bluuebunny/crossref_metadata_2025 huggingface dataset:
Control of Arabidopsis shoot stem cell homeostasis by two antagonistic CLE peptide signalling pathways
Authors: Schlegel Jenia , Denay Grégoire , Pinto Karine Gustavo , Stahl Yvonne , Schmid Julia , Blümke Patrick , Simon Rüdiger
Published: June 2021

Stem cell homeostasis in plant shoot meristems requires tight coordiantion between stem cell proliferation and cell differentiation. In Arabidopsis, stem cells express the secreted dodecapeptide CLAVATA3 (CLV3), which signals through the leucine-rich repeat (LRR)–receptor kinase CLAVATA1 (CLV1) and related CLV1-family members to downregulate expression of the homeodomain transcription factor WUSCHEL (WUS). WUS protein moves from cells below the stem cell domain to the meristem tip and promotes stem cell identity, together with CLV3 expression, generating a negative feedback loop. How stem cell activity in the meristem centre is coordinated with organ initiation and cell differentiation at the periphery is unknown.

We show here that the CLE40 gene, encoding a secreted peptide closely related to CLV3, is expressed in the SAM in differentiating cells in a pattern complementary to that of CLV3. CLE40 promotes WUS expression via BAM1, a CLV1-family receptor, and CLE40 expression is in turn repressed in a WUS-dependent manner. Together, CLE40-BAM1-WUS establish a second negative feedback loop. We propose that stem cell homeostasis is achieved through two intertwined pathways that adjust WUS activity and incorporate information on the size of the stem cell domain, via CLV3-CLV1, and on cell differentiation via CLE40-BAM1.
A need for time-varying models to suppress artefacts of tACS in the M/EEG
Authors: Bland Nicholas S.
Published: June 2021

Rhythmic modulation of brain activity by transcranial alternating current stimulation (tACS) can entrain neural oscillations in a frequency- and phase-specific manner. However, large stimulation artefacts contaminate concurrent ‘online’ neuroimaging measures, including magneto- and electro-encephalography (M/EEG)—restricting most analyses to periods free from stimulation (‘offline’ aftereffects). While many published methods exist for removing artefacts of tACS from M/EEG recordings, they universally assume linear artefacts: either time-invariance (i.e., an artefact is a scaled version of itself from cycle to cycle) or sensor-invariance (i.e., artefacts are scaled versions of one another from sensor to sensor). However, heartbeat and respiration both nonlinearly modulate the amplitude and phase of these artefacts, predominantly via changes in scalp impedance. The spectral symmetry this introduces to the M/EEG spectra may lead to false-positive evidence for entrainment around the frequency of tACS, if not adequately suppressed. Good electrophysiological evidence for entrainment therefore requires that tACS artefacts are fully accounted for before comparing online spectra to a control (e.g., as might be observed during sham stimulation). Here I outline an approach to linearly solve templates for tACS artefacts, and demonstrate how event-locked perturbations to amplitude and phase can be introduced from simultaneous recordings of heartbeat and respiration—effectively forming time-varying models of tACS artefacts. These models are constructed for individual sensors, and can therefore be used in contexts with few EEG sensors and with no assumption of artefact collinearity. I also discuss the feasibility of this approach in the absence of simultaneous recordings of heartbeat and respiration traces.
Increased sensitivity of SARS-CoV-2 to type III interferon in human intestinal epithelial cells
Authors: Kee Carmon , Metz-Zumaran Camila , Doldan Patricio , Guo Cuncai , Stanifer Megan L. , Boulant Steeve
Published: June 2021

The coronavirus SARS-CoV-2 caused the COVID-19 global pandemic leading to 3.5 million deaths worldwide as of June 2021. The human intestine was found to be a major viral target which could have a strong impact on virus spread and pathogenesis since it is one of the largest organs. While type I interferons (IFNs) are key cytokines acting against systemic virus spread, in the human intestine type III IFNs play a major role by restricting virus infection and dissemination without disturbing homeostasis. Recent studies showed that both type I and III IFNs can inhibit SARS-CoV-2 infection, but it is not clear if one IFN controls SARS-CoV-2 infection of the human intestine better or with a faster kinetics. In this study, we could show that both type I and III IFNs possess antiviral activity against SARS-CoV-2 in human intestinal epithelial cells (hIECs), however type III IFN is more potent. Shorter type III IFN pretreatment times and lower concentrations were required to efficiently reduce virus load when compared to type I IFNs. Moreover, type III IFNs significantly inhibited SARS-CoV-2 even 4 hours post-infection and induced a long-lasting antiviral effect in hIECs. Importantly, the sensitivity of SARS-CoV-2 to type III IFNs was virus-specific since type III IFN did not control VSV infection as efficiently. Together these results suggest that type III IFNs have a higher potential for IFN-based treatment of SARS-CoV-2 intestinal infection as compared to type I IFNs.
NEST Desktop - An educational application for neuroscience
Authors: Spreizer Sebastian , Senk Johanna , Rotter Stefan , Diesmann Markus , Weyers Benjamin
Published: June 2021

Simulation software for spiking neuronal network models matured in the past decades regarding performance and flexibility. But the entry barrier remains high for students and early career scientists in computational neuroscience since these simulators typically require programming skills and a complex installation. Here, we describe an installation-free Graphical User Interface (GUI) running in the web browser, which is distinct from the simulation engine running anywhere, on the student’s laptop or on a supercomputer. This architecture provides robustness against technological changes in the software stack and simplifies deployment for self-education and for teachers. Our new open source tool, NEST Desktop, comprises graphical elements for creating and configuring network models, running simulations, and visualizing and analyzing the results. NEST Desktop allows students to explore important concepts in computational neuroscience without the need to learn a simulator control language before. Our experiences so far highlight that NEST Desktop helps advancing both quality and intensity of teaching in computational neuroscience in regular university courses. We view the availability of the tool on public resources like the European ICT infrastructure for neuroscience EBRAINS as a contribution to equal opportunities.

Significance Statement

The graphical user interface NEST Desktop makes neuronal network simulations accessible to non-programmers. It facilitates the interactive exploration of neuronal network models by integrating the whole workflow of wiring up the setup, simulating the neuronal dynamics, and analyzing the recorded activity data into a single tool. NEST Desktop effectively supports teaching the concepts and methods of computational neuroscience. Due to its installation-free web-based implementation, it is in particularly suitable for online courses.
Deciphering Tumour Tissue Organization by 3D Electron Microscopy and machine learning
Authors: de Senneville Baudouin Denis , Khoubai Fatma Zohra , Bevilacqua Marc , Labedade Alexandre , Flosseau Kathleen , Chardot Christophe , Branchereau Sophie , Ripoche Jean , Cairo Stefano , Gontier Etienne , Grosset Christophe F.
Published: June 2021

Despite recent progress in the characterization of tumour components, the tri-dimensional (3D) organization of this pathological tissue and the parameters determining its internal architecture remain elusive. Here, we analysed the spatial organization of patient-derived xenograft tissues generated from hepatoblastoma, the most frequent childhood liver tumour, by serial block-face scanning electron microscopy using an integrated workflow combining 3D imaging, manual and machine learning-based semi-automatic segmentations, mathematics and infographics. By digitally reconstituting an entire hepatoblastoma sample with a blood capillary, a bile canaliculus-like structure, hundreds of tumour cells and their main organelles (e.g. cytoplasm, nucleus, mitochondria), we report unique 3D ultrastructural data about the organization of tumoral tissue. We found that the size of hepatoblastoma cells correlates with the size of their nucleus, cytoplasm and mitochondrial mass. We also discovered that the blood capillary controls the planar alignment and size of tumour cells in their 3D milieu. Finally, a set of tumour cells polarized in the direction of a hot spot corresponding to a bile canaliculus-like structure. In conclusion, this pilot study allowed the identification of bioarchitectural parameters that shape the internal and spatial organization of tumours, thus paving the way for new investigations in an emerging field that we call ‘onconanotomy’.
Genomic features of Mycobacterium avium subsp. hominissuis isolated from pigs in Japan
Authors: Komatsu Tetsuya , Ohya Kenji , Ota Atsushi , Nishiuchi Yukiko , Yano Hirokazu , Matsuo Kayoko , Odoi Justice Opare , Suganuma Shota , Sawai Kotaro , Hasebe Akemi , Asai Tetsuo , Yanai Tokuma , Fukushi Hideto , Wada Takayuki , Yoshida Shiomi , Ito Toshihiro , Arikawa Kentaro , Kawai Mikihiko , Ato Manabu , Baughn Anthony D , Iwamoto Tomotada , Maruyama Fumito
Published: June 2021

Mycobacterium avium subsp. hominissuis (MAH) is one of the most important agents causing non-tuberculosis mycobacterial infection in humans and pigs. Genome analysis on MAH of human isolates has been proceeding, however, those of pigs are limited despite its potential source of infection to human. In the current study, we obtained 30 draft genome sequences of MAH of pigs reared in Japan. The 30 draft genomes consisted of 4,848,678 – 5,620,788 bp length, 4,652 – 5,388 coding genes and 46 – 75 (Med: 47) tRNAs. All isolates had restriction modification associated genes and 185 – 222 predicted virulence genes. Two isolates had tRNA arrays and one isolate had a clustered regularly interspaced short palindromic repeat (CRISPR) region. Our results will be useful for evaluation of the ecology of MAH by providing a foundation for genome-based epidemiological studies.
Evaluation of US state pollinator plans using 3 evidence-based policymaking frameworks
Authors: Whitney Kaitlin Stack , Stringer Briana Burt
Published: June 2021

After the US federal government created a national pollinator protection plan in 2015, many states followed with their own. Since their goal is to promote pollinating insect conservation, we wanted to know whether the state plans are using best practices for evidence-based science policy. In early 2019 we found and downloaded every existing, publicly available US state pollinator protection plan. We then used content analysis to assess the goals, scope, and implementation of state-level pollinator protection plans across the US. This analysis was conducted using three distinct frameworks for evidence-based policymaking: US Department of Interior Adaptive Resources Management (ARM), US Environmental Protection Agency management pollinator protection plan (MP3) guidance, and Pew Trusts Pew-MacAthur Results First Project elements of evidence-based state policymaking (PEW) framework. Then we scored them using the framework criteria, to assess whether the plans were using known best practices for evidence based policymaking. Of the 31 states with a state pollinator plan, Connecticut was the state with the lowest total score across the three evaluation frameworks. The state with the highest overall scores, across the three frameworks, was Missouri. Most states did not score highly on the majority of the frameworks. Overall, many state plans were lacking policy elements that address monitoring, evaluation, and adjustment. These missing elements impact states’ ability to achieve their conservation goals. Our results indicate that states can improve their pollinator conservation policies to better match evidence-based science policy guidance, regardless of which framework is used.
Developing and deploying an integrated workshop curriculum teaching computational skills for reproducible research
Authors: Lapp Zena , Sovacool Kelly L. , Lesniak Nick , King Dana , Barnier Catherine , Flickinger Matthew , Krüger Jule , Armour Courtney R. , Lapp Maya M. , Tallant Jason , Diao Rucheng , Oneka Morgan , Tomkovich Sarah , Anderson Jacqueline Moltzau , Lucas Sarah K. , Schloss Patrick D.
Published: June 2021

Inspired by well-established material and pedagogy provided by The Carpentries (Wilson 2016), we developed a two-day workshop curriculum that teaches introductory R programming for managing, analyzing, plotting and reporting data using packages from the tidyverse (Wickham et al. 2019), the Unix shell, version control with git, and GitHub. While the official Software Carpentry curriculum is comprehensive, we found that it contains too much content for a two-day workshop. We also felt that the independent nature of the lessons left learners confused about how to integrate the newly acquired programming skills in their own work. Thus, we developed a new curriculum that aims to teach novices how to implement reproducible research principles in their own data analysis. The curriculum integrates live coding lessons with individual-level and group-based practice exercises, and also serves as a succinct resource that learners can reference both during and after the workshop. Moreover, it lowers the entry barrier for new instructors as they do not have to develop their own teaching materials or sift through extensive content. We developed this curriculum during a two-day sprint, successfully used it to host a two-day virtual workshop with almost 40 participants, and updated the material based on instructor and learner feedback. We hope that our new curriculum will prove useful to future instructors interested in teaching workshops with similar learning objectives.
Seascape genomics reveals population structure and local adaptation in a widespread coral reef snail,Coralliophila violacea(Kiener, 1836)
Authors: Simmonds Sara E. , Cheng Samantha H. , Fritts-Penniman Allison L. , Mahardika Gusti Ngurah , Barber Paul H.
Published: June 2021

Local adaptation to different environments may reinforce neutral evolutionary divergence, especially in populations in the periphery of a species’ geographic range. Seascape genomics (high-throughput genomics coupled with ocean climate databases) facilitates the exploration of neutral and adaptive variation in concert, developing a clearer picture of processes driving local adaptation in marine populations. This study used a seascape genomics approach to test the relative roles of neutral and adaptive processes shaping population divergence of a widespread coral reef snail,Coralliophila violacea. We collectedC. violaceafrom colonies of their coral host (Poritesspp.) at ten locations spanning a large portion of their geographic range. We used RAD-seq to investigate possible local adaptation via genetic-environmental associations with five ocean climate variables. Four genetic partitions were concordant with regions previously observed in mtDNA (Indian Ocean, Coral Triangle, and Hawaiian Islands), with the addition of Vietnam and varying isolation and admixture levels. We identified outlier loci (FDR = 0.10,N= 72) among individual localities and between regions (FDR = 0.10,N= 34), suggesting that some loci are putatively under divergent selection. Association analyses showed that the two strongest drivers of local adaptation were the annual range and mean of sea surface temperature. Populations that experience lower sea surface temperatures at the periphery ofC. violacea’sgeographic range drive these associations. Our results show that local adaptation to different environments likely reinforces neutral divergence, especially in peripheral populations.
A new adaptive procedure for estimating perceptual thresholds: the effects of observer bias and its correction
Authors: Fioravanti Chiara , Braun Christoph , Lindner Axel , Ruiz Sergio , Sitaram Ranganatha , Kajal Diljit Singh
Published: June 2021

Adaptive threshold estimation procedures sample close to a subject’s perceptual threshold by dynamically adapting the stimulation based on the subject’s performance. Yet, perceptual thresholds not only depend on the observers’ sensory capabilities but also on any bias in terms of their expectations and response preferences, thus distorting the precision of the threshold estimates. Using the framework of signal detection theory (SDT), independent estimates of both, an observer’s sensitivity and internal processing bias can be delineated from threshold estimates. While this approach is commonly available for estimation procedures engaging the method of constant stimuli (MCS), correction procedures for adaptive methods (AM) are only scarcely applied. In this article, we introduce a new AM that takes individual biases into account, and that allows for a bias-corrected assessment of subjects’ sensitivity. This novel AM is validated with simulations and compared to a typical MCS-procedure, for which the implementation of bias correction has been previously demonstrated.

Comparing AM and MCS demonstrates the viability of the presented AM. Besides its feasibility, the results of the simulation reveal both, advantages, and limitations of the proposed AM. The procedure has considerable practical implications, in particular for the design of shaping procedures in sensory training experiments, in which task difficulty has to be constantly adapted to an observer’s performance, to improve training efficiency.
15 years of introgression studies: quantifying gene flow across Eukaryotes
Authors: Dagilis Andrius J. , Peede David , Coughlan Jenn M. , Jofre Gaston I. , D’Agostino Emmanuel R. R. , Mavengere Heidi , Tate Alexander D. , Matute Daniel R.
Published: June 2021

With the rise of affordable next generation sequencing technology, introgression — or the exchange of genetic materials between taxa — is widely perceived to be a ubiquitous phenomenon in nature. Although this claim is supported by several keystone studies, no thorough assessment on the frequency of introgression in nature has been performed to date. In this manuscript, we aim to address this knowledge gap by providing a meta-analysis of the most comprehensive survey of introgression studies in Eukaryotes to date (724 papers with claims of introgression). We first examined the evidence given to support introgression, and if/how the lines of evidence have changed across time. We then collated a single statistic, Patterson’sD, that quantifies the strength of introgression across 123 studies to further assess how taxonomic group, divergence time, and aspects of life history influence introgression. We find three main results. Studies on introgression are much more frequent in plants and mammals than any other taxonomic group. The study of introgression has shifted from a largely qualitative assessment of whether introgression happens, to a focus on when and how much introgression has occurred across taxa. The most often used introgression statistic, Patterson’sD, shows several intriguing patterns suggesting introgression reports may be biased by both differences in reporting criteria and sequencing technology, but may also differ across taxonomic systems and throughout the process of speciation. Together, these results suggest the need for a unified approach to quantifying introgression in natural communities, and highlight important areas of future research that can be better assessed once this unified approach is met.
Cyanolichen microbiome contains novel viruses that encode genes to promote microbial metabolism
Authors: Ponsero Alise J. , Hurwitz Bonnie L. , Magain Nicolas , Miadlikowska Jolanta , Lutzoni François , U’Ren Jana M.
Published: June 2021

Lichen thalli are formed through the symbiotic association of a filamentous fungus and photosynthetic green alga and/or cyanobacterium. Recent studies have revealed lichens also host highly diverse communities of secondary fungal and bacterial symbionts, yet few studies have examined the viral component within these complex symbioses. Here, we describe viral biodiversity and functions in cyanolichens collected from across North America and Europe. As current machine learning viral-detection tools are not trained on complex eukaryotic metagenomes, we first developed efficient methods to remove eukaryotic reads prior to viral detection and a custom pipeline to validate viral contigs predicted with three machine-learning methods. Our resulting high-quality viral data illustrate that every cyanolichen thallus contains diverse viruses that are distinct from viruses in other terrestrial ecosystems. In addition to cyanobacteria, predicted viral hosts include other lichen-associated bacterial lineages and algae, although a large fraction of viral contigs had no host prediction. Functional annotation of cyanolichen viral sequences reveals numerous viral-encoded auxiliary metabolic genes (AMGs) involved in amino acid, nucleotide, and carbohydrate metabolism, including AMGs for secondary metabolism (antibiotics and antimicrobials) and fatty acid biosynthesis. Overall, the diversity of cyanolichen AMGs suggests that viruses may alter microbial interactions within these complex symbiotic assemblages.
A type VII secretion system in Group B Streptococcus mediates cytotoxicity and virulence
Authors: Spencer BL , Tak U , Mendonça JC , Nagao PE , Niederweis M , Doran KS
Published: June 2021

Type VII secretion systems (T7SS) have been identified in Actinobacteria and Firmicutes and have been shown to secrete effector proteins with functions in virulence, host toxicity, or interbacterial killing in a few genera. Bioinformatic analysis indicates that Group B streptococcal (GBS) isolates encode four distinct subtypes of T7SS machinery, three of which encode adjacent putative T7SS effectors with WXG and LXG motifs. However, the function of T7SS in GBS pathogenesis is not known. Here we show that the most abundant GBS T7SS subtype is important for virulence and cytotoxicity in brain endothelium and that these phenotypes are dependent on the WXG100 effector EsxA. We further show that the WXG motif is required for cytotoxicity in brain endothelium and that EsxA is a pore-forming protein. This work reveals the importance of a T7SS in host–GBS interactions and has implications for the functions of T7SS effectors in other Gram-positive bacteria.
Restoring statistical validity in group analyses of motion-corrupted MRI data
Authors: Lutti Antoine , Corbin Nadège , Ashburner John , Ziegler Gabriel , Draganski Bogdan , Phillips Christophe , Kherif Ferath , Callaghan Martina F. , Di Domenicantonio Giulia
Published: June 2021

Motion during the acquisition of magnetic resonance imaging (MRI) data degrades image quality, hindering our capacity to characterize disease in patient populations. Quality control procedures allow the exclusion of the most affected images from analysis. However, the criterion for exclusion is difficult to determine objectively and exclusion can lead to a suboptimal compromise between image quality and sample size. We provide an alternative, data-driven solution that assigns weights to each image, computed from an index of image quality using restricted maximum likelihood. We illustrate this method through the analysis of brain MRI data. The proposed method restores the validity of statistical tests, and performs near optimally in all brain regions, despite local effects of head motion. This method is amenable to the analysis of a broad type of MRI data and can accommodate any measure of image quality.
RASSF1A independence and early Galectin-1 upregulation in PIK3CA induced hepatocarcinogenesis: new therapeutic venues
Authors: Scheiter Alexander , Evert Katja , Reibenspies Lucas , Cigliano Antonio , Annweiler Katharina , Müller Karolina , Pöhmerer Laura-Maria-Giovanna , Itzel Timo , Materna-Reichelt Silvia , Coluccio Andrea , Honarnejad Kamran , Teufel Andreas , Brochhausen Christoph , Dombrowski Frank , Chen Xin , Evert Matthias , Calvisi Diego F. , Utpatel Kirsten
Published: June 2021

Aberrant activation of the PI3K/AKT/mTOR and Ras/Mitogen-Activated Protein Kinase pathways is a hepatocarcinogenesis hallmark. In a subset of hepatocellular carcinomas (HCC), PI3K/AKT/mTOR signaling dysregulation depends on PIK3CA mutations, while RAS/MAPK activation is partly attributed to promoter methylation of the tumor suppressorRASSF1A. To evaluate a possible co-carcinogenic effect of PIK3CA activation andRASSF1Aknockout, plasmids expressing oncogenic forms of PIK3CA (E545K or H1047R mutants) were delivered to the liver of RASSF1A knockout and wildtype mice by hydrodynamic tail vein injection combined with Sleeping Beauty–mediated somatic integration. Transfection of either PIK3CA E545K or H1047R mutants sufficed to induce hepatocellular carcinomas in mice irrespective ofRASSF1Amutational background. The related tumors displayed a lipogenic phenotype with upregulation of Fatty acid synthase and Stearoyl-CoA desaturase-1 (SCD1). Galectin-1, which was commonly upregulated in preneoplastic lesions and tumors, emerged as a regulator of SCD1. Co-inhibitory treatment with PIK3CA inhibitors and the Galectin-1 inhibitor OTX-008 resulted in synergistic cytotoxicity in human HCC cell lines, suggesting novel therapeutic venues.

Graphical Abstract

Hydrodynamic tail vein injection of Phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha (PIK3CA) mutant forms E545K and H1047R induces stepwise hepatocarcinogenesis in mice, independent of Ras association domain-containing protein 1 (RASSF1A) status. Gene expression analyses revealed an early increase in Galectin-1, which regulates the lipogenic enzyme Stearoyl-CoA desaturase-1 (SCD1). PIK3CA- and Galectin1 inhibitors act synergistically, pointing at novel therapeutic strategies.
Prediction of the sex-determination gene in tunas (Thunnus fishes)
Authors: Nakamura Yoji , Higuchi Kentaro , Kumon Kazunori , Yasuike Motoshige , Takashi Toshinori , Gen Koichiro , Fujiwara Atushi
Published: June 2021

Fish species have a variety of sex determination systems. Tunas (genus Thunnus) have an XY genetic sex-determination system. However, the Y chromosome or responsible locus has not yet been identified in males. In a previous study, a female genome of Pacific bluefin tuna (T. orientalis) was sequenced, and candidates for sex-associated DNA polymorphisms were identified by a genome-wide association study using resequencing data. In the present study, we sequenced a male genome of Pacific bluefin tuna by long-read and linked-read sequencing technologies, and explored male-specific loci through a comparison with the female genome. As a result, we found a unique region carrying the male-specific haplotype, where a homolog of estrogen sulfotransferase gene was predicted to be encoded. The genome-wide mapping of previously resequenced data indicated that, among the functionally annotated genes, only this gene, named sult1st6y, was paternally inherited in the males of Pacific bluefin tuna. We reviewed the RNA-seq data of southern bluefin tuna (T. maccoyii) in the public database and found that sult1st6y of southern bluefin tuna was expressed in all male testes, but absent or suppressed in the female ovary. Since estrogen sulfotransferase is responsible for the inactivation of estrogens, it is reasonable to assume that the expression of sult1st6y in gonad cells may inhibit female development, thereby inducing the individuals to become males. Thus, our results raise a promising hypothesis that sult1st6y is the sex-determination gene in Thunnus fishes, or at least functions at a crucial point in the sex-differentiation cascade.
A self-immolative linker for heparanase activatable probes
Authors: Schleyer Kelton A. , Liu Jun , Wang Zhishen , Cui Lina
Published: June 2021

Substrate-based probes utilize known substrate specificity parameters to create a probe that can be activated by a target enzyme. In developing probes for heparanase, an endo-ß-glucuronidase, we previously reported that small, inactive substrate-based probes could be electronically tuned by incorporating electron-withdrawing atoms on the aromatic aglycone fluorophore, ortho- to the cleaved glycosidic bond. However, the installation of electron-withdrawing groups directly onto established fluorophores or other reporters complicates the synthesis of new heparanase probes. In this work we report a new design strategy to expand the toolkit of heparanase imaging probes, in which the installation of an electronically tuned benzyl alcohol linker restored the activity of a previously inactive heparanase probe using 4-methylumbelliferone as the fluorescent reporter, suggesting such a linker can provide a scaffold for facile development of activatable heparanase probes bearing a variety of imaging moieties.
Norwegian Kveik brewing yeasts are adapted to higher temperatures and produce fewer off-flavours under heat stress than commercial Saccharomyces cerevisiae American Ale yeast
Authors: Kits Dimitri , Garshol Lars Marius
Published: June 2021

Norwegian kveik are a recently described family of domesticated Saccharomyces cerevisiae brewing yeasts used by farmhouse brewers in western Norway for generations to produce traditional Norwegian farmhouse ale. Kveik ale yeasts have been domesticated by farmhouse brewers through serial repitching of the yeast in warm wort (>30°C) punctuated by long periods of dry storage. Kveik yeasts are alcohol tolerant, flocculant, capable of utilizing maltose/maltotriose, phenolic off flavour negative, and exhibit elevated thermotolerance when compared to other modern brewer’s yeasts belonging to the ‘Beer 1’ clade. However, the optimal fermentation and growth temperatures (Topt) for kveik ale yeasts and the influence of fermentation temperature of the production of flavour-active metabolites like fusel alcohols and sulfur compounds (H2S, SO2) are not known. Here we show that kveik ale yeasts have an elevated optimal fermentation temperature (Topt) when compared to commercial American Ale yeast (SafAle™ US-05) and that they produce fewer off-flavours at high temperatures (>30°C) when compared to commercial American Ale yeasts. The tested kveik yeasts show significantly higher maximum fermentation rates than American Ale yeast not only at elevated temperatures (>30°C), but also at ‘typical’ ale fermentation temperatures (20°C-25°C). Finally, we demonstrate that kveik ale yeasts are heterogeneous in their Topt and that they attenuate standard wort robustly above their Topt unlike our control American Ale yeast which showed very poor apparent attenuation in our standard wort at temperatures ≫ Topt. Our results provide further support that kveik yeasts may possess favourable fermentation kinetics and sensory properties compared to American Ale yeasts. The observations here provide a roadmap for brewers to fine tune their commercial fermentations using kveik ale yeasts for optimal performance and/or flavour impact.
Differential expression of glycosyltransferases identified through comprehensive pan-cancer analysis
Authors: Dingerdissen Hayley M , Vora Jeet , Cauley Edmund , Bell Amanda , King Charles Hadley , Mazumder Raja
Published: June 2021

Despite accumulating evidence supporting a role for glycosylation in cancer progression and prognosis, the complexity of the human glycome and glycoproteome poses many challenges to understanding glycosylation-related events in cancer. In this study, a multifaceted genomics approach was applied to analyze the impact of differential expression of glycosyltransferases (GTs) in 16 cancers. An enzyme list was compiled and curated from numerous resources to create a consensus set of GTs. Resulting enzymes were analyzed for differential expression in cancer, and findings were integrated with experimental evidence from other analyses, including: similarity of healthy expression patterns across orthologous genes, miRNA expression, automatically-mined literature, curation of known cancer biomarkers, N-glycosylation impact, and survival analysis. The resulting list of GTs comprises 222 human enzymes based on annotations from five databases, 84 of which were differentially expressed in more than five cancers, and 14 of which were observed with the same direction of expression change across all implicated cancers. 25 high-value GT candidates were identified by cross-referencing multimodal analysis results, includingPYGM,FUT6and additional fucosyltransferases, several UDP-glucuronosyltransferases, and others, and are suggested for prioritization in future cancer biomarker studies. Relevant findings are available through OncoMX athttps://data.oncomx.org, and the overarching pipeline can be used as a framework for similarly analysis across diverse evidence types in cancer. This work is expected to improve the understanding of glycosylation in cancer by transparently defining the space of glycosyltransferase enzymes and harmonizing variable experimental data to enable improved generation of data-driven cancer biomarker hypotheses.
HKG: An open genetic variant database of 205 Hong Kong Cantonese exomes
Authors: Ou Min , Leung Henry Chi-Ming , Leung Amy Wing-Sze , Luk Ho-Ming , Yan Bin , Liu Chi-Man , Tong Tony Ming-For , Mok Myth Tsz-Shun , Ko Wallace Ming-Yuen , Law Wai-Chun , Lam Tak-Wah , Lo Ivan Fai-Man , Luo Ruibang
Published: June 2021

HKG is the first fully accessible variant database for Hong Kong Cantonese, constructed from 205 novel whole-exome sequencing data. There has long been a research gap in the understanding of the genetic architecture of southern Chinese subgroups, including Hong Kong Cantonese. HKG detected 196,325 high-quality variants with 5.93% being novel, and 25,472 variants were found to be unique in HKG compared to other Chinese populations (CHN). PCA illustrates the uniqueness of HKG in CHN, and IBD analysis revealed that it is related mostly to southern Chinese with a similar effective population size. An admixture study estimated the ancestral composition of HKG and CHN, with a gradient change from north to south, consistent with their geological distribution. ClinVar, CIViC and PharmGKB annotated 599 clinically significant variants and 360 putative loss-of-function variants, substantiating our understanding of population characteristics for future medical development. Among the novel variants, 96.57% were singleton and 6.85% were of high impact. With a good representation of Hong Kong Cantonese, we demonstrated better variant imputation using reference with the addition of HKG data, thus successfully filling the data gap in southern Chinese to facilitate the regional and global development of population genetics.
Sticking around: plant persistence strategies on edaphic islands
Authors: Ottaviani Gianluigi , Méndez-Castro Francisco E. , Conti Luisa , Zelený David , Chytrý Milan , Doležal Jiři , Jandová Veronika , Altman Jan , Klimešová Jitka
Published: June 2021

Species extinction risk at local scales can be partially offset by strategies promoting in-situ persistence. We explored how persistence-related traits of clonal and non-clonal plants in temperate dry grasslands respond intra- and interspecifically to variation in environmental conditions (soil, climate) and insularity.

We focused on edaphic island specialist species, hypothesizing that plants experiencing harsh soil environments and strong insularity are distinguished by traits supporting enhanced persistence, such as small stature, long lifespan and resource-conservative strategies. We used linear mixed-effect models and bivariate ordinary least squares linear models to explore the response of species triats to environmental and biogeographic predictors.

We found general support for this hypothesis. Soil properties and insularity emerged as the most important drivers of trait patterns. However, clonal species showed more consistent responses to variation in environmental conditions and insularity than non-clonal plants, which were characterized by distinct species-specific responses.

Soil properties and insularity confirmed their major role in shaping the persistence strategies of edaphic island plant species. These drivers may exert their effect on specific functions (e.g. belowground resource conservation captured by BDMC). Additionally, we unambiguously identified that clonal species had different persistence strategies than non-clonal ones.
The use of autologous skeletal muscle derived cells as a sling in the treatment of induced stress urinary incontinence, an experimental study
Authors: Wadie Bassem S. , Aamer Haytham G. , Khater Sherry M. , Gabr Mahmoud M.
Published: June 2021

Introduction & hypothesis

This is an experimental pre-clinical study testing for the applicability of autologous skeletal muscle derived cells as a seeded sling for the treatment of SUI in the canine model

Methods

10 Mongrel dogs: In 4, skeletal muscle biopsy was harvested from Biceps Femoris. 1 month later, incontinence was induced in 8 dogs through surgical disruption of the pubourethral ligaments. Muscle biopsy was incubated in DMEM medium and after expansion for 8 weeks, MDCs were collected. PGA scaffold was immersed in culture medium, coated with matrigel and cells were seeded. The sling was placed suburethrally in 8 dogs; 2 of which were cell-seeded and 4 had the scaffold only.

Urethral pressure (UP) measurement was done at baseline and 2 weeks alter insertion of the sling.

The urethra with its surrounding was harvested 4 weeks after sling insertion for histopathology. 2 dogs were considered as control, in which no urethrolysis or insertion of slings were carried out

Results

UP show increase of maximum urethral pressure during static measurement in all dogs with a scaffold inserted. The increase ranged from 5-40 cmH20 (Median 23 cmH20)

Histopathology shows significant periurethral proliferation of skeletal muscles in 4 dogs with cell-seeded scaffold, as demonstrated by Desmin. This was maximum in dogs # 1& 2. This was not the case in the 4 dogs that had PGA sling only.

Conclusion

The use of skeletal muscle –seeded PGA scaffold is a practical technique with preserved integrity of histological differentiation in canine model at short term.

Brief Summary

Autologous Skeletal muscle-derived cells could be propagated in vitro and seeded to PGS scaffolds and used as slings
Multivariate associations between dopamine receptor availability and risky investment decision making across adulthood
Authors: Green Mikella A. , Seaman Kendra L. , Crawford Jennifer L. , Kuhnen Camelia M. , Samanez-Larkin Gregory R.
Published: June 2021

Pharmacological manipulations have revealed that enhancing dopamine increases financial risk taking across adulthood. However, it is unclear whether baseline individual differences in dopamine function, assessed using PET imaging, are related to performance on risky financial decision making tasks. Here, thirty-five healthy adults completed an incentive-compatible learning-based risky investment decision task and a PET scan at rest using [11C]FLB457 to assess dopamine D2-like receptor availability. In the task, participants made choices between a safe asset (bond) and a risky asset (stock) with either an expected value less than the bond (“bad stock”) or expected value greater than the bond (“good stock”). Five measures of behavioral performance (choice inflexibility, risk seeking, suboptimal investment) and beliefs (absolute error, optimism) were extracted from the task data and average non-displaceable dopamine D2-like binding potential was extracted from four brain regions of interest (midbrain, amygdala, anterior cingulate, insula) from the PET imaging data. Given the presence of multiple independent and dependent variables, we used canonical correlation analysis (CCA) to evaluate multivariate associations between learning-based decision making and dopamine function controlling for age. Decomposition of the first dimension (r = .76) revealed that the strongest associations were between measures of choice inflexibility, incorrect choice, optimism, amygdala binding potential, and age. Follow-up univariate analyses revealed that amygdala binding potential and age were both independently associated with choice inflexibility. The findings reveal latent associations between baseline neural and behavioral measures suggesting that individual differences in dopamine function may be associated with learning-based financial risk taking in healthy adults.
Cryo-EM Structure of a Ferrichrome Importer FhuCDB
Authors: Hu Wenxin , Zheng Hongjin
Published: June 2021

As one of the most elegant biological processes developed in bacteria, the siderophore-mediated iron uptake demands the action of specific ATP-binding cassette (ABC) importers. Although extensive studies have been done on various ABC importers, the molecular basis of these iron-chelated-siderophore importers are still not fully understood. Here, we report the structure of a ferrichrome importer FhuCDB from Escherichia coli at 3.4Å resolution determined by cryo electron microscopy. The structure revealed a monomeric membrane subunit of FhuB with a substrate translocation pathway in the middle. In the pathway, there were unique arrangements of residues, especially layers of methionines. Important residues found in the structure were interrogated by mutagenesis and functional studies. Surprisingly, the importer’s ATPase activity was decreased upon FhuD binding, which deviated from the current understanding about bacterial ABC importers. In summary, our studies not only reveal a new structural twist in the type II ABC importer subfamily, but also provide biological insights in the transport of iron-chelated siderophores.
Validating marker-less pose estimation with 3D x-ray radiography
Authors: Moore Dalton D. , Walker Jeffrey D. , MacLean Jason N. , Hatsopoulos Nicholas G.
Published: June 2021

To reveal the neurophysiological underpinnings of natural movement, neural recordings must be paired with accurate tracking of limbs and postures. Here we validate the accuracy of DeepLabCut (DLC) by comparing it to a 3D x-ray video radiography system that tracks markers placed under the skin (XROMM). We record behavioral data simultaneously with XROMM and high-speed video for DLC as marmosets engage in naturalistic foraging and reconstruct three-dimensional kinematics in a shared coordinate system. We find that DLC tracks position and velocity of 12 markers on the forelimb and torso with low median error (0.272 cm and 1.76 cm/s, respectively) corresponding to 2.9% of the full range of marker positions and 5.9% of the range of speeds. For studies that can accept this relatively small degree of error, DLC and similar marker-less pose estimation tools enable the study of more naturalistic, unconstrained behaviors in many fields including non-human primate motor control.

Summary Statement

We validate the accuracy of DeepLabCut, a widely used marker-less pose estimation tool, using a marker-based 3D x-ray radiography system (XROMM).
Bioengineering a Miniaturized In Vitro 3D Myotube Contraction Monitoring Chip For Modelization of Muscular Dystrophies
Authors: Rose Nicolas , Sonam Surabhi , Nguyen Thao , Grenci Gianluca , Bigot Anne , Muchir Antoine , Ladoux Benoît , Le Grand Fabien , Trichet Léa
Published: June 2021

Quantification of skeletal muscle functional contraction is essential to assess the outcomes of therapeutic procedures for muscular disorders. Muscle three-dimensional “Organ-on-chip” models usually require a substantial amount of biological material, which is problematic in the context of limited patient sample. Here we developed a miniaturized 3D myotube culture chip with contraction monitoring capacity. Optimized micropatterned substrate design enabled to obtain high culture yields in tightly controlled microenvironments. Spontaneous contractions in myotubes derived from primary human myoblasts were observed. Analysis of nuclear morphology confirmed a similar organization between obtained myotubes and in vivo myofibers. LMNA-related Congenital Muscular Dystrophy (L-CMD) was modelled with successful development of mutant 3D myotubes displaying contractile dysfunction. This technology can thus be used to study contraction characteristics and evaluate how diseases affect muscle organization and force generation. Importantly, it requires significantly fewer starting materials than current systems, which should allow to substantially improve drug screening capability.
Rapid high-resolution structure analysis of small, biotechnologically relevant enzymes by cryo-electron microscopy
Authors: Dimos Nicole , Helmer Carl P.O. , Chánique Andrea M. , Wahl Markus C. , Kourist Robert , Hilal Tarek , Loll Bernhard
Published: June 2021

Enzyme catalysis has emerged as a key technology for developing efficient, sustainable processes in the chemical, biotechnological and pharmaceutical industries. Plants provide large and diverse pools of biosynthetic enzymes that facilitate complex reactions, such as the formation of intricate terpene carbon skeletons, with exquisite specificity. High-resolution structural analysis of these enzymes is crucial to understand their mechanisms and modulate their properties by targeted engineering. Although cryo-electron microscopy (cryo-EM) has revolutionized structural biology, its applicability to high-resolution structure analysis of comparatively small enzymes is so far largely unexplored. Here, we show that cryo-EM can reveal the structures of ~120 kDa plant borneol dehydrogenases at or below 2 Å resolution, paving the way for the fast development of new biocatalysts that provide access to bioactive terpenes and terpenoids.
Validating the Representational Space of Deep Reinforcement Learning Models of Behavior with Neural Data
Authors: Bruch Sebastian , McClure Patrick , Zhou Jingfeng , Schoenbaum Geoffrey , Pereira Francisco
Published: June 2021

Deep Reinforcement Learning (Deep RL) agents have in recent years emerged as successful models of animal behavior in a variety of complex learning tasks, as exemplified by Song et al. [2017]. As agents are typically trained to mimic an animal subject, the emphasis in past studies on behavior as a means of evaluating the fitness of models to experimental data is only natural. But the true power of Deep RL agents lies in their ability to learn neural computations and codes that generate a particular behavior—factors that are also of great relevance and interest to computational neuroscience. On that basis, we believe that model evaluation should include an examination of neural representations and validation against neural recordings from animal subjects. In this paper, we introduce a procedure to test hypotheses about the relationship between internal representations of Deep RL agents and those in animal neural recordings. Taking a sequential learning task as a running example, we apply our method and show that the geometry of representations learnt by artificial agents is similar to that of the biological subjects’, and that such similarities are driven by shared information in some latent space. Our method is applicable to any Deep RL agent that learns a Markov Decision Process, and as such enables researchers to assess the suitability of more advanced Deep Learning modules, or map hierarchies of representations to different parts of a circuit in the brain, and help shed light on their function. To demonstrate that point, we conduct an ablation study to deduce that, in the sequential task under consideration, temporal information plays a key role in molding a correct representation of the task.