortical responses to an LED flash decreased in the contralateral hemisphere in the primary visual cortex and in the secondary visual areas following the ONC, but was partially rescued between 3 and 5 days post-ONC, remaining stable thereafter. The connectivity between visual and non-visual regions was disorganized after the crush, as shown by a decorrelation, but correlated activity was restored 31 days after the injury. The number of surviving retinal ganglion cells dramatically dropped and remained low. At the behavioral level, the ONC resulted in visual acuity loss on the injured side and an increase in visual acuity with the non-injured eye. In conclusion, our results show a reorganization of connectivity between visual and associative cortical areas after an ONC, which is indicative of spontaneous cortical plasticity.
Oxidation suppression of Cu in alkaline aluminophosphate glass and the effects for radiation-induced luminescence characteristics
Authors: Shiratori Daiki , Masai Hirokazu , Kato Takumi , Okada Go , Nakauchi Daisuke , Kawaguchi Noriaki , Yanagida Takayuki
Published: December 2020

A glass phosphor is an attractive material for applications in radiation detections because of its high workability and availability with a wide range of chemical compositions. Recently, X-ray-induced luminescence of glasses containing various luminescent activators are actively investigated worldwide. In applications as phosphor, tailoring valence state of activators, which can take multiple valence states in glass, is very important. In this research, we studied effects of glass melting atmosphere on the valence state of copper-activator ion in alkaline aluminophosphate glasses and the radiation-induced luminescence characteristics. Optical absorption and X-ray absorption near edge structure spectra of Cu-doped glasses showed that the glass fused in Ar atmosphere contains higher concentration of Cu+ than those prepared in air. In addition, the presence of Cu+ enhances the photoluminescence (PL) quantum yield and PL kinetic constant. Furthermore, the increase of Cu+ concentration resulted an improvement of the X-ray-induced scintillation and thermally-stimulated luminescence intensity.
Determinants of delay in diagnosis and end stage at presentation among breast cancer patients in Iran: a multi-center study
Authors: Foroozani Elahe , Ghiasvand Reza , Mohammadianpanah Mohammad , Afrashteh Sima , Bastam Dariush , Kashefi Fatemeh , Shakarami Saba , Dianatinasab Mostafa
Published: December 2020

One of the reasons for high mortality of breast cancer (BC) is long delay in seeking medical care and end stage at presentation. This study was designed to measure the association between a wide range of socio-demographic and clinical factors with diagnostic delay in BC and stage at presentation among Iranian patients. From June 2017 to December 2019, 725 patients with newly diagnosed BC in Shiraz and Kermanshah were selected and information on BC diagnosis delay was obtained from the patient’s medical record. Data on socio-economic status was obtained via a structured interview. Our findings suggest that 45.8% of the patients were diagnosed at a late stage (stage 3 or higher). A total of 244 (34%) patients had more than 3 months delay in diagnosis. We found a significant association between stage at diagnosis and place of residence (adjusted odds ratio (aOR rural vs. urban = 1.69, 95% CI 1.49–1.97), marital status (aOR 1.61, 95% CI 1.42–1.88), family history of BC (aOR 1.46, 95% CI 1.01–2.13), and history of benign breast disease (BBD) (aOR 1.94, 95% CI 1.39–2.72) or unaware of breast self-examination (BSE) (aOR 1.42, 95% CI 1.42–1.85), delay time (aOR 3.25, 95% CI 1.04–5.21), and left breast tumor (aOR right vs. left 2.64, 95% CI 1.88–3.71) and smoking (aOR no vs. yes 1.59, 95% CI 1.36–1.97). Also, delay in diagnosis was associated with age, family income, health insurance, place of residence, marital status, menopausal status, history of BBD, awareness of breast self-examination, type of first symptoms, tumor histology type, BMI and comorbidity (p < 0.05 for all). Factors including history of BBD, awareness of BSE, and suffering from chronic diseases were factors associated with both delay in diagnosis and end stage of disease. These mainly modifiable factors are associated with the progression of the disease.
Mild hyperlipidemia in mice aggravates platelet responsiveness in thrombus formation and exploration of platelet proteome and lipidome
Authors: van Geffen Johanna P. , Swieringa Frauke , van Kuijk Kim , Tullemans Bibian M. E. , Solari Fiorella A. , Peng Bing , Clemetson Kenneth J. , Farndale Richard W. , Dubois Ludwig J. , Sickmann Albert , Zahedi René P. , Ahrends Robert , Biessen Erik A. L. , Sluimer Judith C. , Heemskerk Johan W. M. , Kuijpers Marijke J. E.
Published: December 2020

Hyperlipidemia is a well-established risk factor for cardiovascular diseases. Millions of people worldwide display mildly elevated levels of plasma lipids and cholesterol linked to diet and life-style. While the prothrombotic risk of severe hyperlipidemia has been established, the effects of moderate hyperlipidemia are less clear. Here, we studied platelet activation and arterial thrombus formation in Apoe−/− and Ldlr−/− mice fed a normal chow diet, resulting in mildly increased plasma cholesterol. In blood from both knockout mice, collagen-dependent thrombus and fibrin formation under flow were enhanced. These effects did not increase in severe hyperlipidemic blood from aged mice and upon feeding a high-fat diet (Apoe−/− mice). Bone marrow from wild-type or Ldlr−/− mice was transplanted into irradiated Ldlr−/− recipients. Markedly, thrombus formation was enhanced in blood from chimeric mice, suggesting that the hyperlipidemic environment altered the wild-type platelets, rather than the genetic modification. The platelet proteome revealed high similarity between the three genotypes, without clear indication for a common protein-based gain-of-function. The platelet lipidome revealed an altered lipid profile in mildly hyperlipidemic mice. In conclusion, in Apoe−/− and Ldlr−/− mice, modest elevation in plasma and platelet cholesterol increased platelet responsiveness in thrombus formation and ensuing fibrin formation, resulting in a prothrombotic phenotype.
Under the karst: detecting hidden subterranean assemblages using eDNA metabarcoding in the caves of Christmas Island, Australia
Authors: West Katrina M. , Richards Zoe T. , Harvey Euan S. , Susac Robert , Grealy Alicia , Bunce Michael
Published: December 2020

Subterranean ecosystems are understudied and challenging to conventionally survey given the inaccessibility of underground voids and networks. In this study, we conducted a eukaryotic environmental DNA (eDNA) metabarcoding survey across the karst landscape of Christmas Island, (Indian Ocean, Australia) to evaluate the utility of this non-invasive technique to detect subterranean aquatic ‘stygofauna’ assemblages. Three metabarcoding assays targeting the mitochondrial 16S rRNA and nuclear 18S genes were applied to 159 water and sediment samples collected from 23 caves and springs across the island. Taken together, our assays detected a wide diversity of chordates, cnidarians, porifera, arthropods, molluscs, annelids and bryozoans from 71 families across 60 orders. We report a high level of variation between cave and spring subterranean community compositions which are significantly influenced by varying levels of salinity. Additionally, we show that dissolved oxygen and longitudinal gradients significantly affect biotic assemblages within cave communities. Lastly, we combined eDNA-derived community composition and environmental (water quality) data to predict potential underground interconnectivity across Christmas Island. We identified three cave and spring groups that showed a high degree of biotic and abiotic similarity indicating likely local connectivity. This study demonstrates the applicability of eDNA metabarcoding to detect subterranean eukaryotic communities and explore underground interconnectivity.