bluuebunny/crossref_metadata_2025 huggingface dataset:
Expression andin vitroanticancer activity of Lp16-PSP, a member of the YjgF/YER057c/UK114 protein family from the mushroomLentinula edodesC91-3
Authors: Joseph Thomson Patrick , Zhao Qianqian , Chanda Warren , Kanwal Sadia , Fang Yukun , Zhong MinTao , Huang Min
Published: April 2020

Latcripin-16 (Lp16-PSP) is a gene that was extracted as a result ofde novocharacterization of theLentinula edodes strainC91-3transcriptome. The aim of the present study was to clone, express and investigate the selectivein vitroanticancer potential of Lp16-PSP in human cell lines. Lp16-PSP was analyzed using bioinformatics tools, cloned in a prokaryotic expression vector pET32a (+) and transformed intoE. coliRosetta gami. It was expressed and solubilized under optimized conditions. The differential scanning fluorometry (DSF)-guided refolding method was used with modifications to identify the proper refolding conditions for the Lp16-PSP protein. In order to determine the selective anticancer potential of Lp16-PSP, a panel of human cancerous and non-cancerous cell lines was used. Lp16-PSP protein was identified as endoribonuclease L-PSP protein and a member of the highly conserved YjgF/YER057c/UK114 protein superfamily. Lp16-PSP was expressed under optimized conditions (37°C for 4 h following induction with 0.5 mM isopropyl β-D-1-thiogalactopyranoside). Solubilization was achieved with mild solubilization buffer containing 2M urea using the freeze-thaw method. The DSF guided refolding method identified the proper refolding conditions (50 mM Tris-HCl, 100 mM NaCl, 1 mM EDTA, 400 mM Arginine, 0.2 mM GSH and 2 mM GSSG; pH 8.0) for Lp16-PSP, with a melting transition of ~58°C. A final yield of ~16 mg of purified Lp16-PSP from 1 L of culture was obtained following dialysis and concentration by PEG 20,000. A Cell Counting Kit-8 assay revealed the selective cytotoxic effect of Lp16-PSP. The HL-60 cell line was demonstrated to be most sensitive to Lp16-PSP, with an IC50value of 74.4±1.07 μg/ml. The results of the present study suggest that Lp16-PSP may serve as a potential anticancer agent; however, further investigation is required to characterize this anticancer effect and to elucidate the molecular mechanism underlying the action of Lp16-PSP.
ForestSaccharomyces paradoxusare robust to seasonal biotic and abiotic changes
Authors: Boynton Primrose J. , Wloch-Salamon Dominika , Landermann Doreen , Stukenbrock Eva H.
Published: April 2020

Microorganisms are famous for adapting quickly to new environments. However, most evidence for rapid microbial adaptation comes from laboratory experiments or domesticated environments, and it is unclear how rates of adaptation scale from human-influenced environments to the great diversity of wild microorganisms. We examined potential monthly-scale selective pressures in the model forest yeastSaccharomyces paradoxus. Contrary to expectations of seasonal adaptation, theS. paradoxuspopulation was stable over four seasons in the face of abiotic and biotic environmental changes. While theS. paradoxuspopulation was diverse, including 41 unique genotypes among 192 sampled isolates, there was no correlation betweenS. paradoxusgenotypes and seasonal environments. Consistent with observations from otherS. paradoxuspopulations, the forest population was highly clonal and inbred. This lack of recombination, paired with population stability, implies thatS. paradoxusevolved the phenotypic plasticity needed to resist seasonal environmental fluctuations long ago, and that individualS. paradoxusare generalists with regard to seasonal environments. Similarly, while the forest population included diversity among phenotypes related to intraspecific interference competition, there was no evidence for active coevolution among these phenotypes. At least ten percent of the forestS. paradoxusindividuals produced “killer toxins”, which kill sensitiveSaccharomycescells, but the presence of a toxin-producing isolate did not predict resistance to the toxin among nearby isolates. How forest yeasts acclimate to changing environments remains an open question, and future studies should investigate the physiological responses that allow microbial cells to cope with environmental fluctuations in their native habitats.
ProSolo: Accurate Variant Calling from Single Cell DNA Sequencing Data
Authors: Lähnemann David , Köster Johannes , Fischer Ute , Borkhardt Arndt , McHardy Alice C. , Schönhuth Alexander
Published: April 2020

Obtaining accurate mutational profiles from single cell DNA is essential for the analysis of genomic cell-to-cell heterogeneity at the finest level of resolution. However, sequencing libraries suitable for genotyping require whole genome amplification, which introduces allelic bias and copy errors. As a result, single cell DNA sequencing data violates the assumptions of variant callers developed for bulk sequencing, which when applied to single cells generate significant numbers of false positives and false negatives. Only dedicated models accounting for amplification bias and errors will be able to provide more accurate calls.

We present ProSolo, a probabilistic model for calling single nucleotide variants from multiple displacement amplified single cell DNA sequencing data. It introduces a mechanistically motivated empirical model of amplification bias that improves the quantification of genotyping uncertainty. To account for amplification errors, it jointly models the single cell sample with a bulk sequencing sample from the same cell population—also enabling a biologically relevant imputation of missing genotypes for the single cell. Through these innovations, ProSolo achieves substantially higher performance in calling and genotyping single nucleotide variants in single cells in comparison to all state-of-the-art tools. Moreover, ProSolo implements the first approach to control the false discovery rate reliably and flexibly; not only for single nucleotide variant calls, but also for artefacts of single cell methodology that one may wish to identify, such as allele dropout.

ProSolo’s model is implemented into a flexible framework, encouraging extensions. The source code and usage instructions are available at:https://github.com/prosolo/prosolo
The hepatic compensatory response to elevated systemic sulfide promotes diabetes
Authors: Carter Roderick N. , Gibbins Matthew T.G. , Barrios-Llerena Martin E. , Wilkie Stephen E. , Freddolino Peter L. , Libiad Marouane , Vitvitsky Victor , Emerson Barry , Bihan Thierry Le , Brice Madara , Su Huizhong , Denham Scott G. , Homer Natalie Z.M. , Fadden Clare Mc , Tailleux Anne , Faresse Nourdine , Sulpice Thierry , Briand Francois , Gillingwater Tom , Ahn Kyo Han , Singha Subhankar , McMaster Claire , Hartley Richard C. , Staels Bart , Gray Gillian A. , Finch Andrew J. , Selman Colin , Banerjee Ruma , Morton Nicholas M.
Published: April 2020

Impaired hepatic glucose and lipid metabolism are hallmarks of type–2 diabetes. Increased sulfide production from cysteine, or sulfide–donor compounds, may beneficially regulate hepatic metabolism. Disposal of sulfide through the sulfide oxidation pathway (SOP) is critical for maintaining sulfide within a safe physiological range. We show that mice lacking the liver–enriched mitochondrial SOP enzyme thiosulfate sulfur–transferase (Tst−/−mice) exhibit high circulating sulfide, increased gluconeogenesis, hypertriglyceridemia and fatty liver, despite whole–body insulin–sensitisation. Unexpectedly, hepatic sulfide levels were normal inTst−/−mice, a result of homeostatic induction of mitochondrial sulfide disposal and glutathione excretion associated with net suppression of protein persulfidation and nuclear respiratory factor–2 target proteins. Proteomic and persulfidomic profiling converged on gluconeogenesis and hepatic lipid metabolism and revealed a selective deficit in medium–chain fatty acid oxidation inTst−/−mice. We reveal a critical role for TST in hepatic metabolism that raises implications for sulfide-donor strategies in the context of liver function and metabolic disease.
Genomic characterization of a diazotrophic microbiota associated with maize aerial root mucilage
Authors: Higdon Shawn M. , Pozzo Tania , Kong Nguyet , Huang Bihua , Yang Mai Lee , Jeannotte Richard , Brown C. Titus , Bennett Alan B. , Weimer Bart C.
Published: April 2020

A geographically isolated maize landrace cultivated on nitrogen-depleted fields without synthetic fertilizer in the Sierra Mixe region of Oaxaca, Mexico utilizes nitrogen derived from the atmosphere and develops an extensive network of mucilage-secreting aerial roots that harbors a diazotrophic microbiota. Targeting these diazotrophs, we selected nearly 600 microbes from a collection isolated from these plants and confirmed their ability to incorporate heavy nitrogen (15N2) metabolitesin vitro. Sequencing their genomes and conducting comparative bioinformatic analyses showed that these genomes had substantial phylogenetic diversity. We examined each diazotroph genome for the presence ofnifgenes essential to nitrogen fixation (nifHDKENB) and carbohydrate utilization genes relevant to the mucilage polysaccharide digestion. These analyses identified diazotrophs that possessed canonicalnifgene operons, as well as many other operon configurations with concomitant fixation and release of >700 different15N labeled metabolites. We further demonstrated that many diazotrophs possessed alternativenifgene operons and confirmed their genomic potential to derive chemical energy from mucilage polysaccharide to fuel nitrogen fixation. These results confirm that some diazotrophic bacteria associated with Sierra Mixe maize were capable of incorporating atmospheric nitrogen into their small molecule extracellular metabolites through multiplenifgene configurations while others were able to fix nitrogen without the canonical (nifHDKENB) genes.

Data Summary

Genetic resources, including biological materials and nucleic acid sequences, were accessed under an Access and Benefit Sharing (ABS) Agreement between the Sierra Mixe community and the Mars Corporation, and with authorization from the Mexican government. An internationally recognized certificate of compliance has been issued by the Mexican government under the Nagoya Protocol for such activities (ABSCH-IRCC-MX-207343-3). Any party seeking access to the nucleic acid sequences underlying the analysis reported here is subject to the full terms and obligations of the ABS agreement and the authorization from the government of Mexico. Individuals wishing to access nucleic acid sequence data for scientific research activities should contact Mars Incorporated Chief Science Officer atCSO@effem.com.
Mind Wandering in Sensory Cortices
Authors: Hung Shao-Min , Hsieh Po-Jang
Published: April 2020

Mind wandering contains rich phenomenology as we experience moment by moment, however, such linkage between our subjective experiences and the underlying neural mechanism has been missing in the literature. Here we report that the sensory contents of mind wandering recruit corresponding sensory cortices, serving as the neural bases of the sensory contents in mind wandering.
An essential role for MEF2C in the cortical response to loss of sleep
Authors: Bjorness Theresa E. , Kulkarni Ashwinikumar , Rybalchenko Volodymer , Suzuki Ayako , Bridges Catherine , Harrington Adam J. , Cowan Christopher W. , Takahashi Joseph S. , Konopka Genevieve , Greene Robert W.
Published: April 2020

Neuronal activity and gene expression in response to the loss of sleep can provide a window into the enigma of sleep function. Sleep loss is associated with brain differential gene expression, an increase in pyramidal cell mEPSC frequency and amplitude, and a characteristic rebound and resolution of slow wave sleep-slow wave activity (SWS-SWA). However, the molecular mechanism(s) mediating the sleep loss response are not well understood. We show that sleep-loss regulates MEF2C phosphorylation, a key mechanism regulating MEF2C transcriptional activity, and that MEF2C function in postnatal excitatory forebrain neurons is required for the biological events in response to sleep loss. These include altered gene expression, the increase and recovery of synaptic strength, and the rebound and resolution of SWS-SWA, which implicate MEF2C as an essential regulator of sleep function.

One Sentence Summary

MEF2C is critical to the response to sleep loss.
Single-cell RNA-seq analysis of human iPSC-derived motor neurons resolves early and predictive ALS signatures
Authors: Ho Ritchie , Workman Michael J. , Mathkar Pranav , Wu Kathryn , Kim Kevin J. , O’Rourke Jacqueline G. , Kellogg Mariko , Montel Valerie , Banuelos Maria G. , Aladesuyi Olubankole , Garcia Sandra Diaz , Oheb Daniel , Huang Steven , Khrebtukova Irena , Watson Lisa , Ravits John , Taylor Kevin , Baloh Robert H. , Svendsen Clive N.
Published: April 2020

Induced pluripotent stem cell (iPSC) derived neural cultures from amyotrophic lateral sclerosis (ALS) patients can reflect disease phenotypes targetable by treatments. However, widely used differentiation protocols produce mixtures of progenitors, neurons, glia, and other cells at various developmental stages and rostrocaudal neural tube segments. Here we present a methodology using single-cell RNA sequencing analysis to distinguish cell type expression in C9orf72 ALS, sporadic ALS, control, and genome-edited cultures across multiple subjects, experiments, and commercial platforms. Combinations of HOX and developmental gene expression with global clustering classified rostrocaudal, progenitor, and mantle zone fates. This demonstrated that iPSC-differentiated cells recapitulate fetal hindbrain and spinal cord development and resolved early, reproducible, and motor neuron-specific signatures of familial and sporadic ALS. This includes downregulated ELAVL3 expression, which persists into disease endstages. Single-cell analysis thus yielded predictive ALS markers in other human and mouse models which were otherwise undiscovered through bulk omics assays.
The partitioning of symbionts effects on host resource acquisition and developmental plasticity
Authors: Guilhot Robin , Xuéreb Anne , Fellous Simon
Published: April 2020

Many symbionts provide nutrients to their host and/or affect its phenotypic plasticity. Such symbiont effects on host resource acquisition and allocation are often simultaneous and difficult to disentangle. Here we partitioned symbiont effects on host resource acquisition and allocation using a new framework based on the analysis of a well-established trade-off between host fitness components. This framework was used to analyze the effect of symbiotic yeast on the larval development ofDrosophilalarvae in field-realistic conditions. The screening of eighteen yeast fresh isolates showed they had similar effects on the resource acquisition inDrosophila melanogaster, D. simulansandD. suzukiibut species-specific effects on resource allocation between either larval development speed or adult size. These differences shed light on the ecology ofDrosophilaflies and illustrate why distinguishing between these qualitatively different effects of microorganisms on hosts is essential to understand and predict symbiosis evolution.
Tuning parameters of dimensionality reduction methods for single-cell RNA-seq analysis
Authors: Raimundo Felix , Vallot Celine , Vert Jean Philippe
Published: April 2020

Background

Many computational methods have been developed recently to analyze single-cell RNA-seq (scRNA-seq) data. Several benchmark studies have compared these methods on their ability for dimensionality reduction, clustering or differential analysis, often relying on default parameters. Yet given the biological diversity of scRNA-seq datasets, parameter tuning might be essential for the optimal usage of methods, and determining how to tune parameters remains an unmet need.

Results

Here, we propose a benchmark to assess the performance of five methods, systematically varying their tunable parameters, for dimension reduction of scRNA-seq data, a common first step to many downstream applications such as cell type identification or trajectory inference. We run a total of 1.5 million experiments to assess the influence of parameter changes on the performance of each method, and propose two strategies to automatically tune parameters for methods that need it.

Conclusions

We find that principal component analysis (PCA)-based methods like scran and Seurat are competitive with default parameters but do not benefit much from parameter tuning, while more complex models like ZinbWave, DCA and scVI can reach better performance but after parameter tuning.
Single-cell resolution analysis of the crosstalk between chemogenically activated astrocytes and microglia
Authors: Philtjens Stéphanie , Turnbull Marion T. , Thedy Brian P. , Moon Younghye , Kim Jungsu
Published: April 2020

Astrocytes are the most common glial cell type in the brain, yet, it is unclear how their activation affects the transcriptome of neighboring cells. Engineered G protein-coupled receptors (GPCRs) called Designer Receptors Exclusively Activated by Designer Drugs (DREADDs) enable selective activation of specific cell types, such as astrocytes. Here, we combine activation of astrocytes in the hippocampus and cortex of healthy mice with single-cell RNA sequencing. Our data show that long-term activation of astrocytes dramatically alters the transcriptome of astrocytes and microglia. Genes that were differentially expressed in Gq-DREADD-activated astrocytes are involved in neurogenesis and low-density lipoprotein particle biology, while those in the microglia were involved in lipoprotein handling, purinergic receptor activity, and immune cell migration and chemotaxis. Furthermore, network analysis showed that Gq-DREADD-mediated activation in astrocytes resulted in an upregulation of genes involved in the GPCR signaling pathways and calcium ion homeostasis, confirming astrocyte activation. This dataset will serve as a resource for the broader neuroscience community, and our findings highlight the importance of studying transcriptomic alterations in microglia after astrocyte activationin vivo.
DNA damage independent inhibition of NF-κB transcription by anthracyclines
Authors: Chora Ângelo Ferreira , Pedroso Dora , Kyriakou Eleni , Pejanovic Nadja , Colaço Henrique , Gozzelino Raffaella , Barros André , Willmann Katharina , Velho Tiago , Moita Catarina F. , Santos Isa , Pereira Pedro , Carvalho Sílvia , Martins Filipa Batalha , Ferreira João A. , Fernandes de Almeida Sérgio , Benes Vladimir , Anrather Josef , Weis Sebastian , Soares Miguel P. , Geerlof Arie , Neefjes Jacques , Sattler Michael , Messias Ana C. , Neves-Costa Ana , Moita Luís Ferreira
Published: April 2020

Anthracyclines are among the most used and effective anticancer drugs. Their activity has been attributed to DNA double-strand breaks resulting from topoisomerase II poisoning and to eviction of histones from select sites in the genome. Here we show that the extensively used anthracyclines Doxorubicin, Daunorubicin and Epirubicin, decrease the transcription of nuclear factor kappa B (NF-κB)-dependent gene targets, but not interferon responsive genes. Using an NMR-based structural approach, we demonstrate that anthracyclines disturb the complexes formed between the NF-κB subunit RelA and its DNA binding sites. The variant anthracyclines Aclarubicin, Doxorubicinone and the newly developed Dimethyl-doxorubicin, which share anticancer properties with the other anthracyclines but do not induce DNA damage, also suppressed inflammation, thus uncoupling DNA damage from the effects on inflammation. These findings have implications for anticancer therapy and for the development of novel anti-inflammatory drugs with limited side effects for life-threatening conditions such as sepsis.
Genetic dissection of the fermentative and respiratory contributions supportingVibrio choleraehypoxic growth
Authors: Bueno Emilio , Sit Brandon , Waldor Matthew K. , Cava Felipe
Published: April 2020

Both fermentative and respiratory processes contribute to bacterial metabolic adaptations to low oxygen tension (hypoxia). In the absence of O2as a respiratory electron sink, many bacteria utilize alternative electron acceptors such as nitrate (NO3−). During canonical NO3−respiration, NO3−is reduced in a stepwise manner to N2by a dedicated set of reductases.Vibrio cholerae,the etiological agent of cholera, only requires a single periplasmic NO3−reductase (NapA) to undergo NO3−respiration, suggesting that the pathogen possesses a non-canonical NO3−respiratory chain. Here, we used complementary transposon-based screens to identify genetic determinants of general hypoxic growth and NO3−respiration inV. cholerae. We found that while theV. choleraeNO3−respiratory chain is primarily composed of homologues of established NO3−respiratory genes, it also includes components previously unlinked to this process, such as the Na+-NADH dehydrogenase Nqr. The ethanol-generating enzyme AdhE was shown to be the principal fermentative branch required during hypoxic growth inV. cholerae. Relative to singleadhEornapAmutant strains, aV. choleraestrain lacking both genes exhibited severely impaired hypoxic growthin vitroandin vivo.Our findings reveal the genetic bases for interactions between disparate energy production pathways that support pathogen fitness in shifting conditions. Such metabolic specializations inV. choleraeand other pathogens are potential targets for antimicrobial interventions.

IMPORTANCE

Bacteria reprogram their metabolism in environments with low oxygen levels (hypoxia). Typically, this occurs via regulation of two major, but largely independent, metabolic pathways-fermentation and respiration. Here, we found that the diarrheal pathogenVibrio choleraehas a respiratory chain for NO3−that consists largely of components found in other NO3−respiratory systems, but also contains several proteins not previously linked to this process. Both AdhE-dependent fermentation and NO3−respiration were required for efficient pathogen growth in both laboratory conditions and in an animal infection model. These observations provide genetic evidence for fermentative-respiratory interactions and identify metabolic vulnerabilities that may be targetable for new antimicrobial agents inV. choleraeand related pathogens.
A Ribosome Interaction Surface Sensitive to mRNA GCN Periodicity
Authors: Scopino Kristen , Williams Elliot , Elsayed Abdelrahman , Barr William A. , Krizanc Daniel , Thayer Kelly M. , Weir Michael P.
Published: April 2020

GCN codons are over-represented in initial codons of ORFs of prokaryote and eukaryote mRNAs. We describe a ribosome rRNA-protein surface that interacts with an mRNA GCN codon when next-in-line for the ribosome A site. The interaction surface is comprised of the edges of two stacked rRNA bases: the Watson-Crick edge of 16S/18S rRNA C1054 and adjacent Hoogsteen edge of A1196 (Escherichia coli16S rRNA numbering). Also part of the interaction surface, the planar guanidinium group of a conserved Arginine (R146 of yeast ribosomal protein Rps3) is stacked adjacent to A1196. On its other side, the interaction surface is anchored to the ribosome A site through base stacking of C1054 with the wobble anticodon base of the A-site tRNA. Using Molecular Dynamics simulations of a 495-residue subsystem of translocating ribosomes, we observe base pairing of C1054 to nucleotide G at position 1 of the next-in-line codon, consistent with previous cryo-EM observations, and hydrogen bonding of A1196 and R146 to C at position 2. Hydrogen bonding to both of these codon positions is significantly weakened when C at position 2 is changed to G, A or U. These sequence-sensitive mRNA-ribosome interactions at theC1054-A1196-R146 (CAR) surface potentially contribute to GCN-mediated regulation of protein translation.
Kingdom-wide analysis of the evolution of the plant type III polyketide synthase superfamily
Authors: Naake Thomas , Maeda Hiroshi A. , Proost Sebastian , Tohge Takayuki , Fernie Alisdair R.
Published: April 2020

The emergence of type III polyketide synthases (PKSs) was a pre-requisite for the conquest of land by the green lineage. To study the deep evolutionary history of this key family, we used phylogenomic synteny network and phylogenetic analyses of whole-genome data from 126 species spanning the green lineage. This study thereby combined study of genomic location and context with changes in gene sequences. We found that two major clades, CHS and LAP5/6 homologs, evolved early by a segmental duplication event prior to the divergence of Bryophytes and Tracheophytes. We propose that the macroevolution of the type III PKS superfamily is governed by whole-genome duplications and triplications. Intriguingly, the combined phylogenetic and synteny analyses in this study shed new insights into changes in the genomic location and context that are retained for a longer time scale with more recent functional divergence captured by gene sequence alterations.
RNA-GPS Predicts SARS-CoV-2 RNA Localization to Host Mitochondria and Nucleolus
Authors: Wu Kevin , Zou James , Chang Howard Y.
Published: April 2020

The SARS-CoV-2 coronavirus is driving a global pandemic, but its biological mechanisms are less well understood. SARS-CoV-2 is an RNA virus whose multiple genomic and sub-genomic RNA (sgRNA) transcripts hijack the host cell’s machinery, located across distinct cytotopic locations. Subcellular localization of its viral RNA could play important roles in viral replication and host antiviral immune response. Here we perform computational modeling of SARS-CoV-2 viral RNA localization across eight subcellular neighborhoods. We compare hundreds of SARS-CoV-2 genomes to the human transcriptome and other coronaviruses and perform systematic sub-sequence analyses to identify the responsible signals. Using state-of-the-art machine learning models, we predict that the SARS-CoV-2 RNA genome and all sgRNAs are enriched in the host mitochondrial matrix and nucleolus. The 5’ and 3’ viral untranslated regions possess the strongest and most distinct localization signals. We discuss the mitochondrial localization signal in relation to the formation of double-membrane vesicles, a critical stage in the coronavirus life cycle. Our computational analysis serves as a hypothesis generation tool to suggest models for SARS-CoV-2 biology and inform experimental efforts to combat the virus.
Magnetoencephalographic Signatures of Hierarchical Rule Learning in Newborns
Authors: Moser Julia , Schleger Franziska , Weiss Magdalene , Sippel Katrin , Dehaene-Lambertz Ghislaine , Preissl Hubert
Published: April 2020

Estimating the extent to which newborn humans process input from their environment, especially regarding the depth of processing, is a challenging question. To approach this problem, we measured brain responses in 20 newborns with magnetoencephalography (MEG) in a “local-global” auditory oddball paradigm in which two-levels of hierarchical regularities are presented. Results suggest that infants in the first weeks of life are able to learn hierarchical rules, yet a certain level of vigilance seems to be necessary. Newborns detected violations of the first-order regularity and displayed a mismatch response between 200-400ms. Violations of the second-order regularity only evoked a late response in newborns in an active state, which was expressed by a high heart rate variability. These findings are in line with those obtained in human adults and older infants suggesting a continuity in the functional architecture from term- birth on, despite the important immaturity of the human brain at this age.
A transient role of primary cilia in controlling direct versus indirect neurogenesis in the developing cerebral cortex
Authors: Hasenpusch-Theil Kerstin , Laclef Christine , Colligan Matt , Fitzgerald Eamon , Howe Katherine , Carroll Emily , Abrams Shaun R. , Reiter Jeremy F. , Schneider-Maunoury Sylvie , Theil Thomas
Published: April 2020

During the development of the cerebral cortex, neurons are generated directly from radial glial cells or indirectly via basal progenitors. The balance between these division modes determines the number and types of neurons formed in the cortex thereby affecting cortical functioning. Here, we investigate the role of primary cilia in this process. We show that a mutation in the ciliary geneInpp5eleads to a transient increase in direct neurogenesis and subsequently to an overproduction of layer V neurons in newborn mice. Loss ofInpp5ealso affects ciliary structure coinciding with increased Akt and mTOR signalling and reduced Gli3 repressor levels. Genetically re-storing Gli3 repressor rescues the decreased indirect neurogenesis inInpp5emutants. Overall, our analyses reveal how primary cilia determine neuronal subtype composition of the cortex by controlling direct vs indirect neurogenesis. These findings have implications for understanding cortical malformations in ciliopathies withINPP5Emutations.
ROS in tobacco stigma exudate affect pollen proteome and provoke membrane hyperpolarization
Authors: Maria Breygina , Ekaterina Klimenko , Eugeny Shilov , Anna Mamaeva , Viktor Zgoda , Igor Fesenko
Published: April 2020

1.

ROS are known to be accumulated in stigmas of different species and can possibly perform different functions in plant reproduction. Here we confirm the assumption that they affect pollen by altering ion transport through the plasma membrane; as a more deferred effect, pollen proteome is modified. We detected ROS in stigma exudate, found hyperpolarization in exudate-treated growing pollen tubes and used flow cytometry of pollen protoplasts to compare the effects of fresh exudate and exogenous H2O2on pollen tube plasmalemma. Exudate causes plasmalemma hyperpolarization similar to the one provoked by H2O2, which is abolished by catalase treatment and ROS quencher MnTMPP. Inhibitory analysis indicates the participation of Ca2+- and K+-conducting channels in the observed hyperpolarization, linking obtained data with previous patch-clamp studiesin vitro. For a deeper understanding of pollen response to ROS we analyzed proteome alterations in H2O2-treated pollen grains. We found 50 unique proteins and 20 differently accumulated proteins that are mainly involved in cell metabolism, energetics, protein synthesis and folding. Thus, pollen is getting ready for effective resource usage, construction of cellular components and rapid growth.

Highlights

The active substance in stigma exudate is H2O2

H2O2causes hyperpolarization mediated by the activation of cation channels.

H2O2affects pollen proteome; we found 50 unique proteins.
Clearance of senescent cells following cardiac ischemia-reperfusion injury improves recovery
Authors: Dookun Emily , Walaszczyk Anna , Redgrave Rachael , Palmowski Pawel , Tual-Chalot Simon , Suwana Averina , Chapman James , Jirkovsky Eduard , Sosa Leticia Donastorg , Gill Eleanor , Yausep Oliver E , Santin Yohan , Mialet-Perez Jeanne , Owens W Andrew , Grieve David , Spyridopoulos Ioakim , Taggart Michael , Arthur Helen M. , Passos João F. , Richardson Gavin D.
Published: April 2020

A key component of cardiac ischemia-reperfusion injury (IRI) is the increased generation of reactive oxygen species, leading to enhanced inflammation and tissue dysfunction in patients following intervention for myocardial infarction. In this study we hypothesized that oxidative stress, due to ischemia-reperfusion, induces senescence which contributes to the pathophysiology of cardiac IRI. We demonstrate that IRI induces cellular senescence in both cardiomyocytes and interstitial cell populations and treatment with the senolytic drug navitoclax after ischemia-reperfusion improves left ventricular function, increases myocardial vascularization, and decreases scar size. SWATH-MS based proteomics reveal that biological processes associated with fibrosis and inflammation, that were increased following ischemia-reperfusion, were attenuated upon senescent cell clearance. Furthermore, navitoclax treatment reduced the expression of proinflammatory, profibrotic and anti-angiogenic cytokines, including interferon gamma-induced protein-10, TGF-β3, interleukin-11, interleukin-16 and fractalkine. Our study provides proof-of-concept evidence that cellular senescence contributes to impaired heart function and adverse remodeling following cardiac ischemia-reperfusion. We also establish that post-IRI senescent cells play a considerable role in the inflammatory response. Subsequently, senolytic treatment, at a clinically feasible time point, attenuates multiple components of this response and improves clinically important parameters. Thus, cellular senescence represents a potential novel therapeutic avenue to improve patient outcomes following cardiac ischemia-reperfusion.
Multidecadal decline and recovery of aspen experiencing contrasting fire regimes: long-unburned, infrequent and frequent mixed-severity wildfire
Authors: Brewen Cerena J. , Berrill John-Pascal , Ritchie Martin W. , Boston Kevin , Dagley Christa M. , Jones Bobette , Coppoletta Michelle , Burnett Coye L.
Published: April 2020

Quaking aspen (Populus tremuloides) is a valued, minor component on western landscapes. It provides a wide range of ecosystem services and has been in decline throughout the arid west for the last century. This decline may be explained partially by the lack of fire on the landscape as aspen benefit from fire that eliminates conifer competition and stimulates reproduction through root suckering. Managers are interested in aspen restoration but there is a lack of knowledge about their spatial dynamics in response to fire. Our study area in northeastern California on the Lassen, Modoc and Plumas National Forests has experienced recent large mixed-severity wildfires where aspen was present, providing an opportunity to study the re-introduction of fire. We observed two time periods; a 54-year absence of fire from 1941 to 1993 preceding a 24-year period of wildfire activity from 1993 to 2017. We utilized aerial photos to delineate aspen stand size, location and succession to conifers. We chose aspen stands in areas where wildfires overlapped (twice-burned), where only a single wildfire burned, and areas that did not burn within the recent 24-year period. We looked at these same stands within the first period of fire exclusion for comparison (i.e., 1941-1993). In the absence of fire, all aspen stand areas declined and all stands experienced increases in conifer composition. After wildfire, stands that burned experienced a release from conifer competition and increased in stand area. Stands that burned twice or at high severity experienced a larger removal of conifer competition than stands that burned once at low severity, promoting aspen recovery and expansion. Stands with less edge:area ratio also expanded more with fire present. Across both time periods, stand movement, where aspen stand footprints were mostly in new areas compared to footprints of previous years, was highest in smaller stands. In the fire exclusion period, smaller stands exhibited greater changes in area and location (movement), highlighting their vulnerability to loss in the absence of disturbances that provide adequate growing space for aspen over time.
Systematic hormone-metabolite network provides insights of high salinity tolerance inPongamia pinnata(L.) pierre
Authors: Marriboina Sureshbabu , Sharma Kapil , Sengupta Debashree , Yadavalli Anurupa Devi , Sharma Rameshwar Prasad , Reddy Attipalli Ramachandra
Published: April 2020

Salinity stress results significant losses in plant productivity, and loss of cultivable lands. AlthoughPongamia pinnatais reported to be a salt tolerant semiarid tree crop, the adaptive mechanisms to saline environment are elusive. The present investigation describes alterations in hormonal and metabolic responses in correlation with physiological and molecular variations in leaves and roots of Pongamia at sea salinity level (3% NaCl) for 8 days. At physiological level, salinity induced adjustments in plant morphology, leaf gas exchange and ion accumulation patterns were observed. Our study also revealed that phytohormones including JAs and ABA play crucial role in promoting the salt adaptive strategies such as apoplasmic Na+sequestration and cell wall lignification in leaves and roots of Pongamia. Correlation studies demonstrated that hormones including ABA, JAs and SA showed a positive interaction with selective compatible metabolites (sugars, polyols and organic acids) to aid in maintaining osmotic balance and conferring salt tolerance to Pongamia. At the molecular level, our data showed that differential expression of transporter genes as well as antioxidant genes regulate the ionic and ROS homeostasis in Pongamia. Collectively, these results shed new insights on an integrated physiological, structural, molecular and metabolic adaptations conferring salinity tolerance to Pongamia.

High light

Our data, for the first time, provide new insights for an integrated molecular and metabolic adaptation conferring salinity tolerance in Pongamia. The present investigation describes alterations in hormonal and metabolic responses in correlation with physiological and molecular variations in Pongamia at sea salinity level (3% NaCl) for 8 days.
Plant pathogen infection risk tracks global crop yields under climate change
Authors: Chaloner Thomas M. , Gurr Sarah J. , Bebber Daniel P.
Published: April 2020

Global food security is strongly determined by crop production. Climate change-induced losses to production can occur directly, or indirectly, including via the distributions and impacts of plant pathogens. However, the likely changes in pathogen pressure in relation to global crop production are poorly understood. Here we show that temperature-dependent infection risk, r(T), for 80 fungal and oomycete crop pathogens will track projected yield changes in 12 crops over the 21st Century. For most crops, both yields and r(T) are likely to increase at high latitudes. In contrast, while the tropics will see little or no productivity gains, r(T) is also likely to decline. In addition, the USA, Europe and China may experience major changes in pathogen assemblages. The benefits of yield gains may therefore be tempered by the increased burden of crop protection due to increased and unfamiliar pathogens.
Random peptides rich in small and disorder-promoting amino acids are less likely to be harmful
Authors: Kosinski Luke , Aviles Nathan , Gomez Kevin , Masel Joanna
Published: April 2020

Proteins are the workhorses of the cell, yet they carry great potential for harm via misfolding and aggregation. Despite the dangers, proteins are sometimes bornde novofrom non-coding DNA. Proteins are more likely to be born from non-coding regions that produce peptides that do little to no harm when translated than from regions that produce harmful peptides. To investigate which newborn proteins are most likely to “first, do no harm”, we estimate fitnesses from an experiment that competedEscherichia colilineages that each expressed a unique random peptide. A variety of peptide metrics significantly predict lineage fitness, but this predictive power stems from simple amino acid frequencies rather than the ordering of amino acids. Amino acids that are smaller and that promote intrinsic structural disorder have more benign fitness effects. We validate that the amino acids that indicate benign effects in random peptides expressed inE. colialso do so in an independent dataset of random N-terminal tags in which it is possible to control for expression level. The same amino acids are also enriched in young animal proteins.

Significance statement

Proteins are sometimes born de novo. In an experiment to reproduce this process inEscherichia coli, we were able to predict 15% of the variation in random peptide fitness effects from their amino acid frequencies. In contrast, which order the amino acids are in seems to make no difference, adding no predictive power on top of simple amino acid frequencies. Amino acids that are smaller and promote intrinsic structural disorder have more benign fitness effects.
Electron Event Representation (EER) data enables efficient cryoEM file storage with full preservation of spatial and temporal resolution
Authors: Guo Hui , Franken Erik , Deng Yuchen , Benlekbir Samir , Singla Lezcano Garbi , Janssen Bart , Yu Lingbo , Ripstein Zev A. , Tan Yong Zi , Rubinstein John L.
Published: April 2020

Direct detector device (DDD) cameras have revolutionized electron cryomicroscopy (cryoEM) with their high detective quantum efficiency (DQE) and output of movie data. A high ratio of camera frame rate (frames/sec) to camera exposure rate (electrons/pixel/sec) allows electron counting, which further improves DQE and enables recording of super-resolution information. Movie output also allows for computational correction of specimen movement and compensation for radiation damage. However, these movies come at the cost of producing large volumes of data. It is common practice to sum groups of successive camera frames to reduce the final frame rate, and therefore file size, to one suitable for storage and image processing. This reduction in the camera’s temporal resolution requires decisions to be made during data acquisition that may result in the loss of information that could have been advantageous during image analysis. Here we present experimental analysis of a new Electron Event Representation (EER) data format for electron counting DDD movies, which is enabled by new hardware developed by Thermo Fisher Scientific for their Falcon DDD cameras. This format enables recording of DDD movies at the raw camera frame rate without sacrificing either spatial or temporal resolution. Experimental data demonstrate that the method retains super-resolution information and allows correction of specimen movement at the physical frame rate of the camera while maintaining manageable file sizes. The EER format will enable the development of new methods that can utilize the full spatial and temporal resolution of DDD cameras.
VCFdbR: A method for expressing biobank-scale Variant Call Format data in a SQLite database using R
Authors: Koomar Tanner , Michaelson Jacob J
Published: April 2020

As exome and whole-genome sequencing cohorts grow in size, the data they produce strains the limits of current tools and data structures. The Variant Call Format (VCF) was originally created as part of the 1,000 Genomes project. Flexible and concise enough to describe the genetic variations of thousands of samples in a single flat file, the VCF has become the standard for communicating the results of large-scale sequencing experiments. Because of its static and text-based structure, VCFs remain cumbersome to parse and filter in an interactive way, even with the aid of indexing. Iterating on previous concepts, we propose here a pipeline for converting VCFs to simple SQLite databases, which allow for rapid searching and filtering of genetic variants while minimizing memory overhead. Code can be found athttps://github.com/tkoomar/VCFdbR
Large-scale Inference of Population Structure in Presence of Missingness using PCA
Authors: Meisner Jonas , Liu Siyang , Huang Mingxi , Albrechtsen Anders
Published: April 2020

Background

Principal component analysis (PCA) is a commonly used tool in genetics to capture and visualize population structure. Due to technological advances in sequencing, such as the widely used non-invasive prenatal test, massive datasets of ultra-low coverage sequencing are being generated. These datasets are characterized by having a large amount of missing genotype information. We presentEMU, a method for inferring population structure in the presence of rampant non-random missingness.

Results

We show through simulations that several commonly used PCA methods can not handle missing data arisen from various sources, which leads to biased results as individuals are projected into the PC space based on their amount of missingness. In terms of accuracy,EMUoutperforms an existing method that also accommodates missingness while being competitively fast. We further testedEMUon around 100K individuals of the Phase 1 dataset of the Chinese Millionome Project, that were shallowly sequenced to around 0.08x. From this data we are able to capture the population structure of the Han Chinese and to reproduce previous analysis in a matter of CPU hours instead of CPU years.

Conclusions

EMU’s capability to accurately infer population structure in the presence of missingness will be of increasing importance with the rising number of large-scale genetic datasets.EMUis written inPythonand is freely available athttps://github.com/Rosemeis/emu/.
Volt-per-Ångstrom terahertz fields from X-ray free-electron lasers
Authors: Tanikawa T. , Karabekyan S. , Kovalev S. , Casalbuoni S. , Asgekar V. , Bonetti S. , Wall S. , Laarmann T. , Turchinovich D. , Zalden P. , Kampfrath T. , Fisher A. S. , Stojanovic N. , Gensch M. , Geloni G.
Published: April 2020

The electron linear accelerators driving modern X-ray free-electron lasers can emit intense, tunable, quasi-monochromatic terahertz (THz) transients with peak electric fields of V Å−1 and peak magnetic fields in excess of 10 T when a purpose-built, compact, superconducting THz undulator is implemented. New research avenues such as X-ray movies of THz-driven mode-selective chemistry come into reach by making dual use of the ultra-short GeV electron bunches, possible by a rather minor extension of the infrastructure.
Crystal structure of the nucleoid-associated protein Fis (PA4853) fromPseudomonas aeruginosa
Authors: Zhou Juan , Gao Zengqiang , Zhang Heng , Dong Yuhui
Published: April 2020

Factor for inversion stimulation (Fis) is a versatile bacterial nucleoid-associated protein that can directly bind and bend DNA to influence DNA topology. It also plays crucial roles in regulating bacterial virulence factors and in optimizing bacterial adaptation to various environments. Fis fromPseudomonas aeruginosa(PA4853, referred to as PaFis) has recently been found to be required for virulence by regulating the expression of type III secretion system (T3SS) genes. PaFis can specifically bind to the promoter region ofexsA, which functions as a T3SS master regulator, to regulate its expression and plays an essential role in transcription elongation fromexsBtoexsA. Here, the crystal structure of PaFis, which is composed of a four-helix bundle and forms a homodimer, is reported. PaFis shows remarkable structural similarities to the well studiedEscherichia coliFis (EcFis), including an N-terminal flexible loop and a C-terminal helix–turn–helix (HTH) motif. However, the critical residues for Hin-catalyzed DNA inversion in the N-terminal loop of EcFis are not conserved in PaFis and further studies are required to investigate its exact role. A gel-electrophoresis mobility-shift assay showed that PaFis can efficiently bind to the promoter region ofexsA. Structure-based mutagenesis revealed that several conserved basic residues in the HTH motif play essential roles in DNA binding. These structural and biochemical studies may help in understanding the role of PaFis in the regulation of T3SS expression and in virulence.