bluuebunny/crossref_metadata_2025 huggingface dataset:
Scientometric correlates of high-quality reference lists in ecological papers
Authors: Mammola Stefano , Fontaneto Diego , Martínez Alejandro , Chichorro Filipe
Published: March 2020

It is said that the quality of a scientific publication is as good as the science it cites, but the properties of high-quality reference lists have never been numerically quantified. We examined seven numerical characteristics of reference lists of 50,878 primary research articles published in 17 ecological journals between 1997 and 2017. Over this 20-years period, there have been significant changes in reference lists’ properties. On average, more recent ecological papers have longer reference lists, cite more high Impact Factor papers, and fewer non-journal publications. Furthermore, we show that highly cited papers across the ecology literature have longer reference lists, cite more recent and impactful papers, and account for more self-citations. Conversely, the proportion of ‘classic’ papers and non-journal publications cited, as well as the temporal range of the reference list, have no significant influence on articles’ citations. From this analysis, we distill a recipe for crafting impactful reference lists.
Evolutionary analysis of LP3 gene family in conifers: an ASR homolog
Authors: Lecoy Jonathan , García-Gil MR
Published: March 2020

Drought has long been established as a major environmental stress for plants which have in turn developed several coping strategies, ranging from physiological to molecular mechanisms. LP3; a homolog of the Abscisic Acid, Stress and Ripening (ASR) gene was first detected in tomato; and has been shown to be present in four different isoforms in loblolly pine called LP3-0, LP3-1, LP3-2 and LP3-3. While ASR has already been extensively studied notably in tomato, the same cannot be said of LP3. Like ASR, the different LP3 isoforms have been shown to be upregulated in response to water deficit stress and to also act as transcription factors for genes likely involved in hexose transport. In this study we have investigated the evolutionary history of LP3 gene family, with the aim of relating it to that of ASR from a phylogenetic perspective and comparing the differences in selective pressure and codon usage. Phylogenetic analyses of different LP3 homologs compared to ASR show that LP3 is less divergent across species than ASR and that even when comparing the different sub-sections of the gene the divergence rate of LP3 is lower than that of ASR. Analysis of different gene parameters showed that there were differences in GC1% and GC2% but not in total or GC3% content. All genes had a relatively high CAI value associated with a low to moderate ENC value, which is indicative of high translation efficiency found in highly expressed genes. Analysis of codon usage also showed that LP3 preferentially uses different codons than ASR. Selective pressure analysis across most of the LP3 and ASR genes used in this study showed that these genes were principally undergoing purifying selection, with the exception of LP3-3 which seems to be undergoing diversifying selection most probably due to the fact that it likely recently diverged from LP3-0. This study thus provides insight in how ASR and LP3 have diverged from each other while remaining homologous.
The TRF2 General Transcription Factor Is a Key Regulator of Cell Cycle Progression
Authors: Kedmi Adi , Sloutskin Anna , Epstein Natalie , Gasri-Plotnitsky Lital , Ickowicz Debby , Shoval Irit , Doniger Tirza , Darmon Eliezer , Ideses Diana , Porat Ziv , Yaron Orly , Juven-Gershon Tamar
Published: March 2020

TRF2 (TATA-box-binding protein-related factor 2) is an evolutionarily conserved general transcription factor that is essential for embryonic development ofDrosophila melanogaster, C. elegans, zebrafish andXenopus. Nevertheless, the cellular processes that are regulated by TRF2 are largely underexplored.

Here, usingDrosophilaSchneider cells as a model, we discovered that TRF2 regulates cell cycle progression. Using flow cytometry, high-throughput microscopy and advanced imaging-flow cytometry, we demonstrate that TRF2 knockdown regulates cell cycle progression and exerts distinct effects on G1 and specific mitotic phases. RNA-seq analysis revealed that TRF2 regulates the expression ofCyclin Eand the mitotic cyclins,Cyclin A, Cyclin BandCyclin B3, but notCyclin DorCyclin C. To identify proteins that could account for the observed regulation of these cyclin genes, we searched for TRF2-interacting proteins. Interestingly, mass spectrometry analysis of TRF2-containing complexes identified GFZF, a nuclear glutathione S-transferase implicated in cell cycle regulation, and Motif 1 binding protein (M1BP). Furthermore, available ChIP-exo data revealed that TRF2, GFZF and M1BP co-occupy the promoters of TRF2-regulated genes. Using RNAi to knockdown the expression of either M1BP, GFZF, TRF2 or their combinations, we demonstrate that although GFZF and M1BP interact with TRF2, it is TRF2, rather than GFZF or M1BP, that is the main factor regulating the expression ofCyclin Eand the mitotic cyclins. Taken together, our findings uncover a critical and unanticipated role of a general transcription factor as a key regulator of cell cycle.
SCYN: Single cell CNV profiling method using dynamic programming
Authors: Feng Xikang , Chen Lingxi , Qing Yuhao , Li Ruikang , Li Chaohui , Li Shuai Cheng
Published: March 2020

Copy number variation is crucial in deciphering the mechanism and cure of complex disorders and cancers. The recent advancement of scDNA sequencing technology sheds light upon addressing intratumor heterogeneity, detecting rare subclones, and reconstructing tumor evolution lineages at single-cell resolution. Nevertheless, the current circular binary segmentation based approach proves to fail to efficiently and effectively identify copy number shifts on some exceptional trails. Here, we propose SCYN, a CNV segmentation method powered with dynamic programming. SCYN resolves the precise segmentation on twoin silicodatasets. Then we verified SCYN manifested accurate copy number inferring on triple negative breast cancer scDNA data, with array comparative genomic hybridization results of purified bulk samples as ground truth validation. We tested SCYN on two datasets of the newly emerged 10x Genomics CNV solution. SCYN successfully recognizes gastric cancer cells from 1% and 10% spike-ins 10x datasets. Moreover, SCYN is about 150 times faster than state of the art tool when dealing with the datasets of approximately 2000 cells. SCYN robustly and efficiently detects segmentations and infers copy number profiles on single cell DNA sequencing data. It serves to reveal the tumor intra-heterogeneity. The source code of SCYN can be accessed inhttps://github.com/xikanfeng2/SCYN. The visualization tools are hosted onhttps://sc.deepomics.org/.
A naturaltimelesspolymorphism allowing circadian clock synchronization in ‘white nights’
Authors: Lamaze Angelique , Chen Chenghao , Leleux Solene , Xu Min , George Rebekah , Stanewsky Ralf
Published: March 2020

Daily temporal organisation of behavioural and physiological functions offers a fitness advantage for most animals. Optimized temporal niches are determined by an interplay between external environmental rhythms and internal circadian clocks. While daily light:dark cycles serve as a robust time cue (Zeitgeber) to synchronise circadian clocks, it is not clear how animals experiencing only weak environmental cues deal with this problem. Like humans, flies of the genus Drosophila originate in sub-Saharan Africa and spread North in Europe up to the polar circle where they experience extremely long days in the summer or even constant light (LL). LL is known to disrupt clock function, due to constant activation of the deep brain photoreceptor CRYPTOCHROME (CRY), which induces constant degradation of the clock protein TIMELESS (TIM). Temperature cycles are able to overcome these arrhythmia inducing effects of LL, reinstating clock protein oscillations and rhythmic behaviour. We show here that for this to occur a recently evolved natural allele (ls-tim) of thetimelessgene is required, whereby the presence of this allele within the central clock neurons is sufficient. Thels-timallele encodes a longer, less-light sensitive form of TIM (L-TIM) in addition to the shorter (S-TIM) form, the only form encoded by the ancients-timallele. Only after blocking light-input by removing functional CRY,s-timflies are able to synchronise molecular and behavioural rhythms to temperature cycles in LL. Additional removal of light input from the visual system results in a phase advance of molecular and behavioural rhythms, showing that the visual system contributes to temperature synchronization in LL. We show thatls-tim, but nots-timflies can synchronise their behavioural activity to semi-natural LL and temperature cycle conditions reflecting long Northern Europe summer days, the season when Drosophila populations massively expand. Our observations suggest that this functional gain associated withls-timis driving the Northern spread of this allele by directional selection.
Morphological peculiarities of DNA-protein complexes in dormantEscherichia colicells, subjected to prolonged starvation Condensation of DNA in dormant cells ofEscherichia coli
Authors: Loiko Natalia , Danilova Yana , Moiseenko Andrey , Kovalenko Vladislav , Tereshkina Ksenia , El-Registan Galina I. , Sokolova Olga S. , Krupyanskii Yurii F.
Published: March 2020

One of the adaptive strategies for the constantly changing conditions of the environment utilized in bacterial cells involves the condensation of DNA in complex with the DNA-binding protein, Dps. With the use of electron microscopy and electron tomography, we observed several morphologically different types of DNA condensation in dormantEscherichia colicells, namely:nanocrystalline, liquid crystalline, and thefolded nucleosome-like. We confirmed the presence of both Dps and DNA in all of the ordered structures using EDX analysis. The comparison of EDX spectra obtained for the three different ordered structures revealed that innanocrystallineformation the majority of Dps protein is tightly bound to nucleoid DNA. We demonstrated that the population of the dormant cell is structurally heterogeneous, which allows cells to respond flexibly to environmental changes. It increases the ability of the whole bacterial population to survive under extreme stress conditions.
Drivers of change and ecosystem status in a temperate lake over the last Post-Glacial period from 14.5 kyr
Authors: Tõnno I , Freiberg R , Talas L , Kisand A , Belle S , Stivrins N , Alliksaar T , Heinsalu A , Veski S , Kisand V
Published: March 2020

Understanding the long-term dynamics of ecological communities on the centuries-to-millennia scale is important for explaining present-day biodiversity patterns. Placing these patterns in a historical context could yield reliable tools for predicting possible future scenarios. Paleoarchives of macro+ and micro-fossil remains, and most importantly biomarkers such as fossil pigments and ancient DNA present in various sedimentary deposits, allow long term changes in ecological communities to be analysed. We use recent compilations of data including fossil pigments, metabarcoding of sedimentary ancient DNA and microfossils together with data analysis to understand the impact of gradualversusabrupt climate changes on a lake`s ecosystem status over the last 14.5 kyr. We give examples of hypotheses that need long-term data, which can be addressed using well-established paleoproxy variables. These variables describe the climate, together with vegetation change and the appearance of anthropogenic forcing, either as a gradual change or an abrupt event. We were able to detect abrupt changes in the lake ecosystem during the stable period of the Holocene Thermal Maximum and we highlight the increased frequency and degree of perturbation in lakes due to non-immediate human activity over a larger region. Both observations demonstrate an impaired relationship between a gradual external driver and ecosystem response and apply to future scenarios of climate warming and increased human impact in north-eastern Europe.
Disarrangement of Endoplasmic reticulum-mitochondria communication impairs Ca2+homeostasis in FRDA
Authors: Rodríguez Laura R. , Calap-Quintana Pablo , Lapeña-Luzón Tamara , Pallardó Federico V. , Schneuwly Stephan , Navarro Juan A. , Gonzalez-Cabo Pilar
Published: March 2020

Friedreich ataxia (FRDA) is a neurodegenerative disorder characterized by neuromuscular and neurological manifestations. It is caused by mutations in gene FXN, which results in loss of the mitochondrial protein frataxin. Endoplasmic Reticulum-mitochondria associated membranes (MAMs) are inter-organelle structures involved in the regulation of essential cellular processes, including lipid metabolism and calcium signaling. In the present study, we have analyzed in both, unicellular and multicellular models of FRDA, an analysis of calcium management and of integrity of MAMs. We observed that function of MAMs is compromised in our cellular model of FRDA, which was improved upon treatment with antioxidants. In agreement, promoting mitochondrial calcium uptake was sufficient to restore several defects caused by frataxin deficiency in Drosophila Melanogaster. Remarkably, our findings describe for the first time frataxin as a member of the protein network of MAMs, where interacts with two of the main proteins implicated in endoplasmic reticulum-mitochondria communication. These results suggest a new role of frataxin, indicate that FRDA goes beyond mitochondrial defects and highlight MAMs as novel therapeutic candidates to improve patient’s conditions.
Understanding functional consequences of type 2 diabetes risk loci using the universal data integration and visualization R package CONQUER
Authors: Bouland Gerard A , Beulens Joline WJ , Nap Joey , van der Slik Arno R , Zaldumbide Arnaud , Hart Leen M’t , Slieker Roderick C
Published: March 2020

Background

Numerous large genome-wide association studies (GWASs) have been performed to understand the genetic factors of numerous traits, including type 2 diabetes. Many identified risk loci are located in non-coding and intergenic regions, which complicates the understanding how genes and their downstream pathways are influenced. An integrative data approach is required to understand the mechanism and consequences of identified risk loci.

Results

Here, we developed the R-package CONQUER. Data for SNPs of interest (build GRCh38/hg38) were acquired from static- and dynamic repositories, such as, GTExPortal, Epigenomics Project, 4D genome database and genome browsers such as ENSEMBL. CONQUER modularizes SNPs based on the underlying co-expression data and associates them with biological pathways in specific tissues. CONQUER was used to analyze 403 previously identified type 2 diabetes risk loci. In all tissues, the majority of SNPs (mean = 13.50, SD = 11.70) were linked to metabolism. A tissue-shared effect was found for four type 2 diabetes-associated SNPs (rs601945, rs1061810, rs13737, rs4932265) that were associated with differential expression ofHLA-DQA2, HSD17B12, MAN2C1andAP3S2respectively. Seven SNPs were identified that influenced the expression of seven ribosomal proteins in multiple tissues. Finally, one SNP (rs601945) was found to influence multipleHLAgenes in all twelve tissues investigated.

Conclusion

We present an universal R-package that aggregates and visualizes data in order to better understand functional consequences of GWAS loci. Using CONQUER, we showed that type 2 diabetes risk loci have many tissue-shared effects on multiple pathways including metabolism, the ribosome and HLA pathway.
SynaptoPAC, an Optogenetic Tool for Induction of Presynaptic Plasticity
Authors: Oldani Silvia , Moreno-Velasquez Laura , Stumpf Alexander , Rosenmund Christian , Schmitz Dietmar , Rost Benjamin R.
Published: March 2020

Optogenetic manipulations have transformed neuroscience in recent years. While sophisticated tools now exist for controlling the firing patterns of neurons, it remains challenging to optogenetically define the plasticity state of individual synapses. A variety of synapses in the mammalian brain express presynaptic long-term potentiation (LTP) upon elevation of presynaptic cyclic adenosine monophosphate (cAMP), but the molecular expression mechanisms as well as the impact of presynaptic LTP on network activity and behavior are not fully understood. In order to establish optogenetic control of presynaptic cAMP levels and thereby presynaptic potentiation, we developed synaptoPAC, a presynaptically targeted version of the photoactivated adenylyl cyclase bPAC. In cultures of hippocampal granule cells, activation of synaptoPAC with blue light increases action potential-evoked transmission, an effect not seen in hippocampal cultures of non-granule cells. In acute brain slices, synaptoPAC activation immediately triggers a strong presynaptic potentiation at mossy fiber terminals in CA3, but not at Schaffer collateral synapse in CA1. Following light-triggered potentiation, mossy fiber transmission decreases within 20 minutes, but remains enhanced still after 30 min. Optogenetic potentiation alters the short-term plasticity dynamics of release, reminiscent of presynaptic LTP. SynaptoPAC is the first optogenetic tool that allows acute light-controlled potentiation of transmitter release at specific synapses of the brain, and will enable to investigate the role of presynaptic potentiation in network function and the animal’s behavior in an unprecedented manner.

Significance Statement

SynaptoPAC is a novel optogenetic tool that allows increasing synaptic transmission by light-controlled induction of presynaptic plasticity.
Transcriptome analysis uncovers a link between copper metabolism, and both fungal fitness and antifungal sensitivity in the opportunistic yeast Candida albicans
Authors: Khemiri Inès , Tebbji Faiza , Sellam Adnane
Published: March 2020

Copper homeostasis is an important determinant for virulence of many human pathogenic fungi such as the highly prevalent yeast Candida albicans. However, beyond the copper transporter Ctr1, little is known regarding other genes and biological processes that are affected by copper. To gain insight into the cellular processes that are modulated by copper abundance in C. albicans, we monitored the global gene expression dynamic under both copper depletion and excess using RNA-seq. Beyond copper metabolism, other different transcriptional programs related to fungal fitness such as stress responses, antifungal sensitivity, host invasion and commensalism were modulated in response to copper variations. We have also investigated the transcriptome of the mutant of the copper utilization regulator, mac1, and identified potential direct targets of this transcription factor under copper starvation. We also showed that Mac1 was required for the invasion and adhesion to host cells and antifungal tolerance. This study provides a framework for future studies to examine the link between copper metabolism and essential functions that modulate fungal virulence and fitness inside the host.
Hypoxic gene expression in chronic hepatitis B infected patients is not observed in state-of-artin vitroand mouse infection models
Authors: Liu PJ , Harris JM , Marchi E , D’Arienzo V , Michler T , Wing PAC , Magri A , Ortega-Prieto AM , van de Klundert M , Wettengel J , Durantel D , Dorner M , Klenerman P. , Protzer U , Giotis S , McKeating JA
Published: March 2020

Hepatitis B virus (HBV) is the leading cause of hepatocellular carcinoma (HCC) worldwide. The prolyl hydroxylase domain (PHD)-hypoxia inducible factor (HIF) pathway is a key mammalian oxygen sensing pathway and is frequently perturbed by pathological states including infection and inflammation. We discovered a significant upregulation of hypoxia regulated gene transcripts in patients with chronic hepatitis B (CHB) in the absence of liver cirrhosis. We used state-of-the-artin vitroandin vivoHBV infection models to evaluate a role for HBV infection and the viral regulatory protein HBx to drive HIF-signalling. HBx had no significant impact on HIF expression or associated transcriptional activity under normoxic or hypoxic conditions. Furthermore, we found no evidence of hypoxia gene expression in HBVde novoinfection, HBV infected human liver chimeric mice or transgenic mice with integrated HBV genome. Collectively, our data show clear evidence of hypoxia gene induction in CHB that is not recapitulated in existing models for acute HBV infection, suggesting a role for inflammatory mediators in promoting hypoxia gene expression.
Engineered chemotaxis core signaling units indicate a constrained kinase-off state
Authors: Muok Alise R. , Chua Teck Khiang , Srivastava Madhur , Yang Wen , Maschmann Zach , Borbat Petr P. , Chong Jenna , Zhang Sheng , Freed Jack H. , Briegel Ariane , Crane Brian R.
Published: March 2020

Bacterial chemoreceptors, the CheA histidine kinase, and the coupling protein CheW comprise transmembrane molecular arrays with remarkable sensing properties. An unanswered question concerns how receptors turn off CheA kinase activity. Chemoreceptor cytoplasmic regions engineered to assume a trimer-of-receptor-dimers configuration form well-defined complexes with CheA and CheW and promote a kinase-off state. These mimics of core signaling units were assembled to homogeneity and investigated by site-directed spin-labeling with pulse-dipolar ESR spectroscopy (PDS), small-angle x-ray scattering, targeted protein cross-linking, and cryo-electron microscopy. The kinase-off state is especially stable, has relatively low domain mobility and associates the histidine substrate domain P1 and docking domain P2 with the kinase core. Distances measured between spin-labeled ADP molecules bound to the P4 kinase domain provide evidence for a “dipped conformation” that has been previously proposed from molecular dynamics simulations. Taken together, the data provide an experimentally restrained model for the inhibited state of the core-signaling unit and suggest that chemoreceptors indirectly sequester the kinase and substrate domains to limit histidine autophosphorylation.
Apoptosis, G1 phase stall and premature differentiation account for low chimeric competence of Human and rhesus monkey naïve pluripotent stem cells
Authors: Aksoy Irène , Rognard Cloé , Moulin Anaïs , Marcy Guillaume , Masfaraud Etienne , Wianny Florence , Cortay Véronique , Bellemin-Ménard Angèle , Doerflinger Nathalie , Dirheimer Manon , Mayère Chloé , Bourillot Pierre-Yves , Lynch Cian , Raineteau Olivier , Joly Thierry , Dehay Colette , Serrano Manuel , Afanassieff Marielle , Savatier Pierre
Published: March 2020

After reprogramming to naïve pluripotency, human pluripotent stem cells (PSCs) still exhibit very low ability to make interspecies chimeras. Whether this is because they are inherently devoid of the attributes of chimeric competency or because naïve PSCs cannot colonize embryos from distant species remains to be elucidated. Here, we have used different types of mouse, human and rhesus monkey naïve PSCs and analyzed their ability to colonize rabbit and cynomolgus monkey embryos. Mouse embryonic stem cells (ESCs) remained mitotically active and efficiently colonized host embryos. In contrast, primate naïve PSCs colonized host embryos with much lower efficiency. Unlike mouse ESCs, they slowed DNA replication after dissociation and, after injection into host embryos, they stalled in the G1 phase and differentiated prematurely, regardless of host species. We conclude that human and non-human primate naïve PSCs do not efficiently make chimeras because they are inherently unfit to remain mitotically active during colonization.
WNK1 regulates uterine homeostasis and its ability to support pregnancy
Authors: Chi Ru-pin Alicia , Wang Tianyuan , Huang Chou-Long , Wu San-pin , Young Steven , Lydon John , DeMayo Francesco
Published: March 2020

WNK1 is an atypical kinase protein ubiquitously expressed in humans and mice. A mutation in its encoding gene causes hypertension in humans which is associated with abnormal ion homeostasis. Our earlier findings demonstrated that WNK1 is critical forin vitrodecidualization in human endometrial stromal cells – pointing towards an unrecognized role of WNK1 in female reproduction. Here, we employed a mouse model with conditional WNK1 ablation from the female reproductive tract to define itsin vivorole in uterine biology. Loss of WNK1 altered uterine morphology, causing endometrial epithelial hyperplasia, adenomyosis and a delay in embryo implantation, ultimately resulting in compromised fertility. Combining transcriptomic, proteomic and interactomic analyses revealed a novel regulatory pathway whereby WNK1 represses AKT phosphorylation through the phosphatase PP2A in endometrial cells from both humans and mice. We show that WNK1 interacts with PPP2R1A, an isoform of the PP2A scaffold subunit. This interaction stabilizes the PP2A complex, which then dephosphorylates AKT. Therefore, loss of WNK1 reduced PP2A activity, causing AKT hypersignaling. Using FOXO1 as a readout of AKT activity, we demonstrate that there was escalated FOXO1 phosphorylation and nuclear exclusion, leading to a disruption in the regulation of genes that are crucial for embryo implantation.
Transiently structured head domains control intermediate filament assembly
Authors: Zhou Xiaoming , Lin Yi , Liszczak Glen , Sysoev Vasily , Sutherland Lillian , Mori Eiichiro , Murray Dylan , Kato Masato , Tycko Robert , McKnight Steven L.
Published: March 2020

Low complexity (LC) head domains 92 and 108 residues in length are, respectfully, required for assembly of neurofilament light (NFL) and desmin intermediate filaments (IFs). As studied in isolation, these IF head domains interconvert between states of conformational disorder and labile, β-strand-enriched polymers. Solid state nuclear magnetic resonance (ss-NMR) spectroscopic studies of NFL and desmin head domain polymers reveal spectral patterns consistent with structural order. A combination of intein chemistry and segmental isotope labeling allowed preparation of fully assembled NFL and desmin IFs that could also be studied by ss-NMR. Assembled IFs revealed spectra overlapping with those observed for β-strand-enriched polymers formed from the isolated NFL and desmin head domains. Phosphorylation and disease causing mutations reciprocally alter NFL and desmin head domain self-association, yet commonly impede IF assembly. These observations show how facultative structural assembly of LC domains via labile, β-strand-enriched self-interactions may broadly influence cell morphology.
When species trees disagree: an approach consistent with the coalescent that quantifies phylogenomic support for contentious relationships
Authors: Hodel Richard G.J. , Walker Joseph F. , Knowles L. Lacey , Smith Stephen A.
Published: March 2020

Phylogenies inferred using both concatenation- and coalescent-based analyses typically render highly congruent trees. However, when they disagree, they often differ with respect to historically contentious and evolutionarily important relationships. These relationships may also involve etiolated lineages where increased sampling is not possible. Recently, methods aimed at interrogating single relationships or trees have emerged as promising investigative tools to examine these cases. Although recent methods such as “Edge-based Phylogenomic Support analYsis” (EPSY) led to insights into both systematic error and real biological signal, whether they are consistent with the coalescent in cases with high Incomplete Lineage Sorting (ILS) has yet to be characterized. Here, we use simulations and an empirical dataset to test the performance of EPSY, concatenation, and coalescent-based summary analyses under high levels of ILS. We focused on high-ILS scenarios because these represent the typical difficult cases that researchers often face due to the prevalence of ILS in phylogenomic datasets. ILS is known to be a major cause of phylogenomic conflict, which confounds many biological conclusions that depend on a resolved phylogeny, such as inferring ancestral character states, biogeographic reconstructions, and domestication histories. Our study found that EPSY was consistent with the coalescent in a high-ILS empirical dataset. In high-ILS simulations EPSY infers the correct edge more than half the time, whereas coalescent based methods and concatenation methods inferred the actual tree 37.8% and 25% of the time, respectively. All methods have conditions under which they generate the most accurate inferences. Given the levels of ILS in simulations, 26.2% of the time no method recovered the true tree. This zone where no current method can infer the true topology is likely due to properties of the species tree, such as the length of internal edges adjacent to a conflict and/or the length of the shortest branch. Nevertheless, the EPSY approach proves to be a valuable complement to phylogenomic analyses for interrogating regions of the tree with conflicting hypotheses generated from past studies or alternative inference methods. Our analyses highlight that robust phylogenetic trees may not be possible under some scenarios regardless of method and data source.
Prdm8 regulates pMN progenitor specification for motor neuron and oligodendrocyte fates by modulating Shh signaling response
Authors: Scott Kayt , O’Rourke Rebecca , Gillen Austin , Appel Bruce
Published: March 2020

Spinal cord pMN progenitors sequentially produce motor neurons and oligodendrocyte precursor cells (OPCs). Some OPCs differentiate rapidly as myelinating oligodendrocytes whereas others remain into adulthood. How pMN progenitors switch from producing motor neurons to OPCs with distinct fates is poorly understood. pMN progenitors expressprdm8, which encodes a transcriptional repressor, during motor neuron and OPC formation. To determine ifprdm8controls pMN cell fate specification, we used zebrafish as a model system to investigateprdm8function. Our analysis revealed thatprdm8mutant embryos have a deficit of motor neurons resulting from a premature switch from motor neuron to OPC production. Additionally,prdm8mutant larvae have excess oligodendrocytes and a concomitant deficit of OPCs. Notably, pMN cells of mutant embryos have elevated Shh signaling coincident with the motor neuron to OPC switch. Inhibition of Shh signaling restored the number of motor neurons to normal but did not rescue the proportion of oligodendrocytes. These data suggest that Prdm8 regulates the motor neuron-OPC switch by controlling the level of Shh activity in pMN progenitors and also regulates allocation of oligodendrocyte lineage cell fates.

Summary Statement

Prdm8 regulates the timing of a motor neuron-oligodendrocyte switch and oligodendrocyte lineage cell identity in the zebrafish spinal cord.
Multi-resolution imaging using bioluminescence resonance energy transfer identifies distinct biodistribution profiles of extracellular vesicles and exomeres with redirected tropism
Authors: Wu Anthony Yan-Tang , Sung Yun-Chieh , Chen Yen-Ju , Chou Steven Ting-Yu , Guo Vanessa , Chien Jasper Che-Yung , Ko John Jun-Sheng , Yang Alan Ling , Huang Hsi-Chien , Chuang Ju-Chen , Wu Syuan , Ho Meng-Ru , Ericsson Maria , Lin Wan-Wan , Cheung Chantal Hoi Yin , Juan Hsueh-Fen , Ueda Koji , Chen Yunching , Lai Charles Pin-Kuang
Published: March 2020

Extracellular particles (EP) including extracellular vesicles (EVs) and exomeres have been shown to play significant roles in diseases and therapeutic applications. However, their spatiotemporal dynamicsin vivohave remained largely unresolved in detail due to the lack of a suitable method. We therefore created a bioluminescence resonance energy transfer (BRET)-based reporter, PalmGRET, to enable pan-EP labelling ranging from exomeres (< 50 nm) to small (< 200 nm) and medium and large (> 200 nm) EVs. PalmGRET emits robust, sustained signals and allows the visualization, tracking and quantification of the EPs from whole-animal to nanoscopic resolutions under different imaging modalities, including bioluminescence, BRET and fluorescence. Using PalmGRET, we show that EPs released by lung metastatic hepatocellular carcinoma (HCC) exhibit lung tropism with varying distributions to other major organs in immunocompetent mice. We further demonstrate that gene knockdown of lung-tropic membrane proteins, solute carrier organic anion transporter family member 2A1 (Slco2a1), alanine aminopeptidase (Cd13) and chloride intracellular channel (Clic1) decreases HCC-EP distribution to the lungs and yields distinct biodistribution profiles. We anticipate that EP-specific imaging, quantitative assays and detailedin vivocharacterization to be a starting point for more accurate and comprehensivein vivomodels of EP biology and therapeutic design.
Incursion pathways of the Asian tiger mosquito (Aedes albopictus) into Australia contrast sharply with those of the yellow fever mosquito (Aedes aegypti)
Authors: Schmidt Thomas L , Chung Jessica , van Rooyen Anthony R. , Sly Angus , Weeks Andrew R , Hoffmann Ary A
Published: March 2020

BACKGROUND

Understanding pest incursion pathways is critical for preventing new invasions and for stopping the transfer of alleles that reduce the efficacy of local control methods. The mosquitoesAedes albopictus(Skuse) andAe. aegypti(Linnaeus) are both highly invasive disease vectors, and through a series of ongoing international incursions are continuing to colonise new regions and spread insecticide resistance alleles among established populations. This study uses high-resolution molecular markers and a set of 241 reference genotypes to trace incursion pathways ofAe. albopictusinto mainland Australia, where no successful invasions have yet been observed. We contrast these results with incursion pathways ofAe. aegypti, investigated previously.

RESULTS

Assignments successful identified China, Japan, Singapore and Taiwan as source locations. Incursion pathways ofAe. albopictuswere entirely different to those ofAe. aegypti, despite broad sympatry of these species throughout the Indo-Pacific region. Incursions ofAe. albopictusappeared to have come predominantly along marine routes from key trading locations, whileAe. aegyptiwas mostly linked to aerial routes from tourism hotspots.

CONCLUSION

These results demonstrate how genomics can help decipher otherwise cryptic incursion pathways. The inclusion of reference genotypes from the Americas may help resolve some unsuccessful assignments. While many congeneric taxa will share common incursion pathways, this study highlights that this is not always the case, and incursion pathways of important taxa should be specifically investigated. Species differences in aerial and marine incursion rates may reflect the efficacy of ongoing control programs such as aircraft disinsection.
Partnership between epigenetic reader BRD4 and transcription factor CEBPD
Authors: Wang Qingwei , Zhang Mengxue , Urabe Go , Wang Bowen , Ozer Hatice Gulcin , Huang Yitao , Kent K. Craig , Guo Lian-Wang
Published: March 2020

Vascular smooth muscle cell (SMC) state/phenotype transitions underlie neointimal hyperplasia (IH) predisposing to cardiovascular diseases. Bromodomain protein BRD4 is a histone acetylation reader and enhancer mark that co-activates transcription elongation. CCAAT enhancer binding protein delta (CEBPD) is a transcription factor typically studied in adipogenesis and immune cell differentiation. Here we investigated the association between BRD4 and CEBPD in SMC state transition.

Chromatin immunoprecipitation sequencing (ChIPseq) showed enrichment of BRD4 and histone acetylation (H3K27ac) atCebpdand enhancer in rat carotid arteries undergoing IH. In vitro, BRD4 silencing with siRNA reduced SMC expression of CEBPD. Bromodomain-1 but not bromodoamin-2 accounted for this BRD4 function. Endogenous BRD4 co-IP’ed with CEBPD;Cebpdpromoter and enhancer DNA fragments co-IP’ed with CEBPD or endogenous BRD4 (ChIP-qPCR). These co-IPs were abolished by the BRD4 bromodomain blocker JQ1. TNFα upregulated both BRD4 and CEBPD. Silencing CEBPD averted TNFα-induced inflammatory SMC state transition (heightened IL-1β, IL6, and MCP-1 mRNA levels), so did JQ1. CEBPD overexpression increased PDGFRα preferentially over PDGFRβ; so did TNFα, and JQ1 abolished TNFα’s effect.

Our data reveal a BRD4/CEBPD partnership that promotes CEBPD’s own transcription and inflammatory SMC state transition, thus shedding new light on epigenetic reader and transcription factor cooperative actions in SMC pathobiology.
Flexible multivariate linear mixed models for structured multiple traits
Authors: Kim Hyeonju , Farage Gregory , Lovell John T. , Mckay John K. , Juenger Thomas E. , Sen Śaunak
Published: March 2020

Many genetic studies collect structured multivariate traits containing rich information across traits. We present a flexible multivariate linear mixed model for quantitative trait loci mapping (FlxQTL) for multiple correlated traits that adjusts for genetic relatedness and that models information on multiple environments or multiple timepoints using trait covariates. FlxQTL handles genetic mapping of multivariate traits faster with greater flexibility compared to previous implementations.
Evidence of Presence and Activation of the two Cell Cycle Kinases Nek6 and Nek7 in the ciliated Neuroretina
Authors: Janisch Kerstin M , Kasanuki J Mie , Davis Richard J , Tsang Stephen H
Published: March 2020

The serine/threonine NIMA kinases are widely found in eukaryotes. They are cell-cycle kinases that are associated with centrosomes and spindle apparatus and cilia. In cilia, NIMA kinases are reported to play a role in cilia length maintenance and deflagelation. Here we focus on the two Nek homologs, Nek6 and Nek7, and their potential role in retina. We report for the first-time expression ofnek6andnek7mRNA and protein in retinal tissue. In particular, we detect localisation of these kinases to photoreceptors outer segments. Moreover, we are able to show a light-dependent phosphorylation of the activation loop (serine 206) of Nek6/7 in rod outer segments, suggesting activation of these kinases is downstream of the phototransduction pathway. Indeed, we demonstrate that Nek6/7 phosphorylation in the retina is dependent onGrk1function. Furthermore, Nek6/7 phosphorylation can be stimulated in the brain by opiate drugs, suggesting that activation of Nek6/7 lies downstream of G protein coupled receptors activation, in general. Nek6/7 may couple photoreception with outer segment biogenesis through phosphorylation of downstream substrates, which may affect the microtubules of the axoneme.
RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses
Authors: Rangan Ramya , Zheludev Ivan N. , Das Rhiju
Published: March 2020

As the COVID-19 outbreak spreads, there is a growing need for a compilation of conserved RNA genome regions in the SARS-CoV-2 virus along with their structural propensities to guide development of antivirals and diagnostics. Using sequence alignments spanning a range of betacoronaviruses, we rank genomic regions by RNA sequence conservation, identifying 79 regions of length at least 15 nucleotides as exactly conserved over SARS-related complete genome sequences available near the beginning of the COVID-19 outbreak. We then confirm the conservation of the majority of these genome regions across 739 SARS-CoV-2 sequences reported to date from the current COVID-19 outbreak, and we present a curated list of 30 ‘SARS-related-conserved’ regions. We find that known RNA structured elements curated as Rfam families and in prior literature are enriched in these conserved genome regions, and we predict additional conserved, stable secondary structures across the viral genome. We provide 106 ‘SARS-CoV-2-conserved-structured’ regions as potential targets for antivirals that bind to structured RNA. We further provide detailed secondary structure models for the 5’ UTR, frame-shifting element, and 3’ UTR. Last, we predict regions of the SARS-CoV-2 viral genome have low propensity for RNA secondary structure and are conserved within SARS-CoV-2 strains. These 59 ‘SARS-CoV-2-conserved-unstructured’ genomic regions may be most easily targeted in primer-based diagnostic and oligonucleotide-based therapeutic strategies.
The transcriptional aftermath in two independently formed hybrids of the opportunistic pathogenCandida orthopsilosis
Authors: Hovhannisyan Hrant , Saus Ester , Ksiezopolska Ewa , Gabaldón Toni
Published: March 2020

Interspecific hybridization can drive evolutionary adaptation to novel environments. TheSaccharomycotinaclade of budding yeasts includes many hybrid lineages, and hybridization has been proposed as a source for new pathogenic species.Candida orthopsilosisis an emerging opportunistic pathogen for which most clinical isolates are hybrids, each derived from one of at least four independent crosses between the same two parental lineages. To gain insight on the transcriptomic aftermath of hybridization in these pathogens, we analyzed allele-specific gene expression in two independently formed hybrid strains, and in a homozygous strain representative of one parental lineage. Our results show that the effect of hybridization on overall gene expression is rather limited, affecting ~4% of the studied genes. However, we identified a larger effect in terms of imbalanced allelic expression, affecting ~9.5% of the heterozygous genes in the hybrids. Some of these altered genes have functions related to pathogenicity, including zinc transport and superoxide dismutase activities. Additionally, the number of shared genes with imbalanced expression in the two independently formed hybrids was higher than random expectation, suggesting selective retention. While it remains unclear whether the observed imbalanced genes play a role in virulence, our results suggest that differences in allele-specific expression may add an additional layer of phenotypic plasticity to traits related to virulence inC. orthopsilosishybrids.

Importance

How new pathogens emerge is an important question that remains largely unanswered. Some emerging yeast pathogens are hybrids originated through the crossing of two different species, but how hybridization contributes to a higher virulence is unclear. Here we show that hybrids selectively retain gene regulation plasticity inherited from the two parents, and that this plasticity affects genes involved in virulence.
APOBEC3C tandem domain proteins create super restriction factors against HIV-1
Authors: McDonnell Mollie M. , Crawford Kate H.D. , Dingens Adam S. , Bloom Jesse D. , Emerman Michael
Published: March 2020

Humans encode proteins, called restriction factors, that inhibit replication of viruses like HIV-1. One family of antiviral proteins,apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3, shortened to A3) acts by deaminating cytidines to uridines during the reverse transcription reaction of HIV-1. TheA3locus encodes seven genes, namedA3A-A3H. These genes either have one or two cytidine deaminase domains and several of these A3s potently restrict HIV-1. A3C, which has only a single cytidine deaminase domain, however, inhibits HIV-1 only very weakly. We tested novel double domain protein combinations by genetically linking twoA3Cgenes to make a synthetic tandem domain protein. This protein created a “super restriction factor” that had more potent antiviral activity than the native A3C protein, which correlated with increased packaging into virions. Furthermore, disabling one of the active sites of the synthetic tandem domain protein results in an even greater increase in the antiviral activity—recapitulating a similar evolution seen in A3F and A3G (double domain A3s that only use a single catalytically active deaminase domain). These A3C tandem domain proteins do not have an increase in mutational activity, but instead inhibit formation of reverse transcription products which correlates with their ability to form large higher order complexes in cells. Finally, the A3C-A3C super restriction factor largely escaped antagonism by the HIV-1 viral protein, Vif.

Importance

As a part of the innate immune system, humans encode proteins that inhibit viruses like HIV-1. These broadly acting antiviral proteins do not protect humans from viral infections because viruses encode proteins that antagonize the host antiviral proteins to evade the innate immune system. One such example of a host antiviral protein is APOBEC3C (A3C), which weakly inhibits HIV-1. Here, we show that we can improve the antiviral activity of A3C by duplicating the DNA sequence to create a synthetic tandem domain, and furthermore, are relatively resistant to the viral antagonist, Vif. Together, these data give insights about how nature has evolved a defense against viral pathogens like HIV.
Determining structures of biomacromolecular complexes from ambiguous NMR restraints and cryoEM data
Authors: Walser Reto , Milbradt Alexander G.
Published: March 2020

Integrated structural biology aims at combining different techniques to tackle challenging systems. Where individual techniques are not delivering structures of suitable quality, harnessing the strengths of various methods can often overcome this problem. X-ray crystallography and NMR have been the two most widely applied structural biology disciplines. In recent years cryoelectron microscopy (cryoEM) has become ever more powerful and is now capable of providing structures at resolutions comparable to those common in X-ray crystallography. Unfortunately, both NMR and cryoEM have inherent limitations on the system under study. However, the two techniques can be considered somewhat complementary as NMR has an upper and cryoEM a lower molecular weight (MW) limit. Here, we present a joint NMR and cryoEM methodology for the determination of biomacromolecular structures at the boundary region between the MW limits of the two techniques. The method relies on measuring chemical shift perturbations, which is the most readily accessible NMR parameter for characterizing the interaction of biomacromolecular complexes. Low-resolution cryoEM information yields global information on the shape of the complex and is used for complementing the local NMR data. We have successfully applied this method to the model system histidine-containing phosphoprotein (HPr) in complex with the glucose-specific acceptor protein IIAGlcfromEscherichia coli.
Recombination and sterility in inversion homo- and heterokaryotypes under a general counting model of chiasma interference
Authors: Kapperud Øystein
Published: March 2020

It has long been known that chiasmata are not independently generated along the chromosome, a phenomenon known aschiasma interference. In this paper, I suggest a model of chiasma interference that generalizes thePoisson model, thecounting model, thePoisson-skip modeland thetwo-pathway counting modelinto a single framework, and use it to derive infinite series expressions for the sterility and recombination pattern probabilities in inversion homo- and heterokaryotypes, and a closed-form expression for the special case of the two-pathway counting model in homokaryotypes.