bluuebunny/crossref_metadata_2025 huggingface dataset:
Phylogenomic analyses of the East Asian endemicAbelia(Caprifoliaceae) shed insights into the temporal and spatial diversification history with widespread hybridizations
Authors: Sun Qing-Hui , Morales-Briones Diego F. , Wang Hong-Xin , Landis Jacob B. , Wen Jun , Wang Hua-Feng
Published: April 2021

Background and Aims

Abelia(Caprifoliaceae) is a small genus with five species, including one man-made hybrid and several natural hybrids. The genus has a discontinuous distribution in mainland China, Taiwan Island, and the Ryukyu islands, providing a model system to explore mechanisms of species dispersal in the East Asian flora. However, the current phylogenetic relationships withinAbeliaremain uncertain.

Methods

In this study, we reconstructed phylogenetic relationships withinAbeliausing nuclear loci generated by target enrichment and plastomes from genome skimming. Divergence time estimation, ancestral area reconstruction, and ecological niche modelling (ENM) were used to examine the diversification history ofAbelia.

Key Results

We found extensive cytonuclear discordance across the genus. By integrating lines of evidence from molecular phylogenies, divergence times, and morphology, we propose to mergeA. macroteravar.zabelioidesintoA. uniflora.Network analyses suggested that there have been widespread and multiple hybridization events amongAbeliaspecies. These hybridization events may have contributed to the speciation mechanism and resulted in a high observed morphological diversity. The diversification ofAbeliabegan in the early Eocene, followed byA. chinensisvar.ionandracolonizing the island of Taiwan in the Middle Miocene. The ENM results suggested an expansion of climatically suitable areas during the Last Glacial Maximum and range contraction during the Last Interglacial. Disjunction between the Himalayan-Hengduan Mountain region (HHM) and the island of Taiwan is most likely the consequence of topographic isolation and postglacial contraction.

Conclusions

We used genomic data to reconstruct the phylogeny ofAbeliaand found a clear pattern of reticulate evolution in the group. In addition, our results support shrinkage of postglacial range and the heterogeneity of the terrain have led to the disjunction of the mainland China-Taiwan island. This study provides important new insights into the speciation process and taxonomy ofAbelia.
Dynamic Profiling of Binding and Allosteric Propensities of the SARS-CoV-2 Spike Protein with Different Classes of Antibodies: Mutational and Perturbation-Based Scanning Reveal Allosteric Duality of Functionally Adaptable Hotspots
Authors: Verkhivker Gennady M. , Agajanian Steve , Oztas Deniz Yazar , Gupta Grace
Published: April 2021

Structural and biochemical studies of the SARS-CoV-2 spike complexes with highly potent antibodies have revealed multiple conformation-dependent epitopes and a broad range of recognition modes linked to different neutralization responses In this study, we combined atomistic simulations with mutational and perturbation-based scanning approaches to perform in silico profiling of binding and allosteric propensities of the SARS-CoV-2 spike protein residues in complexes with B38, P2B-2F6, EY6A and S304 antibodies representing three different classes. Conformational dynamics analysis revealed that binding-induced modulation of soft modes can elicit the unique protein response to different classes of antibodies. Mutational scanning heatmaps and sensitivity analysis revealed the binding energy hotspots for different classes of antibodies that are consistent with the experimental deep mutagenesis, showing that differences in the binding affinity caused by global circulating variants in spike positions K417, E484 and N501 are relatively moderate and may not fully account for the observed antibody resistance effects. Through functional dynamics analysis and perturbation-response scanning of the SARS-CoV-2 spike protein residues in the unbound form and antibody-bound forms, we examine how antibody binding can modulate allosteric propensities of spike protein residues and determine allosteric hotspots that control signal transmission and global conformational changes. These results show that residues K417, E484, and N501 targeted by circulating mutations correspond to a group of versatile allosteric centers in which small perturbations can modulate collective motions, alter the global allosteric response and elicit binding resistance. We suggest that SARS-CoV-2 S protein may exploit plasticity of specific allosteric hotspots to generate escape mutants that alter response to antibody binding without compromising activity of the spike protein.
Jointex vivoMRI and histology detect iron-rich cortical gliosis in Tau and TDP-43 proteinopathies
Authors: Tisdall M. Dylan , Ohm Daniel T. , Lobrovich Rebecca , Das Sandhitsu R. , Mizsei Gabor , Prabhakaran Karthik , Ittyerah Ranjit , Lim Sydney , McMillan Corey T. , Wolk David A. , Gee James , Trojanowski John Q. , Lee Edward B. , Detre John A. , Yushkevich Paul , Grossman Murray , Irwin David J.
Published: April 2021

Frontotemporal lobar degeneration (FTLD) is a heterogeneous spectrum of age-associated neurodegenerative diseases that include two main pathologic categories of tau (FTLD-Tau) and TDP-43 (FTLD-TDP) proteinopathies. These distinct proteinopathies are often clinically indistinguishable during life, posing a major obstacle for diagnosis and emerging therapeutic trials tailored to disease-specific mechanisms. Moreover, MRI-derived measures have had limited success to date discriminating between FTLD-Tau or FTLD-TDP. T2*-weighted (T2*w)ex vivoMRI has previously been shown to be sensitive to non-heme iron in healthy intracortical lamination and myelin, and to pathological iron deposits in amyloid-beta plaques and activated microglia in Alzheimer’s disease (AD). However, an integrated,ex vivoMRI and histopathology approach is understudied in FTLD. We apply joint, whole-hemisphereex vivoMRI at 7T and histopathology to the study autopsy-confirmed FTLD-Tau (n=3) and FTLD-TDP (n=2), relative to an AD disease-control brain with antemortem clinical symptoms of frontotemporal dementia and an age-matched healthy control. We detect distinct laminar patterns of novel iron-laden glial pathology in both FTLD-Tau and FTLD-TDP brains. We find iron-positive ameboid and hypertrophic microglia and astrocytes largely in deeper GM and adjacent WM in FTLD-Tau. In contrast, FTLD-TDP presents prominent superficial cortical layer iron reactivity in astrocytic processes enveloping small blood vessels with limited involvement of adjacent WM, as well as more diffuse distribution of punctate iron-rich dystrophic microglial processes across all GM lamina. This integrated MRI/histopathology approach revealsex vivoMRI features that are consistent with these pathological observations distinguishing FTLD-Tau and FTLD-TDP, including prominent irregular hypointense signal in deeper cortex in FTLD-Tau whereas FTLD-TDP showed upper cortical layer hypointense bands and diffuse cortical speckling. Moreover, differences in adjacent WM degeneration and iron-rich gliosis on histology between FTLD-Tau and FTLD-TDP were also readily apparent on MRI as hyperintense signal and irregular areas of hypointensity, respectively that were more prominent in FTLD-Tau compared to FTLD-TDP. These unique histopathological and radiographic features were distinct from HC and AD brains, suggesting that iron-sensitive T2*w MRI, adapted toin vivoapplication at sufficient resolution, may offer an opportunity to improve antemortem diagnosis of FTLD proteinopathies using tissue-validated methods.
A divergent nonsense-mediated decay machinery inPlasmodium falciparumis inefficient and non-essential
Authors: McHugh Emma , Bulloch Michaela S. , Batinovic Steven , Sarna Drishti K. , Ralph Stuart A.
Published: April 2021

Nonsense-mediated decay (NMD) is a conserved mRNA quality control process that eliminates transcripts bearing a premature termination codon. In addition to its role in removing erroneous transcripts, NMD is involved in post-transcriptional regulation of gene expression via programmed intron retention in metazoans. The apicomplexan parasitePlasmodium falciparumshows relatively high levels of intron retention, but it is unclear whether these variant transcripts are functional targets of NMD. In this study, we use CRISPR-Cas9 to disrupt and epitope-tag two core NMD components:PfUPF1 (PF3D7_1005500) andPfUPF2 (PF3D7_0925800). Using RNA-seq, we find that NMD inP. falciparumis highly derived and requires UPF2, but not UPF1 for transcript degradation. Furthermore, our work suggests that the majority of intron retention inP. falciparumhas no functional role and that NMD is not required for parasite growthex vivo. We localise bothPfUPF1 andPfUPF2 to puncta within the parasite cytoplasm, which may represent processing bodies - ribonucleoparticles that are sites of cytoplasmic mRNA decay. Finally, we identify a number of mRNA-binding proteins that co-immunoprecipitate with the NMD core complex and propose a model for a divergent NMD that does not requirePfUPF1 and incorporates novel accessory proteins to elicit mRNA decay.
Sodium accumulation in breast cancer predicts malignancy and treatment response
Authors: James Andrew D , Leslie Theresa K , Kaggie Joshua D , Wiggins Laura , Patten Lewis , O’Duinn John Murphy , Langer Swen , Labarthe Marie-Christine , Riemer Frank , Baxter Gabrielle , McLean Mary A. , Gilbert Fiona J , Kennerley Aneurin J , Brackenbury William J
Published: April 2021

Breast cancer is the leading cause of cancer-related death in women worldwide. Development of novel noninvasive diagnostic and predictive pathophysiological biomarkers would represent a significant clinical improvement. Here, we explored the utility of non-invasive23Na MRI to profile tumour physiology using preclinical mouse models of breast cancer. We establish that tissue Na+concentration ([Na+]) is elevated vs non-tumour regions across multiple different tumour models.Ex vivoSBFI fluorescence imaging corroborated that this elevation in tumour [Na+] is due to increased intracellular [Na+]. Effective treatment with cytotoxic chemotherapy reduced tumour tissue [Na+], but was not detected by1H diffusion-weighted imaging (DWI). Moreover, combining23Na MRI and DWI measurements enabled superior classification accuracy of tumour vs non-tumour regions compared to either parameter alone. Quantification of breast tumour tissue [Na+] using23Na MRI thus represents a novel, accurate, non-invasive diagnostic and predictive imaging biomarker.
MG132 induces progerin clearance and improves disease phenotypes in fibroblasts of patients affected with Hutchinson-Gilford Progeria-like syndromes
Authors: Harhouri Karim , Cau Pierre , Casey Frank , Mawuse Guedenon Koffi , Doubaj Yassamine , Van Maldergem Lionel , Mejia-Baltodano Gerardo , Bartoli Catherine , De Sandre-Giovannoli Annachiara , Lévy Nicolas
Published: April 2021

Progeroid Syndromes (PS), including Hutchinson-Gilford Progeria Syndrome (HGPS, OMIM #176670), are premature and accelerated aging that clinically resemble some aspects of advancing physiological aging. Most classical HGPS patients carry ade novopoint mutation within exon 11 of theLMNAgene encoding A-type Lamins. This mutation activates a cryptic splice site leading to the deletion of 50 amino acids at its carboxy-terminal domain, resulting in a truncated and permanently farnesylated Prelamin A called Prelamin A Δ50 or Progerin that accumulates in HGPS cell nuclei and is a hallmark of the disease. Some patients with PS carry otherLMNAmutations affecting exon 11 splicing, leading to defects in nuclear A-type Lamins and are named “HGPS-like” patients. They also produce Progerin and/or other truncated Prelamin A isoforms (Δ35 and Δ90). We recently found that MG132, a proteasome inhibitor, induced progerin clearance in classical HGPS through autophagy activation and splicing regulation. Here, we show that MG132 induces aberrant prelamin A clearance and improves cellular phenotypes in HGPS-like patient cells. These results provide preclinical proof of principle for the use of a promising class of molecules toward a potential therapy for children with HGPS-like, who may therefore be eligible for inclusion in a therapeutic trial based on this approach, together with classical HGPS patients.
Glucose regulates expression of pro-inflammatory genesIL-1βandIL-12through a mechanism involving hexosamine biosynthesis pathway dependent regulation of α-E catenin in the RAW 264.7 macrophage cell line
Authors: Dissanayake Waruni C. , Oh Jin Kyo , Sorrenson Brie , Shepherd Peter R.
Published: April 2021

High glucose levels are associated with changes in macrophage polarization and evidence indicates that the sustained or even short-term high glucose levels modulate inflammatory responses in macrophages. However, the mechanism by which macrophages can sense the changes in glucose levels are not clearly understood. We find that high glucose levels rapidly increase the α-E catenin protein level in RAW264.7 macrophages. We also find an attenuation of glucose induced increase of α-E catenin when hexosamine biosynthesis pathway is inhibited either with glutamine depletion or with the drugs azaserine and tunicamycin. This indicates the involvement of hexosamine biosynthesis pathway in this process. Then, we investigated the potential role of α-E catenin in glucose induced macrophage polarization. We find that the reduction of α-E catenin level using siRNA attenuates the glucose induced change of IL-1β mRNA level under LPS stimulated condition. Further, we identified that the depletion of α-E catenin also decreases theIL-12gene expression in basal glucose conditions leading to a reduction of glucose induced changes inIL-12. Together this indicates that α-E catenin can sense the changes in glucose levels in macrophagesviahexosamine biosynthesis pathway and also can modulate the glucose induced gene expression of inflammatory markers such asIL-1-βandIL-12. This identifies a new part of the mechanism by which macrophages are able to respond to changes in glucose levels.
Convergent selection on hormone signaling shaped social evolution in bees
Authors: Jones Beryl M. , Rubin Benjamin E.R. , Dudchenko Olga , Kingwell Callum J. , Traniello Ian M. , Wang Z. Yan , Kapheim Karen M. , Wyman Eli S. , Adastra Per A. , Liu Weijie , Parsons Lance R. , Jackson S. RaElle , Goodwin Katharine , Davidson Shawn M. , McBride Matthew J. , Webb Andrew E. , Omufwoko Kennedy S. , Van Dorp Nikki , Otárola Mauricio Fernández , Pham Melanie , Omer Arina D. , Weisz David , Schraiber Joshua , Villanea Fernando , Wcislo William T. , Paxton Robert J. , Hunt Brendan G. , Aiden Erez Lieberman , Kocher Sarah D.
Published: April 2021

Sweat bees have repeatedly gained and lost eusociality, a transition from individual to group reproduction. Here, we generate chromosome-length genome assemblies for 17 species and identify genomic signatures of evolutionary trade-offs associated with transitions between social and solitary living. Both young genes and regulatory regions show enrichment for these molecular patterns. We also identify loci that show evidence of complementary signals of positive and relaxed selection linked specifically to the convergent gains and losses of eusociality in sweat bees. This includes two proteins that bind and transport juvenile hormone (JH) – a key regulator of insect development and reproduction. We find one of these JH binding proteins is primarily expressed in subperineurial glial cells that form the insect blood-brain barrier and that brain levels of JH vary by sociality. Our findings are consistent with a role of JH in modulating social behavior and suggest eusocial evolution was facilitated by alteration of the proteins that bind and transport JH, revealing how an ancestral, developmental hormone may have been co-opted during one of life’s major transitions. More broadly, our results highlight how trade-offs have structured the molecular basis of eusociality in these bees and demonstrate how both directional selection and release from constraint can shape trait evolution.
Fish functional diversity as an indicator of resilience to industrial fishing in Patagonia Argentina
Authors: Rincón-Díaz Martha Patricia , Bovcon Nelson D. , Cochia Pablo D. , Góngora María Eva , Galván David E.
Published: April 2021

The relationship between fish functional diversity and fishing levels at which its baselines shift is important to identify the consequences of fishing in ecosystem functioning. For the first time, we implemented a trait-based approach in the Argentine Patagonian sea to identify the vulnerability and spatiotemporal changes in functional diversity of fish assemblages bycatch by a trawling fleet targeting the Argentine red shrimpPleoticus muelleri(Spence Bate, 1888) between 2003 and 2014. We coupled seven fish trophic traits to a reconstructed fish assemblage for the study area and bycatch and evaluated changes in fish species richness and four complementary functional diversity metrics [functional richness, redundancy, dispersion, and community trait values] along with fishing intensity, temporal use, latitudinal location, and depth of fishing grounds. Resident fishes larger than 30 cm in TL, with depressed and fusiform bodies, intermediate to high trophic levels, and feeding in shallow benthic, benthodemersal, and benthopelagic areas were vulnerable to bycatch. Fish assemblages exhibited a low functional trait redundancy, likely related to species influxes in a biogeographic ecotone with tropicalisation signs. Significantly increases in fish trait richness and dispersion polewards and with depth suggested new functional roles in these grounds, matching trends in community body size, reproductive load, maximum depth, trophic level, and diet breadth. Finally, a temporal increase in fish species and functional trait removal in fishing grounds led to trait homogenisation since the first year of trawling. The identified tipping points in temperate fish functional trait diversity highlight trait-based approaches within ecosystem-based fisheries management.
Structural variants contribute to pangenome evolution of a plant pathogenic fungus
Authors: Guo Li , Dong Quanbin , Wang Bo , Guo Mengyao , Ye Kai
Published: April 2021

Genetic variation is the driving force of plant-pathogen co-evolution. Large-scale genetic variations such as structural variations (SVs) often alter genome stability and organismal fitness. However, the pangenomic landscape and functional implications of SVs remain largely unexplored in plant pathogens. Here, we characterized the pangenomic and SV landscape in wheat head blight fungusFusarium graminearumby producing and comparing chromosome-level (average contig N50 of 8.9 Mb) genome assemblies of 98 accessions using a reference-guided approach. Accounting for 29.05% and 19.01% ofF. graminearumpangenome, respectively, accessory and private genomes are enriched with functions related to membrane trafficking, metabolism of fatty acids and tryptophans, with the private also enriched with putative effectors. Furthermore, using chromosome-level assemblies, we detected 52,420 SVs, 69.51% of which are inaccessible using read-mapping based approach. Over a half (55.65%) of 52,645 merged SVs affected 1,660 protein-coding genes, the most variable of which are involved in fungal virulence, cellular contact and communications. Interestingly, highly variable effectors and secondary metabolic enzymes are co-localized with SVs at subtelomeric and centromeric regions. Collectively, this landmark study shows the prevalence and functional relevance of SVs inF. graminearum, providing a valuable resource for future pangenomic studies in this cosmopolitan pathogen of cereal crops.
Fine-tuning heat stress algorithms to optimise global predictions of mass coral bleaching
Authors: Lachs Liam , Bythell John C. , East Holly K. , Edwards Alastair J. , Mumby Peter J. , Skirving William J. , Spady Blake L. , Guest James R.
Published: April 2021

Increasingly severe marine heatwaves under climate change threaten the persistence of many marine ecosystems. Mass coral bleaching events, caused by periods of anomalously warm sea surface temperatures (SST), have led to catastrophic levels of coral mortality globally. Remotely monitoring and forecasting such biotic responses to heat stress is key for effective marine ecosystem management. The Degree Heating Week (DHW) metric, designed to monitor coral bleaching risk, reflects the duration and intensity of heat stress events, and is computed by accumulating SST anomalies (HotSpot) relative to a stress threshold over a 12-week moving window. Despite significant improvements in the underlying SST datasets, corresponding revisions of the HotSpot threshold and accumulation window are still lacking. Here, we fine-tune the operational DHW algorithm to optimise coral bleaching predictions using the 5km satellite-based SSTs (CoralTemp v3.1) and a global coral bleaching dataset (37,871 observations, National Oceanic and Atmospheric Administration). After developing 234 test DHW algorithms with different combinations of HotSpot threshold and accumulation window, we compared their bleaching-prediction ability using spatiotemporal Bayesian hierarchical models and sensitivity-specificity analyses. Peak DHW performance was reached using HotSpot thresholds less than or equal to Maximum Monthly Mean SST and accumulation windows of 4 – 8 weeks. This new configuration correctly predicted up to an additional 310 bleaching observations compared to the operational DHW algorithm, an improved hit rate of 7.9 %. Given the detrimental impacts of marine heatwaves across ecosystems, heat stress algorithms could also be fine-tuned for other biological systems, improving scientific accuracy, and enabling ecosystem governance.
In vivodissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation
Authors: Anania Chiara , Acemel Rafael D. , Jedamzick Johanna , Bolondi Adriano , Cova Giulia , Brieske Norbert , Kühn Ralf , Wittler Lars , Real Francisca M. , Lupiáñez Darío G.
Published: April 2021

Vertebrate genomes organize into topologically associating domains (TADs), delimited by boundaries that insulate regulatory elements from non-target genes. However, how boundary function is established is not well understood. Here, we combine genome-wide analyses and transgenic mouse assays to dissect the regulatory logic of clustered-CTCF boundariesin vivo, interrogating their function at multiple levels: chromatin interactions, transcription and phenotypes. Individual CTCF binding sites (CBS) deletions revealed that the characteristics of specific sites can outweigh other factors like CBS number and orientation. Combined deletions demonstrated that CBS cooperate redundantly and provide boundary robustness. We show that divergent CBS signatures are not strictly required for effective insulation and that chromatin loops formed by non-convergently oriented sites could be mediated by a loop interference mechanism. Further, we observe that insulation strength constitutes a quantitative modulator of gene expression and phenotypes. Our results highlight the modular nature of boundaries and their control over developmental processes.
Evaluation of different concentrations antibiotics on gut bacteria and growth ofEctropis obliquaProut (Lepidoptera: Geometridae)
Authors: Gao Tian , Zhou Xiaomin , Jiang Rui , Zhang Chen , Liu Song , Zhao Tianyu , Li Xiayu , Long Yanhua , Yang Yunqiu
Published: April 2021

The use of antibiotics to remove gut bacteria is a commonly used method to study gut function of insects. We assessed the impact of the artificial diet made from tea powder with different concentrations of antibiotics mixture (containing tetracycline, gentamicin, penicillin, and rifampicin) onEctropis obliquaProut (Lepidoptera: Geometridae) survival, growth, and reproduction. Antibiotic-induced bacterial clearance was monitored by Polymerase Chain Reaction (PCR) and by Colony-counting Methods. The results indicated that administration of the antibiotic mixture at a concentration of 200μg/ml caused the increase of gut bacteria, while a concentration of 300μg/ml was more effective in clearing gut bacteria but the concentration of 400μg/ml caused a large number of larval deaths. The concentration of 300μg/ml had no significant effect on the growth and development ofE. obliqua, but had impact on fecundity. Therefore, we could use 300μg/ml concentrations of the antibiotic mixture to obtain sterileE. obliquato study the function of intestinal microbes.
Evolution of Nuclear Receptors in Platyhelminths
Authors: Wu Wenjie , LoVerde Philip T.
Published: April 2021

Since the first complete set of Platyhelminth nuclear receptors (NRs) fromSchistosoma mansoniwere identified a decade ago, more flatworm genome data is available to identify their NR complement and to analyze the evolutionary relationship of Platyhelminth NRs. NRs are important transcriptional modulators that regulate development, differentiation and reproduction of animals. In this study, NRs are identified in genome databases of thirty-three species including in all Platyhelminth classes (Rhabditophora, Monogenea, Cestoda and Trematoda). Phylogenetic analysis shows that NRs in Platyhelminths follow two different evolutionary lineages: 1) NRs in a free-living freshwater flatworm (Schmidtea mediterranea) and all parasitic flatworms share the same evolutionary lineage with extensive gene loss. 2) NRs in a free-living intertidal zone flatworm (Macrostomum lignano) follow a different evolutionary lineage with a feature of multiple gene duplication and gene divergence. The DNA binding domain (DBD) is the most conserved region in NRs which contains two C4-type zinc finger motifs. A novel zinc finger motif is identified in parasitic flatworm NRs: the second zinc finger of parasitic Platyhelminth HR96b possesses a CHC2 motif which is not found in NRs of all other animals. In this study, novel NRs (members of NR subfamily 3 and 6) are identified in flatworms, this result demonstrates that members of all six classical NR subfamilies are present in the Platyhelminth phylum. NR gene duplication, loss and divergence in Platyhelminths are analyzed along with the evolutionary relationship of Platyhelminth NRs.
Phenotypic divergence between the cultivated apple (Malus domestica) and its primary wild progenitor (Malus sieversii)
Authors: Davies Thomas , Watts Sophie , McClure Kendra , Migicovsky Zoë , Myles Sean
Published: April 2021

An understanding of the relationship between the cultivated apple (Malus domestica) and its primary wild progenitor species (M. sieversii) not only provides an understanding of how apples have been improved in the past, but may be useful for apple improvement in the future. We measured 10 phenotypes in over 1000 unique apple accessions belonging toM. domesticaandM. sieversiifrom Canada’s Apple Biodiversity Collection. Using principal components analysis (PCA), we determined thatM. domesticaandM. sieversiidiffer significantly in phenotypic space and are nearly completely distinguishable as two separate groups. We found thatM. domesticahad a shorter juvenile phase thanM. sieversiiand that cultivated trees produced flowers and ripe fruit later than their wild progenitors. Cultivated apples were also 3.6 times heavier, 43% less acidic, and had 68% less phenolic content than wild apples. Using historical records, we found that apple breeding over the past 200 years has resulted in a trend towards apples that have higher soluble solids, are less bitter, and soften less during storage. Our results quantify the significant changes in phenotype that have taken place since apple domestication, and provide evidence that apple breeding has led to continued phenotypic divergence of the cultivated apple from its wild progenitor species.
A secreted proteomic footprint for stem cell pluripotency
Authors: Lewis Philip , Silajzick Edina , Smith Helen , Bates Nicola , Smith Christopher A , Knight David , Denning Chris , Brison Daniel R , Kimber Susan J
Published: April 2021

With a view to developing a much-needed non-invasive method for monitoring the healthy pluripotent state of human stem cells in culture, we undertook proteomic analysis of the spent medium from cultured embryonic (Man-13) and induced (Rebl.PAT) human pluripotent stem cells (hPSCs). Cells were grown in E8 medium to maintain pluripotency, and then transferred to FGF2 and TGFβ deficient media for 48 hours to replicate an early, undirected dissolution of pluripotency.

We identified a distinct proteomic footprint associated with early loss of pluripotency in both hPSC lines, and a strong correlation with changes in the transcriptome. We demonstrate that multiplexing of 4 E8- against 4 E6- enriched biomarkers provides 16 ratio abundances which are each robustly diagnostic for pluripotent state. These biomarkers were further confirmed by Western blotting which demonstrated consistent correlation with the pluripotent state across cell lines, and in response to recovery assays.
Investigating the Effect of Flow Compensation and Quantitative Susceptibility Mapping Method on the Accuracy of Venous Susceptibility Measurement
Authors: Berg Ronja C. , Preibisch Christine , Thomas David L. , Shmueli Karin , Biondetti Emma
Published: April 2021

Quantitative susceptibility mapping (QSM) is a promising non-invasive method for obtaining information relating to the oxygen metabolism. However, the optimal acquisition sequence and QSM reconstruction method for reliable venous susceptibility measurements are unknown. Full flow compensation is generally recommended to correct for the influence of venous blood flow, although the effect of flow compensation on the accuracy of venous susceptibility values has not been systematically evaluated. In this study, we investigated the effect of different acquisition sequences, including different flow compensation schemes, and different QSM reconstruction methods on venous susceptibilities.

Ten healthy subjects were scanned with five or six distinct QSM sequence designs implementing different flow compensation schemes. All data sets were processed using six different QSM pipelines and venous blood susceptibility was evaluated in whole-brain segmentations of the venous vasculature and single veins. The quality of vein segmentations and the accuracy of venous susceptibility values were analyzed and compared between all combinations of sequences and QSM methods.

The influence of the QSM method on average venous susceptibility values was found to be 2.7 - 11.6 times greater than the influence of the acquisition sequence, including flow compensation. The majority of the investigated QSM reconstruction methods tended to underestimate venous susceptibility values in the vein segmentations that were obtained.

Using multi-echo gradient-echo acquisitions with monopolar readout gradients, we found that sequences without full flow compensation yielded venous susceptibility values comparable to sequences with full flow compensation. However, the QSM method had a great influence on susceptibility values and thus needs to be considered carefully for accurate venous QSM.
Resolving Between Novelty and Homology in the Rapidly Evolving Phallus of Drosophila
Authors: Rice Gavin R. , David Jean R. , Gompel Nicolas , Yassin Amir , Rebeiz Mark
Published: April 2021

The genitalia present some of the most rapidly evolving anatomical structures in the animal kingdom, possessing a variety of parts that can distinguish recently diverged species. In theDrosophila melanogastergroup, the phallus is adorned with several processes, pointed outgrowths, that are similar in size and shape between species. However, the complex three-dimensional nature of the phallus can obscure the exact connection points of each process. Previous descriptions based upon adult morphology have primarily assigned phallic processes by their approximate positions in the phallus and have remained largely agnostic regarding their homology relationships. In the absence of clearly identified homology, it can be challenging to model when each structure first evolved. Here, we employ a comparative developmental analysis of these processes in eight members of themelanogasterspecies group to precisely identify the tissue from which each process forms. Our results indicate that adult phallic processes arise from three pupal primordia in all species. We found that in some cases the same primordia generate homologous structures whereas in other cases, different primordia produce phenotypically similar but remarkably non-homologous structures. This suggests that the same gene regulatory network may have been redeployed to different primordia to induce phenotypically similar traits. Our results highlight how traits diversify and can be redeployed, even at short evolutionary scales.

Research Highlight

By incorporating developmental analysis, we find that genital structures previously identified as homologs are novel structures. This highlights how developmental analysis can help resolve contentious claims of homology.
Analysis of gene expression and mutation data points on contribution of transcription to the mutagenesis by APOBEC enzymes
Authors: Chervova Almira , Fatykhov Bulat , Koblov Alexander , Shvarov Evgeny , Preobrazhenskaya Julia , Vinogradov Dmitry , Ponomarev Gennady V. , Gelfand Mikhail S. , Kazanov Marat D.
Published: April 2021

Since the discovery of the role of the APOBEC enzymes in human cancers, the mechanisms of this type of mutagenesis remain little understood. Theoretically, targeting of single-stranded DNA by the APOBEC enzymes could occur during cellular processes leading to the unwinding of DNA double-stranded structure. Some evidence points to the importance of replication in the APOBEC mutagenesis, while the role of transcription is still underexplored. Here, we analyzed gene expression and whole genome sequencing data from five types of human cancers with substantial APOBEC activity to estimate the involvement of transcription in the APOBEC mutagenesis and compare its impact with that of replication. Using the TCN motif as the mutation signature of the APOBEC enzymes, we observed a correlation of active APOBEC mutagenesis with gene expression, confirmed the increase of APOBEC-induced mutations in early-replicating regions, and estimated the relative impact of transcription and replication on the APOBEC mutagenesis, which turned out to be approximately equal in transcribed regions. We also found that the known effect of higher density of APOBEC-induced mutations on the lagging strand was highest in middle-replicating regions, and observed higher APOBEC mutation density on the sense strand, the latter bias positively correlated with the gene expression level.

Bullet points

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The APOBEC mutagenesis rate is higher in actively expressed genes

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The APOBEC mutation density is higher on the sense strand

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The lagging/leading strand ratio of the APOBEC mutational density is highest in middle-replicating regions
An automated workflow for multiplexed single-cell proteomics sample preparation at unprecedented sensitivity
Authors: Ctortecka Claudia , Hartlmayr David , Seth Anjali , Mendjan Sasha , Tourniaire Guilhem , Mechtler Karl
Published: April 2021

The analysis of single-cell proteomes has recently become a viable complement to transcriptomics and genomics studies. Proteins are the primary driver of cellular functionality and mRNA levels are often an unreliable proxy of such. Therefore, the global analysis of the proteome is essential to study cellular identities. Multiplexed and label-free mass spectrometry-based approaches with single-cell resolution have lately attributed surprising heterogeneity to presumed homogenous cell populations. Even though specialized experimental designs and instrumentation have demonstrated remarkable advances, the efficient sample preparation of single cells still lag. Here, we introduce the proteoCHIP, a universal option for single-cell proteomics sample preparation at surprising sensitivity and throughput. The automated processing using a commercial system combining single-cell isolation and picoliter dispensing, the cellenONE®, reduces final sample volumes to low nanoliters submerged in a hexadecane layer simultaneously eliminating error-prone manual sample handling and overcoming evaporation. The specialized proteoCHIP design allows direct injection of single cells via a standard autosampler resulting in around 1,500 protein groups per analytical run at remarkable reporter ion signal to noise while reducing or eliminating the carrier proteome. We identified close to 2,600 proteins across 170 multiplexed single cells from two highly similar human cell types. This dedicated loss-less workflow allows distinguishingin vitroco-differentiated cell types of self-organizing cardiac organoids based on indicative markers across 150 single cells. In-depth characterization revealed enhanced cellular motility of cardiac endothelial cells and sarcomere organization in cardiomyocytes. Our versatile and automated sample preparation has not only proven to be easily adaptable but is also sufficiently sensitive to drive biological applications of single-cell proteomics.
The SARS-CoV-2 mRNA-1273 vaccine elicits more RBD-focused neutralization, but with broader antibody binding within the RBD
Authors: Greaney Allison J. , Loes Andrea N. , Gentles Lauren E. , Crawford Katharine H.D. , Starr Tyler N. , Malone Keara D. , Chu Helen Y. , Bloom Jesse D.
Published: April 2021

The emergence of SARS-CoV-2 variants with mutations in key antibody epitopes has raised concerns that antigenic evolution will erode immunity. The susceptibility of immunity to viral evolution is shaped in part by the breadth of epitopes targeted. Here we compare the specificity of antibodies elicited by the mRNA-1273 vaccine versus natural infection. The neutralizing activity of vaccine-elicited antibodies is even more focused on the spike receptor-binding domain (RBD) than for infection-elicited antibodies. However, within the RBD, binding of vaccine-elicited antibodies is more broadly distributed across epitopes than for infection-elicited antibodies. This greater binding breadth means single RBD mutations have less impact on neutralization by vaccine sera than convalescent sera. Therefore, antibody immunity acquired by different means may have differing susceptibility to erosion by viral evolution.

One Sentence Summary

Deep mutational scanning shows the mRNA-1273 RBD-binding antibody response is less affected by single viral mutations than the infection response.
Revealing capture sites and movements by strontium isotope analyses in bones of Caiman yacare in the Beni river floodplain, Bolivia
Authors: Pouilly Marc , Gomez Sergio , Pécheyran Christophe , Bérail Sylvain , Alvarez Gustavo , Miranda-Chumacero Guido
Published: April 2021

Studying the distribution of organisms and their movements is fundamental to understand population dynamics. Most studies indicated that crocodilians do not move around much but several studies demonstrated that some species showed movement patterns. Detection of these movements along the individual life is still a challenge. In this study we analyzed the variation of strontium isotopic ratio (87Sr/86Sr) in the femur bones of 70 Caimanya care individuals caught in 16 sites located in five hydrological sectors of the Beni river floodplain in Bolivia. Our results demonstrated for the first time that such a methodology could yield indications about the capture sites and reconstruct individual life history. Analyses of the outer part of the femur of 70 individuals showed that capture sites could be differentiated between sectors and even between sites or groups of sites in each sector. Studies of complete 87Sr/86Sr profiles along the femur, representing the individual’s entire life, were performed on 33 yacares. We found that most of the individuals did not show any significant isotopic variation throughout their lives. This absence of variation could result from a high fidelity to the birth site, and/or from an insignificant isotopic variation between the water bodies through which the animal has potentially moved. However, 24% of the analyzed individuals presented significant variations that can be considered as movements between different habitats. Based on the observed low proportion of moving yacares, we advocated that each water body should be considered an individual management unit.
Targeting Adaptation to Cancer Treatment by Drug Combinations
Authors: Wang Heping , Luna Augustin , Yan Gonghong , Li Xubin , Babur Ozgun , Mills Gordon B. , Sander Chris , Korkut Anil
Published: April 2021

Adaptation of tumors to therapeutic interventions contributes to dismal long-term patient outcomes. Adaptation to therapy involves co-action of functionally related proteins that together activate cell survival programs and compensate for the therapeutic impact. Oncogenic dependencies to such adaptive events, however, can generate new therapeutic vulnerabilities that can be targeted with drug combinations. The precision medicine approaches in which targeted drugs are matched to pre-existing genomic aberrations fail to address the adaptive responses and resulting vulnerabilities. Here, we provide the mathematical formulation, implementation and validation of the TargetScore method. The TargetScore identifies collective adaptive responses to targeted interventions as concurrent changes of phospho-proteins that are connected within a signaling network. Based on the adaptive responses, the method predicts drug-induced vulnerabilities. Using TargetScore, we inferred the adaptive responses with short-term (i.e., days) stress and long-term (i.e., months) acquired resistance to inhibitors of anti-apoptotic mediators, MCL1 and BCL2. With experiments guided by the predictions, we identified synergistic interactions between inhibitors of PARP, SHP2, and MCL1 in breast cancer cells. TargetScore is readily applicable to existing precision oncology efforts by matching targeted drug combinations to emerging molecular signatures under therapeutic stress.
How faculty define quality, prestige, and impact in research
Authors: Morales Esteban , McKiernan Erin , Niles Meredith T. , Schimanski Lesley , Alperin Juan Pablo
Published: April 2021

Despite the calls for change, there is significant consensus that when it comes to evaluating publications, review, promotion, and tenure processes should aim to reward research that is of high “quality,” has an “impact,” and is published in “prestigious” journals. Nevertheless, such terms are highly subjective and present challenges to ascertain precisely what such research looks like. Accordingly, this article responds to the question: how do faculty from universities in the United States and Canada define the terms quality, prestige, and impact? We address this question by surveying 338 faculty members from 55 different institutions. This study’s findings highlight that, despite their highly varied definitions, faculty often describe these terms in overlapping ways. Additionally, results shown that marked variance in definitions across faculty does not correspond to demographic characteristics. This study’s results highlight the need to more clearly implement evaluation regimes that do not rely on ill-defined concepts.

Financial Disclosure

Funding for this project was provided to JPA, MTN, ECM, and LAS from the OpenSociety Foundations (OR2017-39637). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Related Materials

Other publications related to this project, including a series of infographics summarizing findings, can be found at:https://www.scholcommlab.ca/research/rpt-project/

Survey responses can be found at the following publication:

Niles, Meredith T.; Schimanski, Lesley A.; McKiernan, Erin C.; Alperin, Juan Pablo,2020, “Data for: Why we publish where we do”,https://doi.org/10.7910/DVN/MRLHNO,Harvard Dataverse, V1

Data regarding RPT documents can be found at the following data publication:

Alperin, Juan Pablo; Muñoz Nieves, Carol; Schimanski, Lesley; McKiernan, Erin C.;Niles, Meredith T., 2018, “Terms and Concepts found in Tenure and Promotion Guidelines from the US and Canada”,https://doi.org/10.7910/DVN/VY4TJE,Harvard Dataverse, V3, UNF:6:PQC7QoilolhDrokzDPxxyQ== [fileUNF]
Monosodium Urate Crystals regulate a unique JNK-dependent macrophage metabolic and inflammatory response
Authors: Cobo Isidoro , Cheng Anyan , Murillo-Saich Jessica , Coras Roxana , Torres Alyssa , Lana Addison J. , Schlachetzki Johannes , Liu-Bryan Ru , Terkeltaub Robert , Sanchez-Lopez Elsa , Glass Christopher K. , Guma Monica
Published: April 2021

How macrophages are programmed to respond to monosodium urate crystals (MSUc) is incompletely understood partly due to the use of a toll-like receptor-induced priming step. Here, using genome wide transcriptomic analysis and biochemical assays we demonstrate that MSUc alone induces anin vitrometabolic-inflammatory transcriptional program in both human and murine macrophages markedly distinct from that induced by LPS. Genes uniquely up-regulated in response to MSUc belonged to lipids, glycolysis, and transport of small molecules via SLC transporters pathways. Sera from individuals and mice with acute gouty arthritis provided further evidence for this metabolic rewiring. This distinct macrophage activation may explain the initiating mechanisms in acute gout flares and is regulated through JUN binding to the promoter of target genes through activation of JNK –but not by P38-in a process that is independent of inflammasome activation. Finally, pharmacological JNK inhibition limited MSUc-induced inflammation in animal models of acute gouty inflammation.
Characterization of five purine riboswitches in cellular and cell-free expression systems
Authors: Lins Milca Rachel da Costa Ribeiro , Correa Graciely Gomes , Amorim Laura Araujo da Silva , Franco Rafael Augusto Lopes , Ribeiro Nathan Vinicius , de Jesus Victor Nunes , Pedrolli Danielle Biscaro
Published: April 2021

Bacillus subtilisemploys five purine riboswitches for the control of purinede novosynthesis and transport at the transcription level. All of them are formed by a structurally conserved aptamer, and a variable expression platform harboring a rho-independent transcription terminator. In this study, we characterized all five purine riboswitches under the context of active gene expression processes bothin vitroandin vivo. We identified transcription pause sites located in the expression platform upstream of the terminator of each riboswitch. Moreover, we defined a correlation betweenin vitrotranscription readthrough andin vivogene expression. Ourin vitroassay demonstrated that the riboswitches operate in the micromolar range of concentration for the cognate metabolite. Ourin vivoassay showed the dynamics of control of gene expression by each riboswitch. This study deepens the knowledge of the regulatory mechanism of purine riboswitches.
Speech-related auditory salience detection in the posterior superior temporal region
Authors: Brown Erik C. , Stedelin Brittany , Raslan Ahmed M. , Selden Nathan R.
Published: April 2021

Processing auditory human speech requires both detection (early and transient) and analysis (sustained). We analyzed high gamma (70-110Hz) activity of intracranial electroencephalography waveforms acquired during an auditory task that paired forward speech, reverse speech, and signal correlated noise. We identified widespread superior temporal sites with sustained activity responding only to forward and reverse speech regardless of paired order. More localized superior temporal auditory onset sites responded to all stimulus types when presented first in a pair and responded in recurrent fashion to the second paired stimulus in select conditions even in the absence of interstimulus silence; a novel finding. Auditory onset activity to a second paired sound recurred according to relative salience, with evidence of partial suppression during linguistic processing. We propose that temporal lobe auditory onset sites facilitate a salience detector function with hysteresis of 200ms and are influenced by cortico-cortical feedback loops involving linguistic processing and articulation.