bluuebunny/crossref_metadata_2025 huggingface dataset:
A rapidly evolved shift in life history timing during ecological speciation is driven by the transition between developmental phases
Authors: Powell Thomas H. Q. , Nguyen Andrew , Xia Qinwen , Feder Jeffrey L. , Ragland Gregory J. , Hahn Daniel A.
Published: January 2020

For insect species in temperate environments, seasonal timing is often governed by the regulation of diapause, a complex developmental program that allows insects to weather unfavorable conditions and synchronize their lifecycles with available resources. Diapause consists of a series of phases that govern initiation, maintenance, and termination of this developmental pathway. The evolution of insect seasonal timing depends in part on how these phases of diapause development and post-diapause development interact to affect variation in phenology. Here, we dissect the physiological basis of a recently evolved phenological shift inRhagoletis pomonella(Diptera: Tephritidae), a model system for ecological divergence. A recently derived population ofR. pomonellashifted from specializing on native hawthorn fruit to earlier fruiting introduced apples, resulting in a 3-4 week shift in adult emergence timing. We tracked metabolic rates of individual flies across post-winter development to test which phases of development may act either independently or in combination to contribute to this recently evolved divergence in timing. Apple and hawthorn flies differed in a number of facets of their post-winter developmental trajectories. However, divergent adaptation in adult emergence phenology in these flies was due almost entirely to the end of the pupal diapause maintenance phase, with post-diapause development having a very small effect. The relatively simple underpinnings of variation in adult emergence phenology suggest that further adaptation to seasonal change in these flies for this trait might be largely due to the timing of diapause termination unhindered by strong covariance among different components of post-diapause development.

Data accessibility

All data (in the form of tables of all metabolic rate measurements for all individual flies in the study) will be available on DRYAD when the manuscript is published.
A Tug of War Between Condensate Phases in a Minimal Macromolecular System
Authors: Ghosh Archishman , Zhang Xiaojia , Zhou Huan-Xiang
Published: January 2020

Membraneless organelles formed via liquid-liquid phase separation (LLPS) contain a multitude of macromolecular species. A few of these species drive LLPS while most serve as regulators. The LLPS of SH35(S) and PRM5(P), two oppositely charged protein constructs, was promoted by a polyanion heparin (H) but suppressed by a cationic protein lysozyme (L). Here, using these four components alone, we demonstrate complex phase behaviors associated with membraneless organelles and uncover the underlying physical rules. The S:P, S:L, and P:H binaries form droplets, but the H:L binary forms precipitates, therefore setting off a tug of water between different phases within the S:P:H:L quaternary. We observe dissolution of precipitates upon compositional change, transformation from precipitates to droplet-like condensates over time, and segregation of S:L-rich and P:H-rich foci inside droplet-like condensates. A minimal macromolecular system can thus recapitulate membraneless organelles in essential ways and provide crucial physical understanding.
A Minimal Biophysical Model of Neocortical Pyramidal Cells: Implications for Frontal Cortex Microcircuitry and Field Potential Generation
Authors: Herrera Beatriz , Sajad Amirsaman , Woodman Geoffrey F. , Schall Jeffrey D. , Riera Jorge J.
Published: January 2020

Ca2+spikes initiated in the apical dendrites of layer-5 pyramidal cells (PC) underlie nonlinear dynamic changes in the gain of cellular response, which is critical for top-down cognitive control. Detailed models with several compartments and dozens of ionic channels have been proposed to account for this Ca2+spike-dependent gain with its associated critical frequency. However, current models do not account for all known Ca2+-dependent features. Previous attempts to include more features have required increasing complexity, limiting their interpretability and utility for studying large population dynamics. We present a minimal 2-compartment biophysical model, overcoming these limitations. In our model, a basal-dendritic/somatic compartment included typical Na+and K+conductances, while an apical-dendritic/trunk compartment included persistent Na+, hyperpolarization-activated cation (Ih), slow inactivation K+, muscarinic K+, and Ca2+L-type. The model replicated the Ca2+spike morphology and its critical frequency plus three other defining features of layer-5 PC synaptic integration: linear frequency-current relationships, backpropagation-activated Ca2+spike firing, and a shift in the critical frequency by blocking Ih. Simulating 1,000 synchronized layer-5 PCs, we reproduced the current source density patterns evoked by Ca2+-spikes both with and without Ihcurrent. Thus, a 2-compartment model with five non-classic ionic currents in the apical-dendrites reproduces all features of these neurons. We discuss the utility of this minimal model to study the microcircuitry of agranular areas of the frontal lobe involved in cognitive control and responsible for event-related potentials such as the error-related negativity.

Significance Statement

A tractable model of layer-5 pyramidal cells replicates all known features crucial for distal synaptic integration in these neurons. This minimal model enables new multi-scale investigations of microcircuit functions with associated current flows measured by intracranial local field potentials. It thus establishes a foundation for the future computational evaluation of scalp electroencephalogram signatures imprinted by Ca2+spikes in pyramidal cells, a phenomenon underlying many brain cognitive processes.
microRNA-seq of cartilage reveals an over-abundance of miR-140-3p which contains functional isomiRs
Authors: Woods Steven , Charlton Sarah , Cheung Kat , Hao Yao , Soul Jamie , Reynard Louise N , Crowe Natalie , Swingler Tracey E. , Skelton Andrew J. , Piróg Katarzyna A. , Miles Colin G. , Tsompani Dimitra , Jackson Robert M. , Dalmay Tamas , Clark Ian M. , Barter Matt J. , Young David A.
Published: January 2020

MiR-140 is selectively expressed in cartilage. Deletion of the entire miR-140 locus in mice results in growth retardation and early-onset osteoarthritis-like pathology, however the relative contribution of miR-140-5p or miR-140-3p to the phenotype remains to be determined. An unbiased small RNA sequencing approach identified miR-140-3p as significantly more abundant (>10-fold) than miR-140-5p in human cartilage. Analysis of these data identified multiple miR-140-3p isomiRs differing from the miRBase annotation at both the 5’ and 3’ end, with >99% having one of two seed sequences (5 ‘ bases 2-8). Canonical (miR-140-3p.2) and shifted (miR-140-3p.1) seed isomiRs were overexpressed in chondrocytes and transcriptomics performed to identify targets. miR-140-3p.1 and miR-140-3p.2 significantly down-regulated 694 and 238 genes respectively, of which only 162 genes were commonly down-regulated. IsomiR targets were validated using 3 ‘UTR luciferase assays. miR-140-3p.1 targets were enriched within up-regulated genes in rib chondrocytes ofMir140-null mice and within down-regulated genes during human chondrogenesis. Finally, through imputing the expression of miR-140 from the expression of the host geneWWP2in 124 previously published datasets, an inverse correlation with miR-140-3p.1 predicted targets was identified. Together these data suggest the novel seed containing isomiR miR-140-3p.1 is more functional than original consensus miR-140-3p seed containing isomiR.
Pervasive phenotypic impact of a large non-recombining introgressed region in yeast
Authors: Brion Christian , Caradec Claudia , Pflieger David , Friedrich Anne , Schacherer Joseph
Published: January 2020

To explore the origin of the diversity observed in natural populations, many studies have investigated the relationship between genotype and phenotype. In yeast species, especially inSaccharomyces cerevisiae, these studies are mainly conducted using recombinant offspring derived from two genetically diverse isolates, allowing to define the phenotypic effect of genetic variants. However, large genomic variants such as interspecies introgressions are usually overlooked even if they are known to modify the genotype-phenotype relationship. To have a better insight into the overall phenotypic impact of introgressions, we took advantage of the presence of a 1-Mb introgressed region, which lacks recombination and contains the mating-type determinant in theLachancea kluyveribudding yeast. By performing linkage mapping analyses in this species, we identified a total of 89 loci affecting growth fitness in a large number of conditions and 2,187 loci affecting gene expression mostly grouped into two major hotspots, one being the introgressed region carrying the mating-type locus. Because of the absence of recombination, our results highlight the presence of a sexual dimorphism in a budding yeast for the first time. Overall, by describing the phenotype-genotype relationship in theL. kluyverispecies, we expanded our knowledge on how genetic characteristics of large introgression events can affect the phenotypic landscape.
Molecular mechanism of light-driven sodium pumping
Authors: Kovalev K. , Astashkin R. , Gushchin I. , Orekhov P. , Volkov D. , Zinovev E. , Marin E. , Rulev M. , Alekseev A. , Royant A. , Carpentier P. , Vaganova S. , Baeken C. , Sergeev I. , Zabelskii D. , Balandin T. , Bourenkov G. , Borshchevskiy V. , Büldt G. , Bamberg E. , Gordeliy V.
Published: January 2020

Microbial rhodopsins appeared to be the most abundant light-harvesting proteins on the Earth and are the major contributes to the solar energy captured in the sea. They possess highly diverse biological functions. Explosion of research on microbial rhodopsins led to breakthroughs in their applications, in particular, in neuroscience.

An unexpected new discovery was a Na+-pumping KR2 rhodopsin fromKrokinobacter eikastus, the first light-driven non-proton cation pump. A fundamental difference between proton and other cation pumps is that non-proton pumps cannot use tunneling or Grotthuss mechanism for the ion translocation and, therefore, Na+pumping cannot be understood in the framework of classical proton pump, like bacteriorhodopsin. Extensive studies on the molecular mechanism of KR2 failed to reveal mechanism of pumping. The existing high-resolution structures relate only to the ground state of the protein and revealed no Na+inside the protein, which is unusual for active ion transporters.

KR2 is only known non proton cation transporter with demonstrated remarkable potential for optogenetic applications and, therefore, elucidation of the mechanism of cation transport is important. To understand conception of cation pumping we solved crystal structures of the functionally key O-intermediate state of physiologically relevant pentameric form of KR2 and its D116N and H30A key mutants at high resolution and performed additional functional studies.

The structure of the O-state reveals a sodium ion near the retinal Schiff base coordinated by N112 and D116 residues of the characteristic (for the whole family) NDQ triad. The structural and functional data show that cation uptake and release are driven by a switching mechanism. Surprisely, Na+pathway in KR2 is lined with the chain of polar pores/cavities, similarly to the channelrhodopsin-2. Using Parinello fast molecular dynamics approach we obtained a molecular movie of a probable ion release.

Our data provides insight into the mechanism of a non-proton cation light-driven pumping, strongly suggest close relation of sodium pumps to channel rhodopsins and, we believe, expand the present knowledge of rhodopsin world. Certainly they might be used for engineering of cation pumps and ion channels for optogenetics.
Coupling of Ca2+and voltage activation in BK channels through the αB helix/voltage sensor interface
Authors: Geng Yanyan , Deng Zengqin , Zhang Guohui , Budelli Gonzalo , Butler Alice , Yuan Peng , Cui Jianmin , Salkoff Lawrence , Magleby Karl L.
Published: January 2020

Large conductance Ca2+and voltage activated K+(BK) channels control membrane excitability in many cell types. BK channels are tetrameric. Each subunit is comprised of a voltage sensor domain (VSD), a central pore gate domain, and a large cytoplasmic domain (CTD) that contains the Ca2+sensors. While it is known that BK channels are activated by voltage and Ca2+, and that voltage and Ca2+activations interact, less is known about the mechanisms involved. We now explore mechanism by examining the gating contribution of an interface formed between the VSDs and the αB helices located at the top of the CTDs. Proline mutations in the αB helix greatly decreased voltage activation while having negligible effects on gating currents. Analysis with the HCA model indicated a decreased coupling between voltage sensors and pore gate. Proline mutations decreased Ca2+activation for both Ca2+bowl and RCK1 Ca2+sites, suggesting that both high affinity Ca2+sites transduce their effect, at least in part, through the αB helix. Mg2+activation was also decreased. The crystal structure of the CTD with proline mutation L390P showed a flattening of the first helical turn in the αB helix compared to WT, without other notable differences in the CTD, indicating structural change from the mutation was confined to the αB helix. These findings indicate that an intact αB helix/VSD interface is required for effective coupling of Ca2+binding and voltage depolarization to pore opening, and that shared Ca2+and voltage transduction pathways involving the αB helix may be involved.

Significance

Large conductance BK (Slo1) K+channels are activated by voltage, Ca2+, and Mg2+to modulate membrane excitability in neurons, muscle, and other cells. BK channels are of modular design, with pore-gate and voltage sensors as transmembrane domains and a large cytoplasmic domain CTD containing the Ca2+sensors. Previous observations suggest that voltage and Ca2+sensors interact, but less is known about this interaction and its involvement in the gating process. We show that a previously identified structural interface between the CTD and voltage sensors is required for effective activation by both voltage and Ca2+, suggesting that these processes may share common allosteric activation pathways. Such knowledge should help explain disease processes associated with BK channel dysfunction.
Cell polarisation in a bulk-surface model can be driven by both classic and non-classic Turing instability
Authors: Borgqvist Johannes , Malik Adam , Lundholm Carl , Logg Anders , Gerlee Philip , Cvijovic Marija
Published: January 2020

The GTPase Cdc42 is the master regulator of eukaryotic cell polarisation. During this process the active form of Cdc42 is accumulated at a particular site on the cell membrane called thepole. It is believed that the accumulation of the active Cdc42 resulting in a pole is driven by a combination of activation-inactivation reactions and diffusion. It has been proposed using mathematical modelling that this is the result of diffusion-driven instability, originally proposed by Alan Turing. In this study we developed, analysed and validated a 3D bulk-surface model of the dynamics of Cdc42. We show that the model can undergo both classic and non-classic Turing instability by deriving necessary conditions for which this occurs and conclude that the non-classic case can be viewed as a limit case of the classic case of diffusion driven instability. We thoroughly investigate the parameter space. Using three-dimensional spatio-temporal simulation we predicted pole size and time to polarisation, suggesting that cell polarisation is mainly driven by the reaction strength parameter and that the size of the pole is determined by the relative diffusion.
The impediment to replication at tRNA genes inS. cerevisiaedoes not require tRNA transcription, and is facilitated by topoisomerases and Rad18-dependent repair pathways
Authors: Yeung Rani , Smith Duncan J.
Published: January 2020

tRNA genes are widely studied sites of replication-fork pausing and genome instability in the budding yeastSaccharomyces cerevisiae. tRNAs are extremely highly transcribed and serve as constitutive condensin binding sites. tRNA transcription by RNA polymerase III has previously been identified as stimulating replication-fork pausing at tRNA genes, but the nature of the block to replication has not been incontrovertibly demonstrated. Here, we describe a systematic, genome-wide analysis of the contributions of candidates to replication-fork progression at tDNAs in yeast: transcription factor binding, transcription, topoisomerase activity, condensin-mediated clustering, and Rad18-dependent DNA repair. We show that an asymmetric block to replication is maintained even when tRNA transcription is abolished by depletion of one or more subunits of RNA polymerase III. By contrast, analogous depletion of the essential transcription factor TFIIIB removes the obstacle to replication. Therefore, our data suggest that the RNA polymerase III transcription complex itself represents an asymmetric obstacle to replication even in the absence of RNA synthesis. We additionally demonstrate that replication-fork progression past tRNA genes is unaffected by the global depletion of condensin from the nucleus, and can be stimulated by the removal of topoisomerases or Rad18-dependent DNA repair pathways.
Theoretical guidelines for editing ecological communities
Authors: Nguyen Vu , Vural Dervis Can
Published: January 2020

Having control over species abundances and community resilience is of great interest for experimental, agricultural, industrial and conservational purposes. Here, we theoretically explore the possibility of manipulating ecological communities by modifying pairwise interactions. Specifically, we establish which interaction values should be modified, and by how much, in order to alter the composition or resilience of a community towards a favorable direction. While doing so, we also take into account the experimental difficulties in making such modifications by including in our optimization process, a cost parameter, which penalizes large modifications. In addition to prescribing what changes should be made to interspecies interactions given some modification cost, our approach also serves to establish the limits of community control, i.e. how well can one approach an ecological goal at best, even when not constrained by cost.
Analysis of metagenome-assembled genomes from the mouse gut microbiota reveals distinctive strain-level characteristics
Authors: Li Shenghui , Zhang Siyi , Li Bo , Sha Shanshan , Kang Jian , Li Peng , Zhang Aiqin , Ji Qianru , Lv Qingbo , Zhang Xiao-Xuan , Ni Hongbo , Han Xiuyan , Xu Miao , Wang Guangyang , Zhang Wenzhe , Sun Yuanyuan , Xu Roujia , Xin Yi , Yan Qiulong , Ma Yufang
Published: January 2020

The laboratorial mouse harbors a unique gut microbiota with potential value for human microbiota-associated studies. Mouse gut microbiota has been explored at the genus and species levels, but features rarely been showed at the strain level. The identification of 833,051 and 658,438 nonredundant genes of faeces and gut content samples from the laboratorial C57/BL mice showed over half of these genes were newly found compared to the previous mouse gut microbial gene catalogue. Metagenome-assembled genomes (MAGs) was used to reconstruct 46 nonredundant MAGs belonging to uncultured specieses. These MAGs included members across all phyla in mouse gut (i.e. Firmicutes, Bacteroidetes, Proteobacteria, Deferribacteres, Verrucomicrobia, and Tenericutes) and allowed a strain-level delineating of the mouse gut microbiota. Comparison of MAGs with human gut colonies revealed distinctive genomic and functional characteristics of mouse’s Bacteroidetes and Firmicutes strains. Genomic characteristics of rare phyla in mouse gut microbiota were demonstrated by MAG approach, including strains ofMucispirillum schaedleri, Parasutterella excrementihominis, Helicobacter typhlonius, andAkkermansia muciniphila.

Importance

The identification of nonredundant genes suggested the existence of unknown microbes in the mouse gut samples. The metagenome-assembled genomes (MAGs) instantiated the specificity of mouse gut species and revealed an intestinal microbial correlation between mouse and human. The cultivation of faeces and gut contents sample validated the existence of MAGs and estimate their accuracy. Full-length 16S ribosomal RNA gene sequencing enabled taxonomic characterization. This study highlighted a unique ecosystem in the gut of laboratorial mice that obviously differed with the human gut flora at the strain level. The outcomes may be beneficial to researches based on laboratorial mouse models.
Degrees of compositional shift in tree communities vary along a gradient of temperature change rates over one decade: Application of an individual-based temporal beta-diversity concept
Authors: Nakadai Ryosuke
Published: January 2020

Temporal patterns in communities have gained widespread attention recently, to the extent that temporal changes in community composition are now termed “temporal beta-diversity”. Previous studies of beta-diversity have made use of two classes of dissimilarity indices: incidence-based (e.g., Sørensen and Jaccard dissimilarity) and abundance-based (e.g., Bray–Curtis and Ružička dissimilarity). However, in the context of temporal beta-diversity, the persistence of identical individuals and turnover among other individuals within the same species over time have not been considered, despite the fact that both will affect compositional changes in communities. To address this issue, I propose new index concepts for beta-diversity and the relative speed of compositional shifts in relation to individual turnover based on individual identity information. Individual-based beta-diversity indices are novel dissimilarity indices that consider individual identity information to quantitatively evaluate temporal change in individual turnover and community composition. I applied these new indices to individually tracked tree monitoring data in deciduous and evergreen broad-leaved forests across the Japanese archipelago with the objective of quantifying the effect of climate change trends (i.e., rates of change of both annual mean temperature and annual precipitation) on individual turnover and compositional shifts at each site. A new index explored the relative contributions of mortality and recruitment processes to temporal changes in community composition. Clear patterns emerged showing that an increase in the temperature change rate facilitated the relative contribution of mortality components. The relative speed of compositional shift increased with increasing temperature change rates in deciduous forests but decreased with increasing warming rates in evergreen forests. These new concepts provide a way to identify novel and high-resolution temporal patterns in communities.
Population genomic structure in Goodman’s mouse lemur reveals long-standing separation of Madagascar’s Central Highlands and eastern rainforests
Authors: Tiley George P. , Blanco Marina B. , Ralison José M. , Rasoloarison Rodin M. , Stahlke Amanda R. , Hohenlohe Paul A. , Yoder Anne D.
Published: January 2020

The Central Highland Plateau of Madagascar is largely composed of grassland savanna, interspersed with patches of closed-canopy forest. Conventional wisdom has it that these grasslands are anthropogenic in nature, having been created very recently via human agricultural practices. Yet, the ancient origins of the endemic grasses suggest that the extensive savannas are natural biomes, similar to others found around the globe. We use a phylogeographic approach to compare these two competing scenarios. By sampling multiple populations of Goodman’s mouse lemur (Microcebus lehilahytsara), a small-bodied nocturnal primate, we reconstruct the phylogeographic and demographic history of these “environmental metronomes” to estimate the time at which their populations diverged, and thus proximally, when their habitats would have become fragmented. We applied coalescent methods to RADseq data to infer phylogenetic relationships, population structure, and migration corridors among sampling sites. These analyses indicate that forest fragmentation occurred rapidly during a period of decreased precipitation near the last glacial maximum and would have affected both the Central Highlands and eastern forests. Though there is clear genomic structure separating the populations of the Central Highland from those of the eastern rainforests, there is also evidence of historical migration between them. Findings support the hypothesis that the Central Highland savanna predates human arrival, indicating that it is a natural landscape that has long impacted the population dynamics of Goodman’s mouse lemur, and by extension, other forest-dwelling organisms in Madagascar.
metaVaR: introducing metavariant species models for reference-free metagenomic-based population genomics
Authors: Laso-Jadart Romuald , Ambroise Christophe , Peterlongo Pierre , Madoui Mohammed-Amin
Published: January 2020

Motivation

The availability of large metagenomic data offers great opportunities for the population genomic analysis of uncultured organisms, especially for small eukaryotes that represent an important part of the unexplored biosphere while playing a key ecological role. However, the majority of these species lacks reference genome or transcriptome which constitutes a technical barrier for classical population genomic analyses.

Results

We introduce the metavariant species (MVS) model, a representation of the species only by intra-species nucleotide polymorphism. We designed a method combining reference-free variant calling, multiple density-based clustering and maximum weighted independent set algorithms to cluster intra-species variant into MVS directly from multisample metagenomic raw reads without reference genome or reads assembly. The frequencies of the MVS variants are then used to compute population genomic statistics such asFSTin order to estimate genomic differentiation between populations and to identify loci under natural selection. The MVSs construction was tested on simulated and real metagenomic data. MVs showed the required quality for robust population genomics and allowed an accurate estimation of genomic differentiation (ΔFST<0.0001 and < 0.03 on simulated and real data respectively). Loci predicted under natural selection on real data were all found by MVSs. MVSs represent a new paradigm that may simplify and enhance holistic approaches for population genomics and evolution of microorganisms.

Availability

The method was implemented in a R package,metaVaR.https://github.com/madoui/MetaVaR

Contact

amadoui@genoscope.cns.fr
Targeting human Plasmacytoid dendritic cells through BDCA2 prevents inflammation and fibrosis in xenotransplant mouse model of Scleroderma
Authors: Ross Rebecca L. , Corinaldesi Clarissa , Migneco Gemma , Carr Ian , Antanaviciute Agne , Carriero Antonio , Wasson Christopher , Georgiou Ioanna , Distler Jörg H. W. , Holmes Steve , El-Sherbiny Yasser M. , McKimmie Clive S. , Del Galdo Francesco
Published: January 2020

Plasmacytoid dendritic cells (pDC) have been implicated in the pathogenesis of Scleroderma (SSc) through their ability to infiltrate the skin and secrete interferons (IFN) and proinflammatory chemokines. Blood Dendritic Cells Antigen 2 (BDCA2) is an inhibitory type II C-type lectin expressed by human pDC. Here we determined the effects of BDCA2 internalisation on pDC mediated skin inflammation and fibrosis in human preclinical models of skin inflammation and fibrosis in vitro and in vivo. BDCA2 targeting reversed TLR-signalling induced transcriptome and differentiation of pDC and suppressed their ability to induce IFN response in organotypic 3D human skin culturesin vitro.In vivo, xenotransplantation of human pDC into immunocompromised mice (XenoSCID) significantly increased IFN induced responses to topical TLR7/9 agonist and separately enhanced the fibrotic response to bleomycin. Targeting of BDCA2 strongly suppressed both of these pathological responses ameliorating skin inflammation and fibrosis. Together, these preclinical data strongly support the notion that human pDC play a key role in immune driven skin fibrosis, which can be effectively blocked by targeting BDCA2.
Microglia in the developing retina couple phagocytosis with the progression of apoptosis via P2RY12 signaling
Authors: Blume Zachary I. , Lambert Jared M. , Lovel Anna G. , Mitchell Diana M.
Published: January 2020

Background

Microglia colonize the developing vertebrate central nervous system coincident with detection of developmental apoptosis. Our understanding of apoptosis in intact tissue in relation to microglial clearance of dying cells is largely based on fixed samples, which is limiting given that microglia are highly motile and mobile phagocytes. Here, we used a system of microglial depletion andin vivoreal-time imaging in zebrafish to directly address microglial phagocytosis of apoptotic cells during normal retinal development, the relative timing of phagocytosis in relation to apoptotic progression, and the contribution of P2RY12 signaling to this process.

Results

Depletion of microglia resulted in accumulation of numerous apoptotic cells in the retina. Real-time imaging revealed precise timing of microglial engulfment with the progression of apoptosis, and dynamic movement and displacement of engulfed apoptotic cells. Inhibition of P2RY12 signaling delayed microglial clearance of apoptotic cells.

Conclusions

Microglial engulfment of dying cells is coincident with apoptotic progression and requires P2RY12 signaling, indicating that microglial P2RY12 signaling is shared between development and injury response. Our work provides importantin vivoinsight into the dynamics of apoptotic cell clearance in the developing vertebrate retina and provides a basis to understand microglial phagocytic behavior in health and disease.

Bullet Points

Levels and location of developmental apoptosis in the zebrafish retina are elusive due to rapid and efficient clearance by microglia

Microglial clearance of apoptotic cells is timed with the progression of apoptosis of the engulfed cell so that many cells are cleared in relatively early apoptotic stages

P2RY12 signaling is involved in microglial sensing and clearance of cells undergoing normal developmental apoptosis, indicating shared signals in microglial responses to cell death in both healthy and injured tissue

Grant Sponsors

NIH NIGMS Grant No. P20 GM103408
Lnc-ECAL-1controls cerebrovascular homeostasis by targeting endothelium-specific tight junction proteinCldn5b
Authors: Li Fang-Fang , Liang Yu-Lai , Zhang Jing-Jing , Jing Qing
Published: January 2020

Cerebrovascular disorder-induced brain blood flow interruption or intracranial hemorrhage pose a great threaten to health. Emerging roles of long-noncoding RNAs (lncRNAs) in diagnosis and treatment of cardiovascular diseases have been recognized. However, whether and how lncRNAs modulate vascular homeostasis, especially network formation remain largely unknown. Here, we identifiedECAL-1, a long non-coding RNA, as an important determinant for cerebrovascular homeostasis. Using the morpholino- and CRISPR /Cas9-based genetic modifications in combination within vivoconfocal imaging in zebrafish, we claimed that inactivation ofECAL-1induced the apparent distortion of cerebral vascular pattern accompanied by intracranial hemorrhage. These cerebrovascular abnormalities were associated with decreased proliferation and anomalous interconnection of endothelial cells. Importantly, overexpression of Cldn5b, an endothelial cell-specific tight junction protein-encoding gene, could partially rescued the phenotype induced byECAL-1deficiency. Furthermore, bioinformatic analysis and experimental validation revealed thatECAL-1sponged miR-23a, which targeted Cldn5b 3’UTR and modulated Cldn5b expression, to maintain cerebrovascular pattern formation and integrity. Our results presented here revealed thatECAL-1specifically controls cerebrovascular network formation and integrity through targeting miR-23a-Cldn5baxis. These findings provide a new regulation modality for cerebrovascular patterning and the potential neurovascular disorders, andECAL-1-miR-23a axis represents as an attractive therapeutic target for cerebrovascular diseases.
Differentiation genes were governed by DNA methylation during hair follicle morphogenesis in Cashmere goat
Authors: Wang Shanhe , Li Fang , Liu Jinwang , Zhang Yuelang , Zheng Yujie , Ge Wei , Qu Lei , Wang Xin
Published: January 2020

DNA methylation plays a critical role in early embryonic skin development by controlling gene expression. Act as an indirect regulator, long non-coding RNA (lncRNA) recruit DNA methyltransferases to specific genomic sites to methylate DNA. However, the molecular regulation mechanisms underlying hair follicle morphogenesis is unclear in cashmere goat. In this study, RNA-seq and Whole-genome bisulfite sequencing (WGBS) in embryonic day 65 (E65) and E120 skin tissues of cashmere goat were used to reveal this complex regulatory process. RNA-seq, qRT-PCR and immunohistochemistry results showed that Wnt signaling played an important role in both hair follicle induction and differentiation stage, transcriptional factors (TFs) including Hoxc13, Sox9, Sox21, Junb, Lhx2, Vdr and Gata3 participated in hair follicle differentiation via specific expression at E120. Subsequently, combination of WGBS and RNA-seq analysis showed that the expression of hair follicle differentiation genes and TFs genes was negatively correlated with DNA methylation level generally. A portion of hair follicle differentiation genes were methylated and repressed in hair follicle induction stage but were subsequently demethylated and expressed during hair follicle differentiation stage, suggesting DNA methylation play an important role in hair morphogenesis through regulating associated gene expression. Furthermore, the potential differentially expressed lncRNAs associated with DNA methylation on target gene were revealed. LncRNA XR_001918556 may affect the DNA methylation of TFs geneGata3, lnc-003786 may affect the DNA methylation of signaling geneFgfr2. In conclusion, differentiation genes were governed by DNA methylation, resulting in repressed expression in hair follicle induction stage and high expression in hair follicle differentiation stage. Furtherly, potential lncRNAs associated with DNA methylation on target genes were delineated. This study would enrich the regulatory network and molecular mechanisms on hair morphogenesis.
Evolution and variation of 2019-novel coronavirus
Authors: Xiong Chenglong , Jiang Lufang , Chen Yue , Jiang Qingwu
Published: January 2020

Background

The current outbreak caused by novel coronavirus (2019-nCoV) in China has become a worldwide concern. As of 28 January 2020, there were 4631 confirmed cases and 106 deaths, and 11 countries or regions were affected.

Methods

We downloaded the genomes of 2019-nCoVs and similar isolates from the Global Initiative on Sharing Avian Influenza Database (GISAID and nucleotide database of the National Center for Biotechnology Information (NCBI). Lasergene 7.0 and MEGA 6.0 softwares were used to calculate genetic distances of the sequences, to construct phylogenetic trees, and to align amino acid sequences. Bayesian coalescent phylogenetic analysis, implemented in the BEAST software package, was used to calculate the molecular clock related characteristics such as the nucleotide substitution rate and the most recent common ancestor (tMRCA) of 2019-nCoVs.

Results

An isolate numbered EPI_ISL_403928 showed different phylogenetic trees and genetic distances of the whole length genome, the coding sequences (CDS) of ployprotein (P), spike protein (S), and nucleoprotein (N) from other 2019-nCoVs. There are 22, 4, 2 variations in P, S, and N at the level of amino acid residues. The nucleotide substitution rates from high to low are 1·05 × 10−2(nucleotide substitutions/site/year, with 95% HPD interval being 6.27 × 10−4to 2.72 × 10−2) for N, 5.34 × 10−3(5.10 × 10−4, 1.28 × 10−2) for S, 1.69 × 10−3(3.94 × 10−4, 3.60 × 10−3) for P, 1.65 × 10−3(4.47 × 10−4, 3.24 × 10−3) for the whole genome, respectively. At this nucleotide substitution rate, the most recent common ancestor (tMRCA) of 2019-nCoVs appeared about 0.253-0.594 year before the epidemic.

Conclusion

Our analysis suggests that at least two different viral strains of 2019-nCoV are involved in this outbreak that might occur a few months earlier before it was officially reported.
Conventional dose rate spatially-fractionated radiation therapy (SFRT) treatment response and its association with dosimetric parameters – A preclinical study in a Fisher 344 rat model
Authors: Rivera Judith N. , Kierski Thomas M. , Kasoji Sandeep K. , Abrantes Anthony S. , Dayton Paul A. , Chang Sha X.
Published: January 2020

Purpose

To identify key dosimetric parameters that have close associations with tumor treatment response and body weight change in SFRT treatments with a large range of spatial-fractionation scale at dose rates of several Gy/min.

Methods

Six study arms using uniform tumor radiation, half-tumor radiation, 2mm beam array radiation, 0.3mm minibeam radiation, and an untreated arm were used. All treatments were delivered on a 320kV x-ray irradiator. Forty-two female Fischer 344 rats with fibrosarcoma tumor allografts were used. Dosimetric parameters studied are peak dose and width, valley dose and width, peak-to-valley-dose-ratio, volumetric average dose, percentage volume directly irradiated, and tumor- and normal-tissue EUD. Animal survival, tumor volume change, and body weight change (indicative of treatment toxicity) are tested for association with the dosimetric parameters using linear regression and Cox Proportional Hazards models.

Results

The dosimetric parameters most closely associated with tumor response are tumor EUD (R2=0.7923, F-stat=15.26*; z-test=−4.07***), valley/minimum dose (R2=0.7636, F-stat=12.92*; z-test=−4.338***), and percentage tumor directly irradiated (R2=0.7153, F-stat=10.05*; z-test=−3.837***) per the linear regression and Cox Proportional Hazards models, respectively. Tumor response is linearly proportional to valley/minimum doses and tumor EUD. Average dose (R2=0.2745, F-stat=1.514 (no sig.); z-test=−2.811**) and peak dose (R2=0.04472, F-stat=0.6874 (not sig.); z-test=−0.786 (not sig.)) show the weakest associations to tumor response. Only the uniform radiation arm did not gain body weight post-radiation, indicative of treatment toxicity; however, body weight change in general shows weak association with all dosimetric parameters except for valley/min dose (R2=0.3814, F-stat=13.56**), valley width (R2=0.2853, F-stat=8.783**), and peak width (R2=0.2759, F-stat=8.382**).

Conclusions

For a single-fraction SFRT at conventional dose rates, valley, not peak, dose is closely associated with tumor treatment response and thus should be used for treatment prescription. Tumor EUD, valley/min dose, and percentage tumor directly irradiated are the top three dosimetric parameters that exhibited close associations with tumor response.
Niche preference ofEscherichia coliin a peri-urban pond ecosystem
Authors: NandaKafle Gitanjali , Huegen Taylor , Potgieter Sarah C. , Steenkamp Emma , Venter Stephanus N. , Brözel Volker S.
Published: January 2020

Escherichia colicomprises of diverse strains with a large accessory genome, indicating functional diversity and the ability to adapt to a range of niches. Specific strains would display greatest fitness in niches matching their combination of phenotypic traits. Given this hypothesis, we sought to determine whetherE. coliin a peri-urban pond and associated cattle pasture display niche preference. Samples were collected from water, sediment, aquatic plants, water snails associated with the pond as well as bovine feces from cattle in an adjacent pasture. Isolates (120) were obtained after plating on Membrane Lactose Glucuronide Agar (MLGA). We used theuidAandmutSsequences for all isolates to determine phylogeny by maximum likelihood, and population structure through gene flow analysis. PCR was used to allocate isolates to phylogroups and to determine the presence of pathogenicity / virulence genes (stxI, stxII, eaeA, hlyA, ST and LT). Antimicrobial resistance was determined using a disk diffusion assay for Tetracycline, Gentamicin, Ciprofloxacin, Meropenem, Ceftriaxone, and Azitrhomycin. Our results showed that isolates from water, sediment and water plants were similar by phylogroup distribution, virulence gene distribution and antibiotic resistance while both snail and feces populations were significantly different. Few of the feces isolates were significantly similar to aquatic ones, and most of the snail isolates were also different. Population structure analysis indicated three genetic backgrounds associated with bovine, snail and aquatic environments. Collectively these data support niche preference ofE. coliisolates occurring in this ecosystem.
Differential virulence ofTrypanosoma brucei rhodesienseisolates does not influence the outcome of treatment with anti-trypanosomal drugs in the mouse model
Authors: Ndung’u Kariuki , Murilla Grace Adira , Thuita John Kibuthu , Ngae Geoffrey Njuguna , Auma Joanna Eseri , Gitonga Purity Kaari , Thungu Daniel Kahiga , Kurgat Richard Kiptum , Chemuliti Judith Kusimba , Mdachi Raymond Ellie
Published: January 2020

We assessed the virulence and anti-trypanosomal drug sensitivity patterns ofTrypanosoma brucei rhodesiense(Tbr) isolates in the Kenya Agricultural and Livestock Research Organization-Biotechnology Research Institute (KALRO-BioRI) cryobank. Specifically, the study focused onTbrclones originally isolated from the western Kenya/eastern Uganda focus of human African Trypanosomiasis (HAT). Twelve (12)Tbrclones were assessed for virulence using groups(n=10) of Swiss White Mice monitored for 60 days post infection (dpi). Based on survival time, four classes of virulence were identified: (a) very-acute: 0-15, (b) acute: 16-30, (c) sub-acute: 31-45 and (d) chronic: 46-60 dpi. Other virulence biomarkers identified included: prepatent period (pp), parasitaemia progression, packed cell volume (PCV) and body weight changes. The testTbrclones together with KALRO-BioRi reference drug-resistant and drug sensitive isolates were then tested for sensitivity to melarsoprol (mel B) pentamidine, diminazene aceturate and suramin, using mice groups (n= 5) treated with single doses of each drug at 24 hours post infection. Our results showed that the clones were distributed among four classes of virulence as follows: 3/12 (very-acute), 3/12 (acute), 2/12 (sub-acute) and 4/12 (chronic) isolates. Differences in survivorship, parasitaemia progression and PCV were significant (P<0.001) and correlated. The isolate considered to be drug resistant at KALRO-BioRI, KETRI 2538, was confirmed to be resistant to melarsoprol, pentamidine and diminazene aceturate but it was not resistant to suramin. At least 80% cure rates of all the test isolates was achieved with melarsoprol (1mg/Kg and 20 mg/kg), pentamidine (5 and 20 mg/kg), diminazene aceturate (5 mg/kg) and suramin (5 mg/kg) indicating that the isolates were not resistant to any of the drugs despite the differences in virulence. This study provides evidence of variations in virulence ofTbrisolates from a single HAT focus and confirms that these variations are not a significant determinant of isolate sensitivity to anti-trypanosomal drugs.
Robust design capture-recapture analysis of abundance and demographic parameters of Indian River Lagoon common bottlenose dolphins (Tursiops truncatus truncatus)
Authors: Durden Wendy Noke , Stolen Eric D. , Moreland Lydia , Howells Elisabeth , Jablonski Teresa , Sleeman Anne , Denny Matthew , Biedenbach George , Mazzoil Marilyn
Published: January 2020

Accurate estimates of abundance are critical to species management and conservation. Common bottlenose dolphins (Tursiops truncatus truncatus) inhabiting the Indian River Lagoon (IRL) estuarine system along the east coast of Florida are impacted by anthropogenic activities and have had multiple unexplained mortality events, necessitating precise estimates of demographic and abundance parameters to implement management strategies. Mark-recapture methodology following a Robust Design survey was used to estimate abundance, adult survival, and temporary emigration for the IRL estuarine system stock of bottlenose dolphins. Models included a parameter (time since first capture) to assess evidence for transient individuals. Boat-based photo-identification surveys (n= 135) were conducted along predetermined contour and transect lines throughout the entire IRL (2016-2017). The best fitting model included the “transient” parameter to survival, allowed survival to vary by primary period, detection to vary by secondary session, and did not allow temporary emigration. Dolphin abundance ranged from 981 (95% CI: 882-1,090) in winter to 1,078 (95% CI: 968-1,201) in summer with a mean of 1,032 (95% CI: 969 -1,098). Model averaged seasonal survival rate for marked residents ranged from 0.85-1.00. Capture probability ranged from 0.20 to 0.42 during secondary sessions and transient rate from 0.06 to 0.07. This study represents the first Robust design mark-recapture survey effort to estimate abundance for IRL dolphins and provides parameter estimates to optimize sampling design of future studies. Transients included individuals with home ranges extending north of the IRL requiring further assessment of stock delineation. Results were remarkably similar to prior abundance estimates resulting from line-transect aerial surveys and were consistent with a stable population. Data will enable managers to evaluate the impact of fisheries-related takes as well as enable future comparisons of demographic parameters for a dolphin population that continues to sustain large scale mortality events and anthropogenic impacts.
The Mutational Landscape of the SCAN-B Real-World Primary Breast Cancer Transcriptome
Authors: Brueffer Christian , Gladchuk Sergii , Winter Christof , Vallon-Christersson Johan , Hegardt Cecilia , Häkkinen Jari , George Anthony M. , Chen Yilun , Ehinger Anna , Larsson Christer , Loman Niklas , Malmberg Martin , Rydén Lisa , Borg Åke , Saal Lao H.
Published: January 2020

Breast cancer is a disease of genomic alterations, of which the complete panorama of somatic mutations and how these relate to molecular subtypes and therapy response is incompletely understood. Within the Sweden Cancerome Analysis Network–Breast project (SCAN-B; ClinicalTrials.govNCT02306096), an ongoing study elucidating the tumor transcriptomic profiles for thousands of breast cancers prospectively, we developed an optimized pipeline for detection of single nucleotide variants and small insertions and deletions from RNA sequencing (RNA-seq) data, and profiled a large real-world population-based cohort of 3,217 breast tumors. We use it to describe the mutational landscape of primary breast cancer viewed through the transcriptome of a large population-based cohort of patients, and relate it to patient overall survival. We demonstrate that RNA-seq can be used to call mutations in important breast cancer genes such asPIK3CA,TP53, andERBB2, as well as the status of key molecular pathways and tumor mutational burden, and identify potentially druggable genes in 86.8% percent of tumors. To make this rich and growing mutational portraiture of breast cancer available for the wider research community, we developed an open source web-based application, the SCAN-B MutationExplorer, accessible athttp://oncogenomics.bmc.lu.se/MutationExplorer. These results add another dimension to the use of RNA-seq as a potential clinical tool, where both gene expression-based and gene mutation-based biomarkers can be interrogated simultaneously and in real-time within one week of tumor sampling.