bluuebunny/crossref_metadata_2025 huggingface dataset:
Human prostate cancer bone metastases have an actionable immunosuppressive microenvironment
Authors: Baryawno Ninib , Kfoury Youmna , Severe Nicolas , Mei Shenglin , Gustafsson Karin , Hirz Taghreed , Brouse Thomas , Scadden Elizabeth W. , Igolkina Anna A. , Choi Bryan D. , Barkas Nikolas , Shin John H. , Saylor Philip J. , Scadden David T. , Sykes David B. , Kharchenko Peter V. ,   as part of the Boston Bone Metastasis Consortium
Published: March 2020

Bone metastases are devastating complications of cancer. They are particularly common in prostate cancer, represent incurable disease and are refractory to immunotherapy. We sought to define distinct features of the bone marrow microenvironment by analyzing single cells from prostate cancer patients’ involved bone, uninvolved bone and distant bone sites as well as bone from cancer-free, orthopedic patients and healthy individuals. Metastatic prostate cancer was associated with multifaceted immune distortion, specifically exhaustion of distinct T cell subsets, appearance of macrophages with states specific to prostate cancer bone metastases. The chemokine CCL20 was notably overexpressed by myeloid cells, as was its cognate CCR6 receptor on T cells. Disruption of the CCL20-CCR6 axis in mice with syngeneic prostate bone metastases restored T cell reactivity and significantly prolonged animal survival. Comparative high resolution analysis of prostate cancer bone metastasis shows a targeted approach for relieving local immunosuppression for therapeutic effect.
All-in-One Dual CRISPR-Cas12a (AIOD-CRISPR) Assay: A Case for Rapid, Ultrasensitive and Visual Detection of Novel Coronavirus SARS-CoV-2 and HIV virus
Authors: Ding Xiong , Yin Kun , Li Ziyue , Liu Changchun
Published: March 2020

A recent outbreak of novel coronavirus (SARS-CoV-2), the causative agent of COVID-19, has spread rapidly all over the world. Human immunodeficiency virus (HIV) is another deadly virus and causes acquired immunodeficiency syndrome (AIDS). Rapid and early detection of these viruses will facilitate early intervention and reduce disease transmission risk. Here, we present anAll-In-OneDualCRISPR-Cas12a (termed “AIOD-CRISPR”) assay method for simple, rapid, ultrasensitive, one-pot, and visual detection of coronavirus SARS-CoV-2 and HIV virus. In our AIOD CRISPR assay, a pair of crRNAs was introduced to initiate dual CRISPR-Cas12a detection and improve detection sensitivity. The AIOD-CRISPR assay system was successfully utilized to detect nucleic acids (DNA and RNA) of SARS-CoV-2 and HIV with a sensitivity of few copies. Also, it was evaluated by detecting HIV-1 RNA extracted from human plasma samples, achieving a comparable sensitivity with real-time RT-PCR method. Thus, our method has a great potential for developing next-generation point-of-care molecular diagnostics.
Mutational synergy coordinately remodels chromatin accessibility, enhancer landscape and 3-Dimensional DNA topology to alter gene expression during leukemia induction
Authors: Yun Haiyang , Vohra Shabana , Mupo Annalisa , Giotopoulos George , Sasca Daniel , Horton Sarah J. , Agrawal-Singh Shuchi , Meduri Eshwar , Basheer Faisal , Marando Ludovica , Gozdecka Malgorzata , Dovey Oliver M. , Castillo-Venzor Aracely , Wang Xiaonan , Gallipoli Paolo , Müller-Tidow Carsten , Osborne Cameron S. , Vassiliou George S. , Huntly Brian J. P.
Published: March 2020

Altered transcription is a cardinal feature of acute myeloid leukemia (AML), however, exactly how mutations synergize to remodel the epigenetic landscape and rewire 3-Dimensional (3-D) DNA topology is unknown. Here we apply an integrated genomic approach to a murine allelic series that models the two most common mutations in AML,Flt3-ITD andNpm1c. We then deconvolute the contribution of each mutation to alterations of the epigenetic landscape and genome organization, and infer how mutations synergize in the induction of AML. These analyses allow the identification of long-rangecis-regulatory circuits, including a novel super-enhancer of theHoxalocus, as well as larger and more detailed gene-regulatory networks, whose importance we demonstrate through perturbation of network members.
Biochemical paedomorphosis and genetic assimilation in the hypoxia adaptation of Tibetan antelope
Authors: Signore Anthony V. , Storz Jay F.
Published: March 2020

Developmental shifts in stage-specific gene expression can provide a ready mechanism of phenotypic change by altering the rate or timing of ontogenetic events. We discovered that the high-altitude Tibetan antelope (Panthelops hodgsonii) has evolved an adaptive increase in blood–O2affinity by truncating the ancestral ontogeny of globin gene expression such that a high-affinity juvenile hemoglobin isoform (isoHb) completely supplants the lower-affinity isoHb that is expressed in the adult red blood cells of other bovids. This juvenilization of blood properties represents a canalization of an acclimatization response to hypoxia that has been well-documented in adult goats and sheep. We also discovered the genomic mechanism underlying this regulatory isoHb switch, revealing how a reversible acclimatization response became genetically assimilated as an irreversible adaptation to chronic hypoxia.
The Irish potato famine pathogen subverts host vesicle trafficking to channel starvation-induced autophagy to the pathogen interface
Authors: Pandey Pooja , Leary Alexandre Y , Tümtas Yasin , Savage Zachary , Dagvadorj Bayantes , Tan Emily , Khandare Virendrasinh , Duggan Cian , Yusunov Temur , Madalinski Mathias , Mirkin Federico Gabriel , Schornack Sebastian , Dagdas Yasin , Kamoun Sophien , Bozkurt Tolga O.
Published: March 2020

Eukaryotic cells deploy autophagy to eliminate invading microbes. In turn, pathogens have evolved effector proteins to counteract antimicrobial autophagy. How and why adapted pathogens co-opt autophagy for their own benefit is poorly understood. The Irish famine pathogen Phythophthora infestans secretes the effector protein PexRD54 that selectively activates an unknown plant autophagy pathway, while antagonizing antimicrobial autophagy. Here we show that PexRD54 induces autophagosome formation by bridging small GTPase Rab8a-decorated vesicles with autophagic compartments labelled by the core autophagy protein ATG8CL. Rab8a is required for pathogen-triggered and starvation-induced but not antimicrobial autophagy, revealing that specific trafficking pathways underpin selective autophagy. We discovered that Rab8a contributes to basal immunity against P. infestans, but PexRD54 diverts a sub-population of Rab8a vesicles to lipid droplets that associate with autophagosomes. These are then diverted towards pathogen feeding structures that are accommodated within the host cells. We propose that PexRD54 mimics starvation-induced autophagy by channeling host endomembrane trafficking towards the pathogen interface possibly to acquire nutrients. This work reveals that effectors can interconnect independent host compartments to stimulate complex cellular processes that benefit the pathogen.

Graphical abstract
Presynaptically silent synapses are modulated by the density of surrounding astrocytes
Authors: Oyabu Kohei , Takeda Kotomi , Kawano Hiroyuki , Kubota Kaori , Watanabe Takuya , Harata N. Charles , Katsurabayashi Shutaro , Iwasaki Katsunori
Published: March 2020

The astrocyte, a major glial cell type, is involved in formation and maturation of synapses, and thus contributes to sustainable synaptic transmission between neurons. Given that the animals in the higher phylogenetic tree have brains with higher density of glial cells with respect to neurons, there is a possibility that the relative astrocytic density directly influences synaptic transmission. However, the notion has not been tested thoroughly. Here we addressed it, by using a primary culture preparation where single hippocampal neurons are surrounded by a variable but countable number of cortical astrocytes in dot-patterned microislands, and recording synaptic transmission by patch-clamp electrophysiology. Neurons with a higher astrocytic density showed a higher amplitude of evoked excitatory postsynaptic current (EPSC) than that of neurons with a lower astrocytic density. The size of readily releasable pool of synaptic vesicles per neuron was significantly higher. The frequency of spontaneous synaptic transmission (miniature EPSC) was higher, but the amplitude was unchanged. The number of morphologically identified glutamatergic synapses was unchanged, but the number of functional ones was increased, indicating a lower ratio of presynaptically silent synapses. Taken together, the higher astrocytic density enhanced excitatory synaptic transmission by increasing the number of functional synapses through presynaptic un-silencing.
The mid-lateral cerebellum is necessary for reinforcement learning
Authors: Sendhilnathan Naveen , Goldberg Michael E.
Published: March 2020

The cerebellum has long been considered crucial for supervised motor learning and its optimization1-3. However, new evidence has also implicated the cerebellum in reward based learning4-8, executive function9-12, and frontal-like clinical deficits13. We recently showed that the simple spikes of Purkinje cells (P-cells) in the mid-lateral cerebellar hemisphere (Crus I and II) encode a reinforcement error signal when monkeys learn to associate arbitrary symbols with hand movements4. However, it is unclear if the cerebellum is necessary for any process beyond motor learning. To investigate if the mid-lateral cerebellum is actually necessary for learning visuomotor associations, we reversibly inactivated the mid-lateral cerebellum of two primates with muscimol while they learned to associate arbitrary symbols with hand movements. Here we show that cerebellar inactivation impaired the monkey’s ability to learn new associations, although it had no effect on the monkeys’ performance on a task with overtrained symbols. A computational model corroborates our results. Cerebellar inactivation increased the reaction time, but there were no deficits in any motor kinematics such as the hand movement, licking or eye movement. There was no loss of function when we inactivated a more anterior region of the cerebellum that is implicated in motor control. We suggest that the mid-lateral cerebellum, which provides a reinforcement learning error signal4, is necessary for visuomotor association learning. Our results have implications for the involvement of cerebellum in cognitive control, and add critical constraints to brain models of non-motor learning14,15.
Isolation and genome sequencing of 14Spongiasp. bacterial associates expands the taxonomic and functional breadth of the cultivatable marine sponge microbiome
Authors: Karimi Elham , Costa Rodrigo
Published: March 2020

Marine sponges live with complex microbial consortia, which have been considered as potential sources of novel natural products. However, the usual recalcitrance of host-associated microorganisms to cultivation makes studying sponge symbionts challenging. To tackle this complexity, exploration of cultivated sponge-associated bacteria and their coding potential is unavoidable. In this study, we isolate and report the draft genome sequences of 14 bacterial strains from the marine spongeSpongiasp. using R2A and VXA media. The strains belong to the classesActinobacteria, Gammaproteobacteria, Alphaproteobacteria,andCytophagiaspanning 11 formally described genera plus two potentially novel genera in theRhodobacteraceaefamily and one potentially novel family in theCytophagalesorder. Functional genomics revealed presumed symbiosis factors typical of specific taxonomic groups (i.e. taurine metabolism genes among theAlphaproteobacteria,chitinase encoding genes and eukaryotic-like proteins in theCytophagiagenome) while multidrug efflux pumps, also important in host-microbe interactions, were common across all genomes. Moreover, we detected 76 secondary-metabolite biosynthetic gene clusters putatively involved in the production of drug-like compounds or signalling molecules across all genomes, warranting future biotechnologically driven research into their coding potential.
Prefrontal cortex represents heuristics that shape choice bias and its integration into future behavior
Authors: Mochol Gabriela , Kiani Roozbeh , Moreno-Bote Rubén
Published: March 2020

Goal-directed behavior requires integrating sensory information with prior knowledge about the environment. Behavioral biases that arise from these priors could increase positive outcomes when the priors match the true structure of the environment, but mismatches also happen frequently and could cause unfavorable outcomes. Biases that reduce gains and fail to vanish with training indicate fundamental suboptimalities arising from ingrained heuristics of the brain. Here, we report systematic, gain-reducing choice biases in highly-trained monkeys performing a motion direction discrimination task where only the current stimulus is behaviorally relevant. The monkey’s bias fluctuated at two distinct time scales: slow, spanning tens to hundreds of trials, and fast, arising from choices and outcomes of the most recent trials. Our finding enabled single trial prediction of biases, which influenced the choice especially on trials with weak stimuli. The pre-stimulus activity of neuronal ensembles in the monkey prearcuate gyrus represented these biases as an offset along the decision axis in the state space. This offset persisted throughout the stimulus viewing period, when sensory information was integrated, leading to a biased choice. The pre-stimulus representation of history-dependent bias was functionally indistinguishable from the neural representation of upcoming choice before stimulus onset, validating our model of single-trial biases and suggesting that pre-stimulus representation of choice could be fully defined by biases inferred from behavioral history. Our results indicate that the prearcuate gyrus reflects intrinsic heuristics that compute bias signals, as well as the mechanisms that integrate them into the oculomotor decision-making process.
The small DdrR protein directly interacts with the UmuDAb regulator to inhibit the mutagenic DNA damage response inAcinetobacter baumannii
Authors: Pavlin Anja , Bajc Gregor , Fornelos Nadine , Browning Douglas F. , Butala Matej
Published: March 2020

Disclaimer statement:

The authors have withdrawn their manuscript due to observed inconsistent results regarding the DdrR effect on the enhanced binding of UmuDAb to its promoter regions. Further experiments are needed to unravel the biology of DdrR. Therefore, the authors do not wish this work to be cited as a reference for the project. If you have any questions, please contact the corresponding author.
Electrostatic and bending energies predict staggering and splaying in nonmuscle myosin II minifilaments
Authors: Kaufmann Tom , Schwarz Ulrich S.
Published: March 2020

Recent experiments with super-resolution live cell microscopy revealed that nonmuscle myosin II minifilaments are much more dynamic than formerly appreciated, often showing plastic processes such as splitting, concatenation and stacking. Here we combine sequence information, electrostatics and elasticity theory to demonstrate that the parallel staggers at 14.3, 43.2 and 72 nm have a strong tendency to splay their heads away from the minifilament, thus potentially initiating the diverse processes seen in live cells. In contrast, the straight antiparallel stagger with an overlap of 43 nm is very stable and likely initiates minifilament nucleation. Using stochastic dynamics in a newly defined energy landscape, we predict that the optimal parallel staggers between the myosin rods are obtained by a trial-and-error process in which two rods attach and re-attach at different staggers by rolling and zipping motion. The experimentally observed staggers emerge as the configurations with the largest contact times. We find that contact times increase from isoforms C to B to A, that A-B-heterodimers are surprisingly stable and that myosin 18A should incorporate into mixed filaments with a small stagger. Our findings suggest that nonmuscle myosin II minifilaments in the cell are first formed by isoform A and then convert to mixed A-B-filaments, as observed experimentally.

Author summary

Nonmuscle myosin II (NM2) is a non-processive molecular motor that assembles into minifilaments with a typical size of 300 nm to generate force and motion in the actin cytoskeleton. This process is essential for many cellular processes such as adhesion, migration, division and mechanosensing. Due to their small size below the resolution limit, minifilaments are a challenge for imaging with traditional light microscopy. With the advent of super-resolution microscopy, however, it has become apparent that the formation of NM2-minifilaments is much more dynamic than formerly appreciated. Modeling the electrostatic interaction between the rigid rods of the myosin monomers has confirmed the main staggers observed in experiments, but cannot explain these high dynamics. Here we complement electrostatics by elasticity theory and stochastic dynamics to show that the parallel staggers are likely to splay away from the main axis of the minifilament and that monomers attach and deattach with rolling and zipping motions. Based on the sequences of the different NM2-isoforms, we predict that isoform A forms the most stable homofilaments and that A-B-heterofilaments are also very stable.
Reconstruction of the urinary tract at the appropriate time reduces fibrosis of the metanephros in rats as judged by imaging
Authors: Nishi Kotaro , Haji Takafumi , Matsumoto Takuya , Hayakawa Chisato , Maeda Kenichi , Okano Shozo , Yokoo Takashi , Iwai Satomi
Published: March 2020

Chronic kidney disease leads to high morbidity rates among humans. It is a serious disease that requires curative treatments other than kidney transplantation. Recently, we successfully established the iPS-derived generated kidney, which might produce urine. The urine can be directed to the native bladder with a stepwise peristaltic ureter system, followed by anastomosis with the recipient ureter for reconstruction of the urinary tract. However, the growth of the regenerated kidney varies significantly, whereas the time window of the anastomosis is quite narrow. Therefore, this study was conducted to evaluate the growth of transplanted metanephros with bladder periodically and noninvasively using computed tomography and ultrasonography. Ultrasonographic findings showed high correlations with computed tomographic findings and clearly evaluated metanephros with bladder. We found that the degree of growth of the metanephros with bladder after the transplantation differed in each individual. However, most of them reached the appropriate period for urinary tract reconstruction within 3 weeks after transplantation. Optimizing the stepwise peristaltic ureter system anastomosis by ultrasonography reduced long-term tubular dilation of the metanephros, thereby decreasing fibrosis caused by transforming growth factor-β. This may be significantly related to long-term maturation of fetal grafts. These results provide new insights into transplanting regenerated kidneys in higher animals. We are one step closer to the first human trial of kidney generation.
Behavioral response of insecticide-resistant mosquitoes against spatial repellent: a modified self-propelled particle model simulation
Authors: Zhou Guofa , Yu Leonard , Wang Xiaoming , Zhong Daibin , Lee Ming-chieh , Kibret Solomon , Yan Guiyun
Published: March 2020

Rapidly increasing pyrethroid insecticide resistance and changes in vector biting and resting behavior pose serious challenges in malaria control. Mosquito repellents, especially spatial repellents, have received much attention from industry. Many of these repellents contain the same or similar chemicals as those used in insecticides. Does resistance to insecticides affect the efficacy of spatial repellents? We attempted to simulate interactions between mosquitoes and repellents using a machine learning method, the self-propelled particle (SPP) model, which we modified to include attractiveness/repellency effects. We simulated a random walk scenario and scenarios with insecticide susceptible/resistant mosquitoes against repellent alone and against repellent plus attractant (to mimic a human host). We assumed attractant odors and repellent chemicals diffused randomly and omnidirectionally, and that mosquitoes were confined in a cubic cage. We modified the velocity and direction components of SPP using attraction/repulsion rates and concentrations. Simulation results indicated that without attractant/repellent, mosquitoes would fly anywhere in the cage at random. With attractant, mosquitoes might or might not fly toward the source (i.e., the human), depending on the simulation time (and thus the attractant concentration distribution). Eventually, however, all mosquitoes were attracted to the source of the odor. With repellent, results depended on the amount of chemical used and the level of mosquito insecticide resistance. All insecticide-susceptible mosquitoes eventually moved to the corner of the cage farthest from the repellent release point. Surprisingly, a high proportion of highly resistant mosquitoes might reach the attractant release point (the human) earlier in the simulation when repellent was present compare to no repellent was present. At fixed concentration, a high proportion of mosquitoes could be able to reach the host when the relative repellency efficacy (compare to attractant efficacy) was <1, whereas, no mosquitoes reached the host when the relative repellency efficacy was > 1. This result implies that repellent may not be sufficient against highly physiologically insecticide resistant mosquitoes, since very high concentrations of repellent are neither practically feasible nor cost-effective.
The genetic structure of Norway
Authors: Mattingsdal Morten , Ebenesersdóttir S. Sunna , Moore Kristjan H. S. , Andreassen Ole A. , Hansen Thomas F. , Werge Thomas , Kockum Ingrid , Olsson Tomas , Alfredsson Lars , Helgason Agnar , Stefánsson Kári , Hovig Eivind
Published: March 2020

The aim of the present study was to describe the genetic structure of the Norwegian population using genotypes from 6369 unrelated individuals with detailed information about places of residence. Using standard single marker- and haplotype-based approaches, we report evidence of two regions with distinctive patterns of genetic variation, one in the far northeast, and another in the south of Norway, as indicated by fixation indices, haplotype sharing, homozygosity and effective population size. We detect and quantify a component of Uralic Sami ancestry that is enriched in the North. On a finer scale, we find that rates of migration have been affected by topography like mountain ridges. In the broader Scandinavian context, we detect elevated relatedness between the mid- and northern border areas towards Sweden. The main finding of this study is that despite Norway’s long maritime history and as a former Danish territory, the region closest to mainland Europe in the south appears to have been the most isolated region in Norway, highlighting the open sea as a barrier to gene flow.
Arrayed CRISPRi and Quantitative Imaging Describe the Morphotypic Landscape of Essential Mycobacterial Genes
Authors: de Wet Timothy J. , Winkler Kristin R. , Mhlanga Musa M. , Mizrahi Valerie , Warner Digby F.
Published: March 2020

Mycobacterium tuberculosispossesses a large number of genes of unknown or merely predicted function, undermining fundamental understanding of pathogenicity and drug susceptibility. To address this challenge, we developed a high-throughput functional genomics approach combining inducible CRISPR-interference and image-based analyses of morphological features and sub-cellular molecular localizations in the related non-pathogen,M. smegmatis. Applying automated imaging and analysis to an arrayed library of 272 essential gene knockdown mutants, we derive robust, quantitative descriptions of bacillary morphologies consequent on gene silencing. Leveraging statistical-learning, we demonstrate that functionally related genes cluster by morphotypic similarity and that this information can be used to infer gene function. Exploiting this observation, we reveal a previously unknown restriction-modification system, and identify filamentation as a defining mycobacterial response to histidine starvation. Our results support the application of large-scale image-based analyses for mycobacterial functional genomics, simultaneously establishing the utility of this approach for drug mechanism-of-action studies.
Mechanism-based inhibitors of SIRT2: structure–activity relationship, X-ray structures, target engagement, regulation of α-tubulin acetylation and inhibition of breast cancer cell migration
Authors: Nielsen Alexander L. , Rajabi Nima , Kudo Norio , Lundø Kathrine , Moreno-Yruela Carlos , Bæk Michael , Fontenas Martin , Lucidi Alessia , Madsen Andreas S. , Yoshida Minoru , Olsen Christian A.
Published: March 2020

Sirtuin 2 (SIRT2) is a protein deacylase enzyme that removes acetyl groups and longer chain acyl groups from post-translationally modified lysine residues. It affects diverse biological functions in the cell and has been considered a drug target in relation to both neurodegenerative diseases and cancer. Therefore, access to well-characterized and robust tool compounds is essential for the continued investigation of the complex functions of this enzyme. Here, we report a collection of probes that are potent, selective, stable in serum, water-soluble, amenable to cell culture experiments, and inhibit both SIRT2 deacetylation and demyristoylation. Compared to the current landscape of SIRT2 inhibitors, this is a unique ensemble of features built into a single compound. We expect the developed chemotypes to find broad application in the interrogation of SIRT2 functions in both healthy and diseased cells, and to provide a foundation for the development of future therapeutics.
IDH1 Mutations Induce Organelle Defects Via Dysregulated Phospholipids
Authors: Lita Adrian , Pliss Artem , Kuzmin Andrey , Yamasaki Tomohiro , Zhang Lumin , Dowdy Tyrone , Burks Christina , de Val Natalia , Celiku Orieta , Ruiz-Rodado Victor , Nicoli Elena-Raluca , Kruhlak Michael , Andresson Thorkell , Das Sudipto , Yang Chunzhang , Schmitt Rebecca , Herold-Mende Christel , Gilbert Mark R. , Prasad Paras N. , Larion Mioara
Published: March 2020

Cytosolic IDH1 enzyme plays a key, but currently unexplored, role in lipid biosynthesis. Using Raman imaging microscopy, we identified heterogeneous lipid profiles in cellular organelles attributed uniquely to IDH1 mutations. Via organelle lipidomics, we found an increase in saturated and monounsaturated fatty acids in the endoplasmic reticulum of IDH1mutcells compared with IDHWTglioma. We showed that these fatty acids incorporate into phospholipids and induce organelle dysfunctions, with prominent dilation of Golgi apparatus, which can be restored by transient knockdown of stearyl-CoA desaturase or inhibition of D-2-hydroxyglutarate (D-2HG) formation. We validated these findings using tissue from patients with glioma. Oleic acid addition led to increased sensitivity to apoptosis of IDH1mutcells compared with IDHWT. Addition of D-2HG to U251WTcells lead in increased ER and Golgi apparatus dilation. Collectively, these studies provide clinically relevant insights into the functional link between IDH1mut-induced lipid alterations and organelle dysfunction, with therapeutic implications.

Significance

Gliomas are devastating tumors, with the most aggressive form—glioblastoma multiforme— correlated with a mean patient survival of 14.5 months. No curative treatment exists to date. Low-grade glioma (LGG) with the isocitrate dehydrogenase 1 (IDH1) mutation, R132H, provides a survival benefit to patients. Understanding the unique metabolic profile of IDH1mutcould provide clues regarding its association with longer survival and information about therapeutic targets. Herein, we identified lipid imbalances in organelles, generated by IDHmutin cells and patient tissue, that were responsible for Golgi dilation and that correlated with increased survival. Addition of oleic acid, which tilted the balance towards elevated levels of monounsaturated fatty acids produced IDH1mut-specific cellular apoptosis.

Highlights

Single-organelle omics revealed unique alterations in lipid metabolism due to IDH1-mutations.

IDH mutation leads to organelle-wide structural defects.

IDH1 mutation leads to increased monounsaturated fatty acids levels in glioma cells and oligodendroglioma patient samples.

Lipid alterations affect the membrane integrity of the Golgi apparatus.

Increased D-2HG induced SCD expression and elevated monounsaturated fatty acids

Tilting the balance toward more-abundant monounsaturated fatty acids leads to specific IDH1mutglioma apoptosis.
Metabolite Quantitative Trait Loci for flavonoids provide new insights into the genetic architecture of strawberry (Fragariaxananassa) fruit quality
Authors: Labadie Marc , Vallin Guillaume , Petit Aurélie , Ring Ludwig , Hoffmann Thomas , Gaston Amèlia , Potier Aline , Schwab Wilfried , Rothan Christophe , Denoyes Béatrice
Published: March 2020

Flavonoids are products from specialized metabolism that contribute to fruit sensorial (colour) and nutritional (antioxidant properties) quality. Here, using a pseudo full-sibling F1progeny previously studied for fruit sensorial quality of cultivated strawberry (Fragariaxananassa), we explored over two successive years the genetic architecture of flavonoid-related traits using LC-ESI-MS (13 compounds including anthocyanins, flavonols and flavan-3-ols) and colorimetric assays (anthocyanins, flavonoids, phenolics, FRAP and TEAC antioxidant capacity). Network correlation analysis highlighted the high connectivity of flavonoid compounds within each chemical class and low correlation with colorimetric traits except anthocyanins. Mapping onto the female and male linkage maps of 152 flavonoid metabolic QTLs (mQTLs) and of 26 colorimetric QTLs indicated co-localization on few linkage groups of major flavonoid- and taste-related QTLs previously uncovered. These results pave the way for the discovery of genetic variations underlying flavonoid mQTLs and for marker-assisted selection of strawberry varieties with improved sensorial and nutritional quality.
The influence of the phylogenetic inference pipeline on murine antibody repertoire sequencing data following viral infection
Authors: Yermanos Alexander , Greiff Victor , Stadler Tanja , Oxenius Annette , Reddy Sai T.
Published: March 2020

Understanding B cell evolution following vaccination or infection is crucial for instructing targeted immunotherapies when searching for potential therapeutic or virus-neutralizing antibodies. Antibody phylogenetics holds the potential to quantify both clonal selection and somatic hypermutation, two key players shaping B cell evolution. A wide range of bioinformatic pipelines and phylogenetic inference methods have been utilized on antibody repertoire sequencing datasets to delineate B cell evolution. Although the majority of B cell repertoire studies incorporate some aspect of antibody evolution, how the chosen computational methods affect the results is largely ignored. Therefore, we performed an extensive computational analysis on time-resolved antibody repertoire sequencing data to better characterize how commonly employed bioinformatic practices influence conclusions regarding antibody selection and evolution. Our findings reveal that different combinations of clonal lineage assignment strategies, phylogenetic inference methods, and biological sampling affect the inferred size, mutation rates, and topologies of B cell lineages in response to virus infection.
Area from image analyses accurately estimates dry-weight biomass of juvenile moss tissue
Authors: Burtscher Wesley P. , List Marna A. , Payton Adam C. , McDaniel Stuart F. , Carey Sarah B.
Published: March 2020

Mosses have long served as models for studying many areas of plant biology. Investigators have used two-dimensional measurements of juvenile growth from photographs as a surrogate for dry-weight biomass. The relationship between area and biomass, however, has not been critically evaluated.

Here we grew axenic tissue cultures of tenCeratodon purpureusisolates to study the relationship between these parameters. We measured area and biomass on replicate cultures with two distinct starting inoculum sizes each week for three weeks and examined the correlation between area and biomass as well as the influence of variation in inoculum size on both parameters.

We found a strong correlation between area and biomass after two weeks of growth. Furthermore, we found inoculum size affected biomass during the first week of growth but not subsequent weeks and inoculum size had no detectible effect on area.

These analyses provide experimental confirmation that area is a suitable proxy for biomass and provide clear guidelines for when inoculum size variation may affect downstream growth estimates.
Motor neurons involved in fine motor control are labeled by tracingAtoh1-lineage neurons in the spinal cord
Authors: Ogujiofor Osita W. , Pop Iliodora V. , Espinosa Felipe , Durodoye Razaq O. , Viacheslavov Michael L. , Jarvis Rachel , Landy Mark A. , Fishell Gordon , Machold Robert P. , Lai Helen C.
Published: March 2020

Motor neurons (MNs) innervating the digit muscles of the intrinsic hand and foot (IH and IF) control fine motor movements. Previous studies suggest that the IH and IF MN pools have a unique developmental history in comparison to limb MN pools. Consistent with having this unique development, we find that the IH and IF MN pools are labeled postnatally using a CRE knock-in mouse line ofAtoh1, a developmentally expressed basic helix-loop-helix (bHLH) transcription factor, while limb-innervating MN pools are not. Approximately 60% of the IH and IF MN pools are labeled and are a mixture of alpha and gamma-MNs. In addition, becauseAtoh1is known developmentally to specify many cerebellar-projecting neurons, we tested the hypothesis that IH and IF MNs can send axon collaterals to the cerebellum as a mechanism of corollary discharge. Using intersectional genetic, viral labeling, and retrograde labeling strategies, we were unable to provide evidence in support of this idea. As a secondary finding of our viral labeling experiments, we report here that injection of both AAV and Lentiviruses in the periphery can cross the blood-brain barrier to infect Purkinje cells within the central nervous system. Altogether, though, we find that labeling of the IH and IF motor neurons using theAtoh1CRE knock-in mouse suggests that IH and IF MNs have a unique developmental history and that this mouse strain might be a useful tool to target these specific sets of neurons allowing for functional studies of fine motor control.

Significance Statement

Motor neurons (MNs) of the intrinsic hand and foot (IH and IF) are labeled postnatally using a CRE knock-in mouse line of the basic helix-loop-helix (bHLH) transcription factorAtoh1indicating a unique developmental history. We tested whether IH and IF MNs send axon collaterals rostrally to the cerebellum as a mechanism of direct corollary discharge from MNs, but the question remains unresolved. As a resource for the community, we report that injection of both AAV and Lentiviruses in the periphery can cross the blood-brain barrier and infect Purkinje cells within the central nervous system.
Selective interferon responses of intestinal epithelial cells minimize TNFα cytotoxicity
Authors: Van Winkle Jacob A. , Constant David A. , Li Lena , Nice Timothy J.
Published: March 2020

Interferon (IFN) family cytokines stimulate genes (ISGs) that are integral to antiviral host defense. Type I IFNs act systemically whereas type III IFNs act preferentially at epithelial barriers. Among barrier cells, intestinal epithelial cells (IECs) are particularly dependent on type III IFN for control and clearance of virus infection, but the physiological basis of this selective IFN response is not well understood. Here, we confirm that type III IFN treatment elicits robust and uniform ISG expression in neonatal mouse IECs and inhibits replication of IEC-tropic rotavirus. In contrast, type I IFN elicits a marginal ISG response in neonatal mouse IECs and does not inhibit rotavirus replication.In vitrotreatment of IEC organoids with type III IFN results in ISG expression that mirrors thein vivotype III IFN response. However, the response of IEC organoids to type I IFN is strikingly increased relative to type III IFN in magnitude and scope. The expanded type I IFN-specific response includes pro-apoptotic genes and potentiates toxicity triggered by tumor necrosis factor alpha (TNFα). The ISGs stimulated in common by types I and III IFN have strong interferon-stimulated response element (ISRE) promoter motifs, whereas the expanded set of type I IFN-specific ISGs, including pro-apoptotic genes, have weak ISRE motifs. Thus, preferential responsiveness of IECs to type III IFNin vivoenables selective ISG expression during infection that confers antiviral protection but minimizes disruption of intestinal homeostasis.
COVID-19 Vaccine Candidates: Prediction and Validation of 174 SARS-CoV-2 Epitopes
Authors: Prachar Marek , Justesen Sune , Steen-Jensen Daniel Bisgaard , Thorgrimsen Stephan , Jurgons Erik , Winther Ole , Bagger Frederik Otzen
Published: March 2020

The recent outbreak of SARS-CoV-2 (2019-nCoV) virus has highlighted the need for fast and efficacious vaccine development. Stimulation of a proper immune response that leads to protection is highly dependent on presentation of epitopes to circulating T-cells via the HLA complex. SARS-CoV-2 is a large RNA virus and testing of all overlapping peptidesin vitroto deconvolute an immune response is not feasible. Therefore HLA-binding prediction tools are often used to narrow down the number of peptides to test. We tested 19 epitope-HLA-binding prediction tools, and using anin vitropeptide MHC stability assay, we assessed 777 peptides that were predicted to be good binders across 11 MHC allotypes. In this investigation of potential SARS-CoV-2 epitopes we found that current prediction tools vary in performance when assessing binding stability, and they are highly dependent on the MHC allotype in question. Designing a COVID-19 vaccine where only a few epitope targets are included is therefore a very challenging task. Here, we present 174 SARS-CoV-2 epitopes with high prediction binding scores, validated to bind stably to 11 HLA allotypes. Our findings may contribute to the design of an efficacious vaccine against COVID-19.
Mechanical memory in cells emerges from mechanotransduction with transcriptional feedback and epigenetic plasticity
Authors: Mathur Jairaj , Shenoy Vivek B. , Pathak Amit
Published: March 2020

Emerging evidence shows that cells are able to sense and store a memory of their past mechanical environment. Since existing mechanotransduction models are based on adhesion and cytoskeletal dynamics that occurs over seconds and minutes, they do not capture memory observed over days or weeks. We postulate that transcriptional activity and epigenetic plasticity, upstream of adhesion-based signaling, need to be invoked to explain long-term mechanical memory. Here, we present a theory for mechanical memory in cells governed by three key components. First, cells on a stiff matrix are primed by a transcriptional reinforcement of cytoskeletal signaling. Second, longer stiff-priming progressively produces more memory-regulating factors and reduces epigenetic plasticity. Third, when stiff-primed cells move to soft matrix, the reduced epigenetic plasticity blocks new transcription required for cellular adaptation to the new matrix. This stalled transcriptional state gives rise to memory. We validate this model against previous experimental findings of memory storage and decay in epithelial cell migration and stem cell differentiation. We also predict wide-ranging memory responses for different cell types of varying protein kinetics and priming conditions. This theoretical framework for mechanical memory expands the timescales of mechanotransduction captured by conventional models by integrating cytoskeletal signaling with transcriptional activity and epigenetic plasticity. Our model predictions explain mechanical memory and propose new experiments to test spatiotemporal regulation of cellular memory in diverse contexts ranging from cell differentiation to migration and growth.
Emergence of SARS-CoV-2 through Recombination and Strong Purifying Selection
Authors: Li Xiaojun , Giorgi Elena E. , Marichann Manukumar Honnayakanahalli , Foley Brian , Xiao Chuan , Kong Xiang-Peng , Chen Yue , Korber Bette , Gao Feng
Published: March 2020

COVID-19 has become a global pandemic caused by a novel coronavirus SARS-CoV-2. Understanding the origins of SARS-CoV-2 is critical for deterring future zoonosis and for drug discovery and vaccine development. We show evidence of strong purifying selection around the receptor binding motif (RBM) in the spike gene and in other genes among bat, pangolin and human coronaviruses, indicating similar strong evolutionary constraints in different host species. We also demonstrate that SARS-CoV-2’s entire RBM was introduced through recombination with coronaviruses from pangolins, possibly a critical step in the evolution of SARS-CoV-2’s ability to infect humans. Similar purifying selection in different host species and frequent recombination among coronaviruses suggest a common evolutionary mechanism that could lead to new emerging human coronaviruses.

One Sentence Summary

Extensive Recombination and Strong Purifying Selection among coronaviruses from different hosts facilitate the emergence of SARS-CoV-2
K2Pchannel C-type gating involves asymmetric selectivity filter order-disorder transitions
Authors: Lolicato Marco , Natale Andrew M. , Abderemane-Ali Fayal , Crottès David , Capponi Sara , Duman Ramona , Wagner Armin , Rosenberg John M. , Grabe Michael , Minor Daniel L.
Published: March 2020

K2Pchannels regulate nervous, cardiovascular, and immune system functions1,2through the action of their selectivity filter (C-type) gate3-6. Although structural studies show K2Pconformations that impact activity7-13, no selectivity filter conformational changes have been observed. Here, combining K2P2.1 (TREK-1) X-ray crystallography in different potassium concentrations, potassium anomalous scattering, molecular dynamics, and functional studies, we uncover the unprecedented, asymmetric, potassium-dependent conformational changes underlying K2PC-type gating. Low potassium concentrations evoke conformational changes in selectivity filter strand 1 (SF1), selectivity filter strand 2 (SF2), and the SF2-transmembrane helix 4 loop (SF2-M4 loop) that destroy the S1 and S2 ion binding sites and are suppressed by C-type gate activator ML335. Shortening the uniquely long SF2-M4 loop to match the canonical length found in other potassium channels or disrupting the conserved Glu234 hydrogen bond network supporting this loop blunts C-type gate response to various physical and chemical stimuli. Glu234 network destabilization also compromises ion selectivity, but can be reversed by channel activation, indicating that the ion binding site loss reduces selectivity similar to other channels14. Together, our data establish that C-type gating occurs through potassium-dependent order-disorder transitions in the selectivity filter and adjacent loops that respond to gating cues relayed through the SF2-M4 loop. These findings underscore the potential for targeting the SF2-M4 loop for the development of new, selective K2Pchannel modulators.
Ciliation of muscle stem cells is critical to maintain regenerative capacity and is lost during aging
Authors: Palla A.R. , Hilgendorf K.I. , Yang A.V. , Kerr J.P. , Hinken A.C. , Demeter J. , Kraft P. , Mooney N.A. , Yucel N. , Jackson P.K. , Blau H.M.
Published: March 2020

During aging, the regenerative capacity of muscle stem cells (MuSCs) decreases, diminishing the ability of muscle to repair following injury. We performed a small molecule library screen and discovered that the proliferation and expansion of aged MuSCs is regulated by signal transduction pathways organized by the primary cilium, a cellular protrusion that serves as a sensitive sensory organelle. Abolishing MuSC ciliain vivoseverely impaired injury-induced muscle regeneration. In aged muscle, a cell intrinsic defect in MuSC ciliation leading to impaired Hedgehog signaling was associated with the decrease in regenerative capacity. This deficit could be overcome by exogenous activation of Hedgehog signaling which promoted MuSC expansion, bothin vitroandin vivo. Delivery of the small molecule Smoothened agonist (SAG) to muscles of aged mice restored regenerative capacity leading to increased strength post-injury. These findings provide fresh insights into the signaling dysfunction in aging and identify the ciliary Hedgehog signaling pathway as a potential therapeutic target to counter the loss of muscle regenerative capacity which accompanies aging.
DIRECT RT-qPCR DETECTION OF SARS-CoV-2 RNA FROM PATIENT NASOPHARYNGEAL SWABS WITHOUT AN RNA EXTRACTION STEP
Authors: Bruce Emily A. , Huang Meei-Li , Perchetti Garrett A. , Tighe Scott , Laaguiby Pheobe , Hoffman Jessica J. , Gerrard Diana L. , Nalla Arun K. , Wei Yulun , Greninger Alexander L. , Diehl Sean A. , Shirley David J. , Leonard Debra G. B. , Huston Christopher D. , Kirkpatrick Beth D. , Dragon Julie A. , Crothers Jessica W. , Jerome Keith R. , Botten Jason W.
Published: March 2020

The ongoing COVID-19 pandemic has caused an unprecedented need for rapid diagnostic testing. The Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) recommend a standard assay that includes an RNA extraction step from a nasopharyngeal (NP) swab followed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to detect the purified SARS-CoV-2 RNA. The current global shortage of RNA extraction kits has caused a severe bottleneck to COVID-19 testing. We hypothesized that SARS-CoV-2 RNA could be detected from NP samples via a direct RT-qPCR assay that omits the RNA extraction step altogether, and tested this hypothesis on a series of blinded clinical samples. The direct RT-qPCR approach correctly identified 92% of NP samples (n = 155) demonstrated to be positive for SARS-CoV-2 RNA by traditional clinical diagnostic RT-qPCR that included an RNA extraction. Thus, direct RT-qPCR could be a front-line approach to identify the substantial majority of COVID-19 patients, reserving a repeat test with RNA extraction for those individuals with high suspicion of infection but an initial negative result. This strategy would drastically ease supply chokepoints of COVID-19 testing and should be applicable throughout the world.