bluuebunny/crossref_metadata_2025 huggingface dataset:
Epidemiological and clinical characteristics of COVID-19 in adolescents and young adults
Authors: Liao Jiaqiang , Fan Shibing , Chen Jing , Wu Jianglin , Xu Shunqing , Guo Yuming , Li Chunhui , Zhang Xianxiang , Wu Chuansha , Mou Huaming , Song Chenxi , Li Feng , Wu Guicheng , Zhang Jingjing , Guo Lian , Liu Huawen , Lv Jinglong , Xu Lixin , Lang Chunhui
Published: March 2020

Background

Adolescents and young adults might play a key role in the worldwide spread of Coronavirus Disease 2019 (COVID-19), because they are more involved in overseas studying, business, working, and travelling. However, the epidemiological and clinical characteristics of them are still unknown.

Methods

We collected data of 46 confirmed COVID-19 patients aged 10 to 35 years from the study hospital. The demographics, epidemiological, and clinical data were collected. Several key epidemiological parameters, the asymptomatic cases and transmission to their family members and the clinical characteristics at admission, and during treatment were summarized.

RESULTS

Of 46 confirmed patients, 14 patients (47.3%) were aged from 10 to 24 years, and 24 (52.7%) patients were male. The mean incubation period for symptomatic cases was 6.6 days (95% confidence interval (CI) 4.4 - 9.6). The median serial interval was 1.9 days (95% CI 0.4 - 6.2). Three of asymptomatic cases showed the transmission to their family members. Only 1 patient was identified as severe cases at admission. The common symptoms at admission were dry cough (34, 91.0%), and fever (29, 69.0%). Nearly 60% of the patients had showed ground-glass opacity by chest CT findings. Three patients developed acute kidney injury during treatment. Majority of patients (78.3%) were discharged by the end of the follow-up.

Conclusions

The adolescent and young adult patients of COVID-19 had a long incubation period, and a short serial interval. The transmission to their family contactors occurred in asymptomatic cases. Few of the study patients have developed complications during treatment.
Non-canonical open reading frames encode functional proteins essential for cancer cell survival
Authors: Prensner John R. , Enache Oana M. , Luria Victor , Krug Karsten , Clauser Karl R. , Dempster Joshua M. , Karger Amir , Wang Li , Stumbraite Karolina , Wang Vickie M. , Botta Ginevra , Lyons Nicholas J. , Goodale Amy , Kalani Zohra , Fritchman Briana , Brown Adam , Alan Douglas , Green Thomas , Yang Xiaoping , Jaffe Jacob D. , Roth Jennifer A. , Piccioni Federica , Kirschner Marc W. , Ji Zhe , Root David E. , Golub Todd R.
Published: March 2020

A key question in genome research is whether biologically active proteins are restricted to the ∼20,000 canonical, well-annotated genes, or rather extend to the many non-canonical open reading frames (ORFs) predicted by genomic analyses. To address this, we experimentally interrogated 553 ORFs nominated in ribosome profiling datasets. Of these 553 ORFs, 57 (10%) induced a viability defect when the endogenous ORF was knocked out using CRISPR/Cas9 in 8 human cancer cell lines, 257 (46%) showed evidence of protein translation when ectopically expressed in HEK293T cells, and 401 (73%) induced gene expression changes measured by transcriptional profiling following ectopic expression across 4 cell types. CRISPR tiling and start codon mutagenesis indicated that the biological effects of these non-canonical ORFs required their translation as opposed to RNA-mediated effects. We selected one of these ORFs,G029442--renamedGREP1(Glycine-Rich Extracellular Protein-1)--for further characterization. We found thatGREP1encodes a secreted protein highly expressed in breast cancer, and its knock-out in 263 cancer cell lines showed preferential essentiality in breast cancer derived lines. Analysis of the secretome of GREP1-expressing cells showed increased abundance of the oncogenic cytokine GDF15, and GDF15 supplementation mitigated the growth inhibitory effect ofGREP1knock-out. Taken together, these experiments suggest that the non-canonical ORFeome is surprisingly rich in biologically active proteins and potential cancer therapeutic targets deserving of further study.
Small Molecule Targeting IRES Domain Inhibits Enterovirus 71 Replication via an Allosteric Mechanism that Stabilizes a Ternary Complex
Authors: Davila-Calderon Jesse , Patwardhan Neeraj , Chiu Liang-Yuan , Sugarman Andrew , Cai Zhengguo , Penutmutchu Srinivasa R. , Li Mei-Ling , Brewer Gary , Hargrove Amanda E. , Tolbert Blanton S.
Published: March 2020

We herein report an RNA-targeting antiviral small molecule that reduces replication of the human enterovirus 71 (EV71) via stabilization of an inhibitory small molecule-RNA-protein ternary complex. The EV71 virus poses serious threats to human health, particularly in regions of Southeast Asia, and no FDA approved drugs or vaccines are available. We first screened an RNA-biased small molecule library using a peptide-displacement assay to identify ligands for the stem loop II structure of the EV71 internal ribosomal entry site, which was previously shown to impact viral translation and replication. One ligand, DMA-135, decreased viral translation and replication in cell-based studies in a dose-dependent manner with no significant toxicity. Structural, biophysical, and biochemical characterization support an allosteric mechanism in which DMA-135 induces a conformational change in the RNA structure that stabilizes a ternary complex with the AUF1 protein that then represses translation. This mechanism was further supported by pull-down experiments in cell culture. These detailed studies establish enterovirus RNA structures as promising drug targets while revealing an approach and mechanism of action that should be broadly applicable to functional RNA targeting.
The superoxide dismutase mimetic GC4419 enhances tumor killing when combined with stereotactic ablative radiation
Authors: Sishc Brock J. , Ding Lianghao , Heer Collin , Saha Debabrata , Spitz Douglas R. , Story Michael D.
Published: March 2020

The penta-aza macrocyclic manganese compound GC4419 is in phase 3 clinical trials as a modifier of mucositis in H&N cancer treated by radio-chemotherapy based upon its properties as a superoxide dismutase mimetic. In studies to address the potential for tumor radioprotection, a significant anti-tumor effect was identified in tumors generated from the non-small cell lung cancer (NSCLC) cell line H1299, when GC4419 was combined with radiation. This effect was directly related to the size of the radiation dose as demonstrated by greater efficacy in tumor growth delay when biologically equivalent irradiation regimens using a limited number of dose fractions was substantially more effective compared to regimens where the fraction number was higher and dose per fraction decreased. Furthermore, a TCD50 assay using H1299 tumors that tested the combination of GC4419 with radiation revealed a Dose Enhancement Factor of 1.67. Based upon these results the hypothesis that GC4419 was generating cytotoxic levels of hydrogen peroxide during the superoxide dismutation process. Peroxide flux did increase in cells exposed to GC4419 as did the expression of the oxidative stress markers 4-HNE and 3-NT. H1299 cells that overexpressed catalase were then challenged as tumors by the combination of radiation and GC4419 and the tumoricidal effect was nearly eliminated. The enhanced radiation response was not specific to NSCLC as similar findings were observed in human head and neck squamous cell carcinoma and pancreatic ductal adenocarcinoma xenografts. RNA sequencing analysis revealed that GC4419, in addition to generating high levels of hydrogen peroxide in irradiated cells, alters inflammatory and differentiation signaling in the tumor following irradiation. Together, these findings provide abundant evidence that the radioprotector GC4419 has dual functionality and will increase tumor response rates when combined with agents that generate high levels of superoxide like stereotactic ablative body radiotherapy (SAbR). Combining SAbR with GC4419 may be an effective strategy to enhance tumor response in general but may also allow for fully potent radiation doses to tumors that might not necessarily be able to tolerate such doses. The potential for protection of organs at risk may also be exploitable.
Detection of Penicillin G Produced byPenicillium chrysogenumKF 425 in Vivo with Raman Microspectroscopy and Multivariate Curve Resolution-Alternating Least Squares Methods
Authors: Horii Shumpei , Ando Masahiro , Samuel Ashok Z. , Take Akira , Nakashima Takuji , Matsumoto Atsuko , Takahashi Yōko , Takeyama Haruko
Published: March 2020

Raman microspectroscopy is a minimally invasive technique that can identify molecular structure without labeling. In this study, we demonstrate in vivo detection of the bioactive compound penicillin G insidePenicillium chrysogenumKF425 fungus cells. Highly overlapped spectroscopic signatures acquired using Raman microspectroscopic imaging are analyzed using a multivariate curve resolution-alternating least squares (MCR-ALS) method to extract the pure spectra of individual molecular constituents. In addition to detecting multiple constituents such as proteins and lipids, we observe the subcellular localization of penicillin G like granule particle inside the fungus body. To date, there have been no reports of direct visualization of intracellular localization of penicillin G. The methodology we present in this article is expected to be applied as a screening tool for the production of bioactive compounds by microorganisms.
Subventricular zone adult mouse neural stem cells and human glioblastoma stem cells require insulin receptor for self-renewal
Authors: Chidambaram Shravanthi , Rothbard Deborah , Deshpande Kaivalya , Cajuste Yvelanda , Snyder Kristin M. , Fajardo Eduardo , Fiser Andras , Tapinos Nikos , Levison Steven W. , Wood Teresa L.
Published: March 2020

The insulin receptor (IR) is an evolutionarily conserved signaling protein that regulates development and cellular metabolism. IR signaling regulates neurogenesis inDrosophila; however, a specific role for the IR in maintaining adult neural stem cells (NSCs) in mammals has not been investigated. We show that conditionally deleting the IR reduces adult NSCs of the subventricular zone by ∼70% accompanied by a corresponding increase in progenitors. IR deletion produced hyposmia due to aberrant olfactory bulb neurogenesis. Interestingly, hippocampal neurogenesis was not perturbed nor were hippocampal dependent behaviors. Highly aggressive proneural and mesenchymal glioblastomas (GBMs) had high IR/insulin-like growth factor (IGF) pathway gene expression, and isolated glioma stem cells had an aberrantly high ratio of IR:IGF1R receptors. Moreover, IR knockdown inhibited proneural and mesenchymal GBM tumorsphere growth. Altogether, these data demonstrate that the IR is essential for a subset of normal NSCs as well as for brain tumor cancer stem cell self-renewal.
Variability in mitochondrial import, mitochondrial health and mtDNA copy number using Type II and Type V CRISPR effectors
Authors: Antón Zuriñe , Mullally Grace , Ford Holly , van der Kamp Marc W. , Szczelkun Mark D. , Lane Jon D.
Published: March 2020

Current methodologies for targeting the mitochondrial genome for basic research and/or therapeutic strategy development in mitochondrial diseases are restricted by practical limitations and technical inflexibility. The development of a functional molecular toolbox for CRISPR-mediated mitochondrial genome editing is therefore desirable, as this could enable precise targeting of mtDNA haplotypes using the precision and tuneability of CRISPR enzymes; however, published reports of “MitoCRISPR” systems have, to date, lacked reproducibility and independent corroboration. Here, we have explored the requirements for a functional MitoCRISPR system in human cells by engineering several versions of CRISPR nucleases, including the use of alternative mitochondrial protein targeting sequences and smaller paralogues, and the application of gRNA modifications that reportedly induce mitochondrial import. We demonstrate varied mitochondrial targeting efficiencies and influences on mitochondrial dynamics/function of different CRISPR nucleases, withLachnospiraceaebacterium ND2006 (Lb) Cas12a being better targeted and tolerated than Cas9 variants. We also provide evidence of Cas9 gRNA association with mitochondria in HeLa cells and isolated yeast mitochondria, even in the absence of a targeting RNA aptamer. Finally, we present evidence linking mitochondrial-targeted LbCas12a/crRNA with increased mtDNA copy number dependent upon DNA binding and cleavage activity. We discuss reproducibility issues and the future steps necessary if MitoCRISPR is to be realised.
Single-chain lanthanide luminescence biosensors for cell-based imaging and screening of protein-protein interactions
Authors: Chen Ting , Pham Ha T. , Mohamadi Ali , Miller Lawrence W.
Published: March 2020

Research tools that enable imaging or analysis of protein-protein interactions (PPIs) directly within living cells provide unique and valuable biological insights and can also aid drug discovery efforts. Here, we present lanthanide-based, Förster resonance energy transfer (lanthanide-based FRET, or LRET) biosensors for time-gated luminescence (TGL) imaging or multiwell plate analysis of PPIs. Polypeptide chains comprised of an alpha helical linker flanked by a Tb(III) complex, GFP and two binding domains exhibit large differences in long-lifetime, Tb(III)-to-GFP LRET-sensitized emission between open (unbound) and closed (bound) states. We used TGL microscopy to image ca. 500% increases in Tb(III)-to-GFP LRET following rapamycin addition to NIH 3T3 cells that expressed biosensors bearing FKBP12 and the rapamycin binding domain of m-Tor (FRB) at each terminus. Much larger signal changes, up to ca. 2500%, were observed when cells were grown in 96-well or 384-well plates and analyzed using a TGL plate reader. We also measured the interaction of p53 and HDM2 and its inhibition within intact HeLa cells grown in 96-well plates and estimated a z’-factor of 0.5 for the assay. The modular design and high dynamic range of Tb(III)-based LRET biosensors will facilitate versatile imaging and cell-based screening of PPIs.
SCENITH: A flow cytometry based method for functional profiling energy metabolism with single cell resolution
Authors: Argüello Rafael J. , Combes Alexis J. , Char Remy , Bousiquot Evens , Gigan Julien-Paul , Camosseto Voahirana , Samad Bushra , Tsui Jessica , Yan Peter , Boissonneau Sebastien , Figarella-Branger Dominique , Tabouret Emeline , Gatti Evelina , Krummel Matthew F. , Pierre Philippe
Published: March 2020

Energetic metabolism reprogramming is critical for cancer and immune responses. Current methods to functionally profile the global metabolic capacities and dependencies of cells are performed in bulk. We designed a simple method for complex metabolic profiling called SCENITH, for Single Cell ENergetIc metabolism by profilIng Translation inHibition. SCENITH allows for the study of metabolic responses in multiple cell types in parallel by flow cytometry. SCENITH is designed to perform metabolic studies ex vivo, particularly for rare cells in whole blood samples, avoiding metabolic biases introduced by culture media. We analyzed myeloid cells in solid tumors from patients and identified variable metabolic profiles, in ways that are not linked to their lineage nor their activation phenotype. SCENITH ability to reveal global metabolic functions and determine complex and linked immune-phenotypes in rare cell subpopulations will contribute to the information needed for evaluating therapeutic responses or patient stratification.
The Demographic History of Micro-endemics: Have Rare Species Always Been Rare?
Authors: Helmstetter Andrew J. , Cable Stuart , Rakotonasolo Franck , Rabarijaona Romer , Rakotoarinivo Mijoro , Eiserhardt Wolf L. , Baker William J. , Papadopulos Alexander S.T.
Published: March 2020

Extinction has increased as human activities impact ecosystems. Conservation assessments for the IUCN red list are a fundamental tool in aiding the prevention of further extinction, yet, relatively few species have been thoroughly assessed. To increase the efficiency of assessments, novel approaches are needed to highlight threatened species that are currently data deficient. Many Madagascan plant species currently have extremely narrow ranges, but this may not have always been the case. To assess this, we used high-throughput DNA sequencing for 2-5 individuals of each species - reflecting the paucity of samples available for rare species. We estimated effective population size (Ne) for each species and compared this to census population(Nc) sizes when known. In each case,Newas an order of magnitude larger thanNc– a signature of rapid, recent population decline. We then estimated the demographic history of each species, tracking changes inNeover time. Five out of ten species displayed significant population declines towards the present (68–90% decreases). Our results for palm trees indicate that it is possible to predict extinction risk, particularly in the most threatened species. We performed simulations to show that our approach has the power to detect population decline during the Anthropocene, but performs less well when less data is used. Similar declines to those in palms were observed in data deficient species or those assessed as of least concern. These analyses reveal that Madagascar’s narrow endemics were not always rare, having experienced rapid decline in their recent history. Our approach offers the opportunity to target species in need of conservation assessment with little prior information, particularly in regions where human modification of the environment has been rapid.

Current IUCN conservation assessment methods are reliant on observed declines in species population and range sizes over the last one hundred years, but for the majority of species this information is not available. We used a population genetic approach to reveal historical demographic decline in the rare endemic flora of Madagascar. These results show that it is possible to predict extinction risk from demographic patterns inferred from genetic data and that destructive human influence is likely to have resulted in the very high frequency of narrow endemics present on the island. Our approach will act as an important tool for rapidly assessing the threatened status of poorly known species in need of further study and conservation, particularly for tropical flora and fauna.
A Deep Learning Approach for Tissue Spatial Quantification and Genomic Correlations of Histopathological Images
Authors: Lu Zixiao , Zhan Xiaohui , Wu Yi , Cheng Jun , Shao Wei , Ni Dong , Han Zhi , Zhang Jie , Feng Qianjin , Huang Kun
Published: March 2020

Epithelial and stromal tissue are components of the tumor microenvironment and play a major role in tumor initiation and progression. Distinguishing stroma from epithelial tissues is critically important for spatial characterization of the tumor microenvironment. We propose an image analysis pipeline based on a Convolutional Neural Network (CNN) model to classify epithelial and stromal regions in whole-slide images. The CNN model was trained using well-annotated breast cancer tissue microarrays and validated with images from The Cancer Genome Atlas (TCGA) project. Our model achieves a classification accuracy of 91.02%, which outperforms other state-of-the-art methods. Using this model, we generated pixel-level epithelial/stromal tissue maps for 1,000 TCGA breast cancer slide images that are paired with gene expression data. We subsequently estimated the epithelial and stromal ratios and performed correlation analysis to model the relationship between gene expression and tissue ratios. Gene Ontology enrichment analyses of genes that were highly correlated with tissue ratios suggest the same tissue was associated with similar biological processes in different breast cancer subtypes, whereas each subtype had its own idiosyncratic biological processes governing the development of these tissues. Taken all together, our approach can lead to new insights in exploring relationships between image-based phenotypes and their underlying genomic data and biological processes for all types of solid tumors.
Single cell RNA-seq analysis reveals compartment-specific heterogeneity and plasticity of microglia
Authors: Zheng Junying , Ru Wenjuan , Adolacion Jay R , Spurgat Michael S , Liu Xin , Yuan Subo , Liang Rommel X , Dong Jianli , Potter Andrew S , Potter S Steven , Varadarajan Navin , Tang Shao-Jun
Published: March 2020

Microglia are heterogeneous and ubiquitous CNS-resident macrophages that maintain homeostasis of neural tissues and protect them from pathogen attacks. Yet, their differentiation in different compartments remains elusive. We performed single cell RNA-seq (scRNA-seq) analysis to compare the transcriptomes of microglia in adult mouse (C57/Bl) brains and spinal cords to identify microglial subtypes in these CNS compartments. Cortical microglia from 2-month mice consisted of a predominant population of the homeostatic subtype (HOM-M) and a small population (4%) of the inflammatory subtype (IFLAM-M), while spinal microglia consisted of 55% HOM-M and 45% IFLAM-M subtype. Comparison of cortical and spinal microglia at 2, 4 and 8 months revealed consistently a higher composition of the IFLAM-M subtype in the spinal cord. At 8-month, cortical microglia differentiated a small new subtype with interferon response phenotypes (INF-M), while spinal microglia polarized toward a proinflammatory phenotype, as indicated by the increase of microglia expressing IL-1β. To further characterize the differential plasticity of cortical and spinal microglial heterogeneity, we determined the microglial transcriptomes from HIV-1 gp 120 transgenic (Tg) mice, a model of HIV-associated neurological disorders. Compared with wild-type (Wt) cortical microglia, the gp120Tg cortical microglia had three new subtypes, with signatures of interferon I response (INF-M), cell proliferation (PLF-M), and myelination or demyelination (MYE-M) respectively; while INF-M and PLF-M subtypes presented at all ages, the MYE-M only at 4-month. In contrast, only the INF-M subtype was observed in the spinal microglia from 2- and 4-month gp120tg mice. Bioinformatic analysis of regulated molecular pathways of individual microglial subtypes indicated that gp120 more severely impaired the biological function of microglia in cortices than in the spinal cord. The results collectively reveal differential heterogeneity and plasticity of cortical and spinal microglia, and suggest functional differentiation of microglia in different CNS compartments.
VarStack: a Web Tool for Data Retrieval to Interpret Somatic Variants in Cancer
Authors: Howard Morgan , Kane Bruce , Lepry Mary , Stey Paul , Ragavendran Ashok , Gamsiz Uzun Ece D.
Published: March 2020

Background and objective

Advances in tumor genome sequencing created an urgent need for bioinformatics tools to support the interpretation of the clinical significance of the variants detected. VarStack is a web tool which is a base to retrieve somatic variant data in cancer from existing databases.

Methods

VarStack incorporates data from several publicly available databases and presents them with an easy-to-navigate user-interface. It currently supports data from the Catalogue of Somatic Mutations in Cancer (COSMIC), gnomAD, cBioPortal, ClinVar, OncoKB and UCSC Genome browser. It retrieves the data from these databases and returns back to the user in a fraction of the time it would take to manually navigate each site independently.

Results

Users submit a variant with gene symbol, peptide change, and coding sequence change. They may select a variety of tumor specific studies in cBioportal to search through in addition to their original query. The results from the databases are presented in tabs. Users can export the results as a CSV file. VarStack also has the batch search feature in which user submits a list of variants and download a CSV file with the data from the databases. With the batch search and data download options users can easily incorporate VarStack into their workflow or tools. VarStack saves time by providing variant data to the user from multiple databases in an easy-to-export and interpretable format.

Availability

VarStack is freely available underhttps://varstack.brown.edu.
LED Zappelin’: An open source LED controller for arbitrary spectrum visual stimulation and optogenetics during 2-photon imaging
Authors: Zimmermann M.J.Y. , Chagas A.M. , Bartel P. , Pop S. , Godino L.L. Prieto , Baden T.
Published: March 2020

Two-photon (2P) microscopy is a cornerstone technique in neuroscience research. However, combining 2P imaging with spectrally arbitrary light stimulation can be challenging due to crosstalk between stimulation light and fluorescence detection. To overcome this limitation, we present a simple and low-cost electronic solution based on an ESP32 microcontroller and a TLC5947 LED driver to rapidly time-interleave stimulation and detection epochs during scans. Implemented for less than $100, our design can independently drive up to 24 arbitrary spectrum LEDs to meet user requirements. We demonstrate the utility of our stimulator for colour vision experiments on thein vivotetrachromatic zebrafish retina and for optogenetic circuit mapping inDrosophila.

https://github.com/BadenLab/LED-Zappelin
RainbowSTORM: An open-source ImageJ plugin for spectroscopic single-molecule localization microscopy (sSMLM) data analysis and image reconstruction
Authors: Davis Janel L. , Soetikno Brian , Song Ki-Hee , Zhang Yang , Sun Cheng , Zhang Hao F.
Published: March 2020

Spectroscopic single-molecule localization microscopy (sSMLM) simultaneously captures the spatial locations and full spectra of stochastically emitting fluorescent single molecules. It provides an optical platform to develop new multi-molecular and functional imaging capabilities. While several open-source software suites provide sub-diffraction localization of fluorescent molecules, software suites for spectroscopic analysis of sSMLM data remain unavailable. RainbowSTORM is an open-source, user-friendly ImageJ/FIJI plugin for end-to-end spectroscopic analysis and visualization for sSMLM images. RainbowSTORM allows users to calibrate, preview, and quantitatively analyze emission spectra acquired using different reported sSMLM system designs and fluorescent labels.

Availability

RainbowSTORM is a java plugin for ImageJ (https://imagej.net)/FIJI (http://fiji.sc) freely available through:https://github.com/FOIL-NU/RainbowSTORM. RainbowSTORM has been tested with Windows and Mac operating systems and ImageJ/FIJI version 1.52.

Supplementary information

Supplementary data are available online.
Charge density of cation determines inner versus outer shell coordination to phosphate in RNA
Authors: Nguyen Hung T. , Thirumalai D.
Published: March 2020

Divalent cations are often required to fold RNA, which is a highly charged polyanion. Condensation of ions, such as Mg2+or Ca2+, in the vicinity of RNA renormalizes the effective charges on the phosphate groups, thus minimizing the intra RNA electrostatic repulsion. The prevailing view is that divalent ions bind diffusively in a non-specific manner. In sharp contrast, we arrive at the exact opposite conclusion using a theory for the interaction of ions with the phosphate groups using RISM theory in conjunction with simulations based on an accurate Three Interaction Site RNA model. The divalent ions bind in a nucleotide-specific manner using either the inner (partially dehydrated) or outer (fully hydrated) shell coordination. The high charge density Mg2+ion has a preference to bind to the outer shell whereas the opposite is the case for Ca2+. Surprisingly, we find that bridging interactions, involving ions that are coordinated to two or more phosphate groups, play a crucial role in maintaining the integrity of the folded state. Their importance could become increasingly prominent as the size of the RNA increases. Because the modes of interaction of divalent ions with DNA are likely to be similar, we propose that specific inner and outer shell coordination could play a role in DNA condensation, and perhaps genome organization as well.
SUMOylation of rice DELLA SLR1 modulates transcriptional responses and improves yield under salt stress
Authors: Gonçalves Nuno M. , Fernandes Telma , Nunes Cátia , Rosa Margarida T. G. , Matiolli Cleverson C. , Rodrigues Mafalda A. A. , Barros Pedro M. , Oliveira M. Margarida , Abreu Isabel A.
Published: March 2020

DELLA proteins modulate GA signalling and are major regulators of plant plasticity to endure stress. DELLAs are mostly regulated at the post-translational level, and their activity relies on the interaction with upstream regulators and transcription factors (TFs). SUMOylation is a post-translational modification (PTM) capable of changing protein interaction and found to influence DELLA activity in Arabidopsis. We determined that SUMOylation of the single rice DELLA SLENDER RICE1 (SLR1) occurs in a lysine residue different from the one previously identified in Arabidopsis REPRESSOR OF GA (RGA). Remarkably, artificially increasing SUMOylated SLR1 (SUMO1SLR1) levels attenuated the penalty of salt stress on plant yield. Gene expression analysis revealed that the overexpression of SUMOylated SLR1 regulates key dioxygenases that modulate active GA levels, namelyGA20ox2andGA2ox3, which could partially explain the sustained productivity upon salt stress imposition. Besides, SLR1 SUMOylation blocked the interaction with the growth regulator YAB4, which may fine-tuneGA20ox2expression. Mechanistically, we propose that SLR1 SUMOylation disrupts the interaction with members of several transcription factor families to modulate gene expression. We found that SLR1 SUMOylation represents a novel mechanism modulating DELLA activity, which attenuates the impact of stress on plant performance.

One sentence summary

Rice plants show increased yield under salt stress when its gibberellin transcriptional regulator DELLA protein is artificially SUMOylated.
Distinguish between Duplication of Essential Genes and Duplication of Dispensable Genes
Authors: Gu Xun
Published: March 2020

When a dispensable gene is duplicated (ancestral dispensability), genetic buffering and duplicate compensation together maintain the gene dispensability, whereas duplicate compensation is the only mechanism when an essential gene is duplicated (ancestral essentiality). To explore the distinct pattern of genetic robustness between these evolutionary scenarios, we formulated a probabilistic model with some biologically reasonable assumptions for analyzing a set of duplicate pairs with three possible states: double-dispensable (DD), semi-dispensable (one dispensable one essential, DE) or double-essential (EE). A computational pipeline is then developed to predict the distribution of three states (DD, DE and EE) conditional of ancestral dispensability or essentiality, respectively. This model was applied to yeast duplicate pairs from a whole-genome duplication, revealing that the process of essentiality of those duplicated from essential genes could be significantly higher than that of those duplicated from dispensable genes. We thus proposed a hypothesis that the process of sub-functionalization may be faster than neo-functionalization. Our analysis may provide some new insights about the role of duplicate compensation on genetic robustness.
Graphical-Model Framework for Automated Annotation of Cell Identities in Dense Cellular Images
Authors: Chaudhary Shivesh , Lee Sol Ah , Li Yueyi , Patel Dhaval S. , Lu Hang
Published: March 2020

Although identifying cell names in dense image stacks is critical in analyzing functional whole-brain data enabling comparison across experiments, unbiased identification is very difficult, and relies heavily on researchers’ experiences. Here we present a probabilistic-graphical-model framework, CRF_ID, based on Conditional Random Fields, for unbiased and automated cell identification. CRF_ID focuses on maximizing intrinsic similarity between shapes. Compared to existing methods, CRF_ID achieves higher accuracy on simulated and ground-truth experimental datasets, and better robustness against challenging noise conditions common in experimental data. CRF_ID can further boost accuracy by building atlases from annotated data in highly computationally efficient manner, and by easily adding new features (e.g. from new strains). We demonstrate cell annotation in C. elegans images across strains, animal orientations, and tasks including gene-expression localization, multi-cellular and whole-brain functional imaging experiments. Together, these successes demonstrate that unbiased cell annotation can facilitate biological discovery, and this approach may be valuable to annotation tasks for other systems.
Selection of forage oat genotypes through GGE Biplot and BLUP
Authors: Santos Franklin , Marza y Félix
Published: March 2020

In Bolivia, there is a low predominance of forage oat productivity. Therefore, it was proposed to select more productive and stable genotypes through statistical methods of GGE Biplot and BLUP. The research was conducted in three environments in Bolivia and six commercial varieties of forage oats were evaluated; three of them correspond to INIA Peru and the rest of Bolivia. Data were analyzed through GGE Biplot and BLUP (Best Linear Unbiased Prediction) and an average yield of 10.29 ±3.51 t ha−1of dry matter was obtained. BLUP accumulated greater variance than GGE Biplot in the first two components. In terms of productivity and stability values, both models have the same selection trend. Thus, Tayco and Texas were selected for their outstanding characteristic in dry matter yield and phenotypic stability.
A surface metric and software toolbox for EEG electrode grids in the macaque
Authors: Li Fan , Teichert Tobias
Published: March 2020

Background

The past years have seen increased appreciation of non-invasive extracranial electroencephalographic (EEG) recordings in non-human primates (NHP) as a tool for translational research. In humans, the international 10-20 system or extensions thereof provide standardized electrode positions that enable easy comparison of data between subjects and laboratories. In the NHP, no such generally accepted, standardized placement system is available.

New Method

Here we introduce a surface metric and software package (NHP1020) that automates the planning of large, approximately evenly spaced electrode grids on the NHP skull.

Results

The system is based on one CT and one MRI image and requires the user to specify two intracranial markers. Based on this, the software defines electrode positions on the brain surface using a surface-based spherical metric similar to the one used by the international 10-20 system. The electrode positions are then projected to the surface of the skull. Standardized electrode grids can be shared, imported or defined with few high-level commands.

Existing Methods

NHP EEG electrodes are often placed on an individual basis relative to extracranial markers, or relative to underlying neural structures. Both approaches are time-consuming and require manual intervention. Furthermore, the use of extracranial markers in this species may be more problematic than in humans, because cranial muscles and ridges are larger and keep maturing long into adulthood thus potentially affecting electrode positions.

Conclusion

The key advantage of the current approach is the automated and objective identification of corresponding electrode positions in different animals. Automation was made possible by the use of a two-dimensional metric on the brain surface which has a simpler, i.e., more convex and sphere-like anatomy than the skull. This enables fast and efficient planning, optimization and calculation of large electrode grids.
Molecular mechanism of the pH-dependent calcium affinity in langerin
Authors: Joswig Jan-O. , Anders Jennifer , Zhang Hengxi , Rademacher Christoph , Keller Bettina G.
Published: March 2020

The C-type lectin receptor langerin plays a vital role in the mammalian defense against invading pathogens. Its function hinges on the affinity to its co-factor Ca2+which in turn is regulated by the pH. We studied the structural consequences of protonating the allosteric pH-sensor histidine H294 by molecular dynamics simulations (total simulation time: about 120 µs) and Markov models. We discovered a mechanism in which the signal that the pH has dropped is transferred to the Ca2+-binding site without transferring the initial proton. Instead, protonation of H294 unlocks a conformation in which a protonated lysine side-chain forms a hydrogen bond with a Ca2+-coordinating aspartic acid. This destabilizes Ca2+in the binding pocket, which we probed by steered molecular dynamics. After Ca2+-release, the proton is likely transferred to the aspartic acid and stabilized by a dyad with a nearby glutamic acid, triggering a conformational transition and thus preventing Ca2+-rebinding.
Cerebellar Purkinje cells can differentially modulate coherence between sensory and motor cortex depending on region and behavior
Authors: Lindeman Sander , Kros Lieke , Hong Sungho , Mejias Jorge F. , Romano Vincenzo , Negrello Mario , Bosman Laurens W.J. , De Zeeuw Chris I.
Published: March 2020

Coherence among sensory and motor cortices is indicative of binding of critical functions in perception, motor planning, action and sleep. Evidence is emerging that the cerebellum can impose coherence between cortical areas, but how and when it does so is unclear. Here, we studied coherence between primary somatosensory (S1) and motor (M1) cortices during sensory stimulation of the whiskers in the presence and absence of optogenetic stimulation of cerebellar Purkinje cells in awake mice. Purkinje cell activation enhanced and reduced sensory-induced S1-M1 coherence in the theta and gamma bands, respectively. This impact only occurred when Purkinje cell stimulation was given simultaneously with sensory stimulation; a 20 ms delay was sufficient to alleviate its impact, suggesting the existence of a fast, cerebellar sensory pathway to S1 and M1. The suppression of gamma band coherence upon Purkinje cell stimulation was significantly stronger during trials with relatively large whisker movements, whereas the theta band changes did not show this correlation. In line with the anatomical distribution of the simple spike and complex spike responses to whisker stimulation, this suppression also occurred following focal stimulation of medial crus 2, but not of lateral crus 1. Granger causality analyses and computational modeling of the involved networks suggest that Purkinje cells control S1-M1 coherence most prominently via the ventrolateral thalamus and M1. Our results indicate that coherences between sensory and motor cortices in different frequency ranges can be dynamically modulated by cerebellar input, and that the modulation depends on the behavioral context and is site-specific.

Significance Statement

Coherent activity between sensory and motor areas is essential in sensorimotor integration. We show here that the cerebellum can differentially affect cortical theta and gamma band coherences evoked by whisker stimulation via a fast ascending and predictive pathway. In line with the functional heterogeneity of its modular organization, the impact of the cerebellum is region-specific and tuned to ongoing motor responses. These data highlight site-specific and context-dependent interactions between the cerebellum and the cerebral cortex that can come into play during a plethora of sensorimotor functions.
Multiple midfrontal thetas revealed by source separation of simultaneous MEG and EEG
Authors: Zuure Marrit B. , Hinkley Leighton B.N. , Tiesinga Paul H.E. , Nagarajan Srikantan S. , Cohen Michael X
Published: March 2020

Theta-band (∼6 Hz) rhythmic activity within and over the medial prefrontal cortex (“midfrontal theta”) has been identified as a distinctive signature of “response conflict,” the competition between multiple actions when only one action is goal-relevant. Midfrontal theta is traditionally conceptualized and analyzed under the assumption that it is a unitary signature of conflict that can be uniquely identified at one electrode (typically FCz). Here we recorded simultaneous MEG and EEG (total of 328 sensors) in nine human subjects (7 female) and applied a feature-guided multivariate source-separation decomposition to determine whether conflict-related midfrontal theta is a unitary or multidimensional feature of the data. For each subject, a generalized eigendecomposition (GED) yielded spatial filters (components) that maximized the ratio between theta and broadband activity. Components were retained based on significance thresholding and midfrontal EEG topography. All of the subjects individually exhibited multiple (mean 5.89, SD 2.47) midfrontal components that contributed to sensor-level midfrontal theta power during the task. Component signals were temporally uncorrelated and asynchronous, suggesting that each midfrontal theta component was unique. Our findings call into question the dominant notion that midfrontal theta represents a unitary process. Instead, we suggest that midfrontal theta spans a multidimensional space, indicating multiple origins, but can manifest as a single feature at the sensor level due to signal mixing.

Significance statement

“Midfrontal theta” is a rhythmic electrophysiological signature of the competition between multiple response options. Midfrontal theta is traditionally considered to reflect a single process. However, this assumption could be erroneous due to “mixing” (multiple sources contributing to the activity recorded at a single electrode). We investigated the dimensionality of midfrontal theta by applying advanced multivariate analysis methods to a multimodal M/EEG dataset. We identified multiple topographically overlapping neural sources that drove response conflict-related midfrontal theta. Midfrontal theta thus reflects multiple uncorrelated signals that manifest with similar EEG scalp projections. In addition to contributing to the cognitive control literature, we demonstrate both the feasibility and the necessity of signal de-mixing to understand the neural dynamics underlying cognitive processes.
Conditional repeatability and the variance explained by reaction norm variation in random slope models
Authors: Schielzeth Holger , Nakagawa Shinichi
Published: March 2020

Individuals differ in average phenotypes and in sensitivity to environmental variation. Such context-sensitivity can be modelled as random-slope variation. Random-slope variation implies that the proportion of between-individual variation varies across the range of a covariate (environment/context/time/age) and has thus been called ‘conditional’ repeatability. We propose to put conditional repeatabilities in perspective of the total phenotypic variance and suggest a way of standardization using the random-slope coefficient of determination. Furthermore, we illustrate that the marginalized repeatabilityRmaraveraged across an environmental gradient offers a biologically relevant description of between-individual variation. We provide simple equations for calculating key descriptors of conditional repeatabilities, clarify the difference between random-intercept variation and average between-individual variation and make recommendations for comprehensive reporting. While we introduce the concept with individual variation in mind, the framework is equally applicable to other type of between-group/cluster variation that varies across some (environmental) gradient.
Super-enhancer switching drives a burst in germline gene expression at the mitosis-to-meiosis transition
Authors: Maezawa So , Yukawa Masashi , Chen Xiaoting , Sakashita Akihiko , Alavattam Kris G. , Weirauch Matthew T. , Barski Artem , Namekawa Satoshi H.
Published: March 2020

The testis has the most diverse and complex transcriptome of all organs due to bursts in expression of thousands of germline-specific genes. Much of this unique gene expression takes place when mitotic germ cells differentiate and enter into meiotic prophase. Here, we demonstrate that the genome-wide reorganization of super-enhancers (SEs) drives bursts of germline genes after the mitosis-to-meiosis transition. At the mitosis-to-meiosis transition, mitotic SEs dissolve while meiotic SEs are established. Meiotic SEs are associated with the activation of key germline genes, defining the cellular identity of germ cells. This SE switching is regulated by the establishment of meiotic SEs via A-MYB (MYBL1), a key transcription factor for germline genes, and by the resolution of mitotic SEs via SCML2, a germline-specific Polycomb protein required for spermatogenesis-specific gene expression. Prior to the entry into meiosis, meiotic SEs are preprogrammed in mitotic spermatogonia, serving to direct the unidirectional differentiation of spermatogenesis. We identify key regulatory factors for both mitotic and meiotic enhancers, revealing a molecular logic for the concurrent activation of mitotic enhancers and suppression of meiotic enhancers in the somatic and/or mitotically proliferating phase.
Mapping the Structural and Dynamic Determinants of pH-sensitive Heparin Binding to Granulocyte Macrophage-colony Stimulating Factor
Authors: Cui Jennifer Y. , Zhang Fuming , Linhardt Robert J. , Lisi George P.
Published: March 2020

GMCSF is an immunomodulatory cytokine that is harnessed as a therapeutic. GMCSF is known to interact with other clinically important molecules, such as heparin, suggesting that endogenous and administered GMCSF has the potential to modulate orthogonal treatment outcomes. Thus, molecular level characterization of GMCSF and its interactions with other biologically active compounds is critical to understanding these mechanisms and predicting clinical outcomes. Here, we dissect the molecular motions and structural contributions that facilitate the GMCSF-heparin interaction, previously shown to be pH-dependent, using NMR spectroscopy, SPR, and molecular docking. We find that GMCSF and heparin binding is related to a change in flexibility reflected in the dynamic profile of GMCSF at acidic pH. The molecular motions driving this interaction largely occur on the ms-µs timescale. Interestingly, we find that GMCSF and heparin binding is not only pH-dependent but is also heparin chain length dependent. We propose a mechanism where a positive binding pocket that is not fully solvent accessible at neutral pH becomes more accessible at acidic pH, allowing heparin to dock with the protein.