bluuebunny/crossref_metadata_2025 huggingface dataset:
SambaR: an R package for fast, easy and reproducible population-genetic analyses of biallelic SNP datasets
Authors: de Jong Menno J. , de Jong Joost F. , Hoelzel A. Rus , Janke Axel
Published: July 2020

Background

SNP datasets can be used to infer a wealth of information about natural populations, including information about their structure, genetic diversity, and the presence of loci under selection. However, SNP data analysis can be a time-consuming and challenging process, not in the least because at present many different software packages are needed to execute and depict the wide variety of mainstream population-genetic analyses. Here we present SambaR, an integrative and user-friendly R package which automates and simplifies quality control and population-genetic analyses of biallelic SNP datasets. SambaR allows users to perform mainstream population-genetic analyses and to generate a wide variety of ready to publish graphs with a minimum number of commands (less than ten). These wrapper commands call functions of existing packages (including adegenet, ape, LEA, poppr, pcadapt and StAMPP) as well as new tools uniquely implemented in SambaR.

Results

We tested SambaR on online available SNP datasets and found that SambaR can process datasets of millions of SNPs and hundreds of individuals within hours, given sufficient computing power. Newly developed tools implemented in SambaR facilitate optimization of filter settings, objective interpretation of ordination analyses, enhance comparability of diversity estimates from reduced representation library SNP datasets, and generate reduced SNP panels and structure-like plots with Bayesian population assignment probabilities.

Conclusion

SambaR facilitates rapid population genetic analyses on biallelic SNP datasets by removing three major time sinks: file handling, software learning, and data plotting. In addition, SambaR provides a convenient platform for SNP data storage and management, as well as several new utilities, including guidance in setting appropriate data filters.

Availability and implementation

The SambaR source script, manual and example datasets are distributed through GitHub:https://github.com/mennodejong1986/SambaR
Transmission efficiency drives host-microbe associations
Authors: Leftwich Philip T. , Edgington Matthew P. , Chapman Tracey
Published: July 2020

Sequencing technologies have fueled a rapid rise in descriptions of microbial communities associated with hosts, but what is often harder to ascertain is their evolutionary significance. Here we review the existing literature on the role of vertical (VT), horizontal (HT), environmental acquisition, and mixed modes (MMT) of transmission for establishing animal host-microbe associations. We then modelled four properties of gut microbiota proposed as key to promoting animal host-microbe relationships: modes of transmission, host reproductive mode, host mate choice, and host fitness. We found: (i) MMT led to the highest frequencies of host-microbe associations, and some environmental acquisition or HT of microbes was required for persistent associations to form unless VT was perfect; (ii) host reproductive mode (sexual vs asexual) and host mate choice (for microbe carriers vs non-carriers) had little impact on the establishment of host-microbe associations; (iii) host mate choice did not itself lead to reproductive isolation, but could reinforce it; (iv) changes in host fitness due to host-microbe associations had a minimal impact upon the formation of co-associations. When we introduced a second population, into which host-microbe carriers could disperse but in which environmental acquisition did not occur, highly efficient VT was required for host-microbe co-associations to persist. Our study reveals that transmission mode is of key importance in establishing host-microbe associations.
A reference tissue atlas for the human kidney
Authors: Hansen Jens , Sealfon Rachel , Menon Rajasree , Eadon Michael T. , Lake Blue B. , Steck Becky , Dobi Dejan , Parikh Samir , Sigdel Tara K. , Zhang Guanshi , Velickovic Dusan , Barwinska Daria , Alexandrov Theodore , Rashmi Priyanka , Otto Edgar A. , Rose Michael P. , Anderton Christopher R. , Shapiro John P. , Pamreddy Annapurna , Winfree Seth , He Yongqun , de Boer Ian H. , Hodgin Jeffrey B. , Barisoni Laura , Naik Abhijit S. , Sharma Kumar , Sarwal Minnie M. , Zhang Kun , Himmelfarb Jonathan , Rovin Brad , El-Achkar Tarek M. , Laszik Zoltan , He John Cijiang , Dagher Pierre C. , Valerius M. Todd , Jain Sanjay , Satlin Lisa , Troyanskaya Olga G. , Kretzler Matthias , Iyengar Ravi , Azeloglu Evren U. ,   for the Kidney Precision Medicine Project
Published: July 2020

Abstract

Kidney Precision Medicine Project (KPMP) is building a spatially-specified human tissue atlas at the single-cell resolution with molecular details of the kidney in health and disease. Here, we describe the construction of an integrated reference tissue map of cells, pathways and genes using unaffected regions of nephrectomy tissues and undiseased human biopsies from 55 subjects. We use single-cell and -nucleus transcriptomics, subsegmental laser microdissection bulk transcriptomics and proteomics, near-single-cell proteomics, 3-D nondestructive and CODEX imaging, and spatial metabolomics data to hierarchically identify genes, pathways and cells. Integrated data from these different technologies coherently describe cell types/subtypes within different nephron segments and interstitium. These spatial profiles identify cell-level functional organization of the kidney tissue as indicative of their physiological functions and map different cell subtypes to genes, proteins, metabolites and pathways. Comparison of transcellular sodium reabsorption along the nephron to levels of mRNAs encoding the different sodium transporter genes indicate that mRNA levels are largely congruent with physiological activity.This reference atlas provides an initial framework for molecular classification of kidney disease when multiple molecular mechanisms underlie convergent clinical phenotypes.
Robust partitioning of microRNA targets from downstream regulatory changes
Authors: Patel Ravi K. , West Jessica D. , Jiang Ya , Fogarty Elizabeth A. , Grimson Andrew
Published: July 2020

The biological impact of microRNAs (miRNAs) is determined by their targets, and robustly identifying direct miRNA targets remains challenging. Existing methods suffer from high falsepositive rates and are unable to effectively differentiate direct miRNA targets from downstream regulatory changes. Here, we present an experimental and computational framework to deconvolute post-transcriptional and transcriptional changes using a combination of RNA-seq and PRO-seq. This novel approach allows us to systematically profile the regulatory impact of a miRNA. We refer to this approach as CARP:CombinedAnalysis ofRNA-seq andPRO-seq. We apply CARP to multiple miRNAs and show that it robustly distinguishes direct targets from downstream changes, while greatly reducing false positives. We validate our approach using Argonaute eCLIP-seq and ribosome profiling, demonstrating that CARP defines a comprehensive repertoire of targets. Using this approach, we identify miRNA-specific activity of target sites within the open reading frame. Additionally, we show that CARP facilitates the dissection of complex changes in gene regulatory networks triggered by miRNAs and identification of transcription factors that mediate downstream regulatory changes. Given the robustness of the approach, CARP would be particularly suitable for dissecting miRNA regulatory networksin vivo.
A semi-automated organoid screening method demonstrates epigenetic control of intestinal epithelial differentiation
Authors: Ostrop Jenny , Zwiggelaar Rosalie , Pedersen Marianne Terndrup , Gerbe François , Bösl Korbinian , Lindholm Håvard T. , Díez-Sánchez Alberto , Parmar Naveen , Radetzki Silke , von Kries Jens Peter , Jay Philippe , Jensen Kim B. , Arrowsmith Cheryl , Oudhoff Menno J.
Published: July 2020

Intestinal organoids are an excellent model to study epithelial biology. Yet, the selection of analytical tools to accurately quantify heterogeneous organoid cultures remains limited. Here, we developed a semi-automated organoid screening method, which we applied to a library of highly specific chemical probes to identify epigenetic regulators of intestinal epithelial biology. The role of epigenetic modifiers in adult stem cell systems, such as the intestinal epithelium, is still undefined. Based on this resource data, we identified several targets that affected epithelial cell differentiation, including HDACs, EP300/CREBBP, LSD1, and type I PRMTs, which were verified by complementary methods. For example, we show that inhibiting type I PRMTs, which leads enhanced epithelial differentiation, blocks the growth of adenoma but not normal organoid cultures. Thus, epigenetic probes are powerful tools to study intestinal epithelial biology and may have therapeutic potential.
Network and synaptic mechanisms underlying high frequency oscillations in the rat and cat olfactory bulb under ketamine-xylazine anesthesia
Authors: Średniawa Władysław , Wróbel Jacek , Kublik Ewa , Wójcik Daniel Krzysztof , Whittington Miles Adrian , Hunt Mark Jeremy
Published: July 2020

High frequency oscillations (HFO) are receiving increased attention for their role in health and disease. Ketamine-dependent HFO have been identified in cortical and subcortical regions in rodents, however, the mechanisms underlying their generation and whether they occur in higher mammals is unclear. Here, we show under ketamine-xylazine anesthesia, classical gamma oscillations diminish and a prominent > 80 Hz oscillation emerges in the olfactory bulb of rats and cats. In cats negligible HFO was observed in the thamalus and visual cortex indicating the OB was a suitable site for further investigation. Simultaneous local field potential and thermocouple recordings demonstrated HFO was dependent on nasal airflow. Silicon probe mapping studies spanning almost the entire dorsal ventral aspect of the OB revealed this rhythm was strongest in ventral areas of the bulb and associated with microcurrent sources about the mitral layer. Pharmacological microinfusion studies revealed HFO was dependent on excitatory-inhibitory synaptic activity, but not gap junctions. Finally, we showed HFO was preserved despite surgical removal of the piriform cortex. We conclude that ketamine-dependent HFO in the OB are driven by nasal airflow and local dendrodendritic interactions. The relevance of our findings to ketamine’s model of psychosis in awake state are also discussed.
Data-guided Multi-Map variables for ensemble refinement of molecular movies
Authors: Vant John W. , Sarkar Daipayan , Streitwieser Ellen , Fiorin Giacomo , Skeel Robert , Vermaas Josh V. , Singharoy Abhishek
Published: July 2020

Driving molecular dynamics simulations with data-guided collective variables offer a promising strategy to recover thermodynamic information from structure-centric experiments. Here, the 3-dimensional electron density of a protein, as it would be determined by cryo-EM or X-ray crystallography, is used to achieve simultaneously free-energy costs of conformational transitions and refined atomic structures. Unlike previous density-driven molecular dynamics methodologies that determine only the best map-model fits, our work uses the recently developedMulti-Mapmethodology to monitor concerted movements within equilibrium, non-equilibrium, and enhanced sampling simulations. Construction of all-atom ensembles along chosen values of the Multi-Map variable enables simultaneous estimation of average properties, as well as real-space refinement of the structures contributing to such averages. Using three proteins of increasing size, we demonstrate that biased simulation along reaction coordinates derived from electron densities can serve to induce conformational transitions between known intermediates. The simulated pathways appear reversible, with minimal hysteresis and require only low-resolution density information to guide the transition. The induced transitions also produce estimates for free energy differences that can be directly compared to experimental observables and population distributions. The refined model quality is superior compared to those found in the Protein DataBank. We find that the best quantitative agreement with experimental free-energy differences is obtained using medium resolution (~5 Å) density information coupled to comparatively large structural transitions. Practical considerations for generating transitions with multiple intermediate atomic density distributions are also discussed.
Retinal optic flow during natural locomotion
Authors: Matthis Jonathan Samir , Muller Karl S , Bonnen Kathryn , Hayhoe Mary M
Published: July 2020

We examine the structure of visual motion on the retina during natural locomotion in real world environments. Natural locomotion generates a rhythmic translation and rotation profile of the head in space, which means that visually specified heading varies throughout the gait cycle. This presents a challenge if optic flow is to be used to control heading towards a goal. The complex, phasic head movements that occur through the gait cycle create a highly unstable pattern of flow relative to the head. In contrast, vestibular-ocular-reflex mediated fixation simplifies patterns of optic flow on the retinae, resulting in regular features that may be valuable for the control of locomotion. In particular, the sign and magnitude of foveal curl in retinal flow fields specifies the body’s trajectory relative to the fixation point. In addition, the peak in the divergence of the retinal flow field specifies the walker’s instantaneous overground velocity/momentum vector in retinotopic coordinates. Assuming that walkers can determine the body position relative to fixation, this time-varying retinotopic cue for the body’s momentum could provide a visual control signal for foot placement over complex terrain. In contrast, the temporal variation of heading is large enough to be problematic for use in steering towards a goal. Consideration of optic flow in the context of natural locomotion therefore suggests a re-evaluation of the role of optic flow in the visual control of locomotion.
Microbial drama in four acts - Extreme rain events cause cyclic succession in plankton communities
Authors: Shabarova Tanja , Salcher Michaela M. , Porcal Petr , Znachor Petr , Nedoma Jiří , Grossart Hans-Peter , Seďa Jaromír , Hejzlar Josef , Šimek Karel
Published: July 2020

Highly abundant, small waterbodies contribute substantially to global freshwater shoreline and surface area. They are strongly interlinked with the terrestrial surrounding, thus controlling the flow of energy, nutrients and organisms through the landscape. Disturbance events can have severe consequences for these ecosystems and the entire downstream freshwater network and require more attention in the context of global change-induced increases in weather extremes. Here we show that extreme rain events (floods) cause cyclic successions in microbial communities and the planktonic food web of a small forest pond. We analyzed the dynamics of nutrients and the entire plankton community during two flood events and subsequent quasi-stable conditions. Floods induced a repeated washout of resident organisms and hundred-fold increases in nutrient load. However, within two weeks, the microbial community recovered to a pre-disturbance state through four well-defined succession phases. Reassembly of phyto- and especially zooplankton took considerably longer and displayed both repetitive and adaptive patterns. Release of dissolved nutrients from the pond was associated with inflow rates and state of community recovery, and it returned to pre-disturbance levels earlier than microbial composition. Our study exemplifies extraordinary compositional and functional resilience of small waterbodies and presents the detailed mechanism of the underlying processes.
Detection of homozygous and hemizygous partial exon deletions by whole-exome sequencing
Authors: Bigio Benedetta , Seeleuthner Yoann , Kerner Gaspard , Migaud Melanie , Rosain Jérémie , Boisson Bertrand , Nasca Carla , Puel Anne , Bustamante Jacinta , Casanova Jean-Laurent , Abel Laurent , Cobat Aurelie
Published: July 2020

The detection of copy number variations (CNVs) in whole-exome sequencing (WES) data is important, as CNVs may underlie a number of human genetic disorders. The recently developed HMZDelFinder algorithm can detect rare homozygous and hemizygous (HMZ) deletions in WES data more effectively than other widely used tools. Here, we present HMZDelFinder_opt, an approach that outperforms HMZDelFinder for the detection of HMZ deletions, including partial exon deletions in particular, in typical laboratory cohorts that are generated over time under different experimental conditions. We show that using an optimized reference control set of WES data, based on a PCA-derived Euclidean distance for coverage, strongly improves the detection of HMZ deletions both in real patients carrying validated disease-causing deletions and in simulated data. Furthermore, we develop a sliding window approach enabling HMZDelFinder-opt to identify HMZ partial deletions of exons that are otherwise undiscovered by HMZDelFinder. HMZDelFinder_opt is a timely and powerful approach for detecting HMZ deletions, particularly partial exon deletions, in laboratory cohorts, which are typically heterogeneous.
Identifying signal and noise structure in neural population activity with Gaussian process factor models
Authors: Keeley Stephen L. , Aoi Mikio C. , Yu Yiyi , Smith Spencer L. , Pillow Jonathan W.
Published: July 2020

Neural datasets often contain measurements of neural activity across multiple trials of a repeated stimulus or behavior. An important problem in the analysis of such datasets is to characterize systematic aspects of neural activity that carry information about the repeated stimulus or behavior of interest, which can be considered “signal”, and to separate them from the trial-to-trial fluctuations in activity that are not time-locked to the stimulus, which for purposes of such analyses can be considered “noise”. Gaussian Process factor models provide a powerful tool for identifying shared structure in high-dimensional neural data. However, they have not yet been adapted to the problem of characterizing signal and noise in multi-trial datasets. Here we address this shortcoming by proposing “signal-noise” Poisson-spiking Gaussian Process Factor Analysis (SNP-GPFA), a flexible latent variable model that resolves signal and noise latent structure in neural population spiking activity. To learn the parameters of our model, we introduce a Fourier-domain black box variational inference method that quickly identifies smooth latent structure. The resulting model reliably uncovers latent signal and trial-to-trial noise-related fluctuations in large-scale recordings. We use this model to show that predominantly, noise fluctuations perturb neural activity within a subspace orthogonal to signal activity, suggesting that trial-by-trial noise does not interfere with signal representations. Finally, we extend the model to capture statistical dependencies across brain regions in multi-region data. We show that in mouse visual cortex, models with shared noise across brain regions out-perform models with independent per-region noise.
The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle
Authors: Ando-Kuri Masami , Arzate-Mejía Rodrigo G. , Morf Jorg , Cairns Jonathan , Poot-Hernández Cesar A. , Andrews Simon , Várnai Csilla , Virk Boo , Wingett Steven W. , Fraser Peter , Furlan-Magaril Mayra
Published: July 2020

Circadian gene expression is essential for organisms to adjust cellular responses and anticipate daily changes in the environment. In addition to its physiological importance, the clock circuit represents an ideal, temporally resolved, system to study transcription regulation. Here, we analysed changes in spatial mouse liver chromatin conformation using genome-wide and promoter-capture Hi-C alongside daily oscillations in gene transcription in mouse liver. We found circadian topologically associated domains switched assignments to the transcriptionally active, open chromatin compartment and the inactive compartment at different hours of the day while their boundaries stably maintain their structure over time. Individual circadian gene promoters displayed maximal chromatin contacts at times of peak transcriptional output and the expression of circadian genes and contacted transcribed regulatory elements, or other circadian genes, was phase-coherent. Anchor sites of promoter chromatin loops were enriched in binding sites for liver nuclear receptors and transcription factors, some exclusively present in either rhythmic or stable contacts. The circadian 3D chromatin maps provided here identify the scales of chromatin conformation that parallel oscillatory gene expression and protein factors specifically associated with circadian or stable chromatin configurations.
PKA-mediated phosphorylation of Neuroligin-2 regulates its cell surface expression and synaptic stabilisation
Authors: Halff Els F. , Hannan Saad , Smart Trevor G. , Kittler Josef T.
Published: July 2020

The trans-synaptic adhesion molecule Neuroligin-2 (NL2) is essential for the development and function of inhibitory synapses. NL2 recruits the postsynaptic scaffold protein gephyrin, which in turn stabilises GABAAreceptors (GABAARs) in the postsynaptic domain. Dynamic regulation of synaptic GABAAR concentration is crucial for inhibitory neurotransmission efficacy. Changes in synaptic levels of NL2 contribute to regulating GABAAR synaptic concentration, however the mechanisms that control NL2 synaptic stabilisation are mostly unknown. Here, by combining biochemistry, imaging, single particle tracking and electrophysiology, we identify a key role for cAMP-dependent protein kinase (PKA) in synaptic stabilisation of NL2. We show that PKA-mediated phosphorylation of NL2 at S714 causes its dispersal from the synapse and reduces NL2 surface levels, leading to a loss of synaptic GABAARs. Conversely, enhanced stability of NL2 at synapses through abolishing phosphorylation leads to increased inhibitory signalling. Thus, PKA plays a key role in regulating NL2 function and synaptic inhibition.
Identification of a meiosis-specific chromosome movement pattern induced by persistent DNA damage
Authors: León-Periñán Daniel , Fernández-Álvarez Alfonso
Published: July 2020

As one of the main events occurring during meiotic prophase, the dynamics of meiotic chromosome movement is not yet well understood. Currently, although it is well-established that chromosome movement takes an important role during meiotic recombination promoting the pairing between homologous chromosomes and avoiding excessive chromosome associations, it is mostly unclear whether those movements follow a particular fixed pattern, or are stochastically distributed. UsingSchizosaccharomyces pombeas a model organism, which exhibits dramatic meiotic nuclear oscillations, we have developed a computationally automatized statistical analysis of three-dimensional time-lapse fluorescence information in order to characterize nuclear trajectories and morphological patterns during meiotic prophase. This approach allowed us to identify a patterned oscillatory microvariation during the meiotic nuclear motion. Additionally, we showed evidence suggesting that this unexpected oscillatory motif might be due to the detection of persistent DNA damage during the nuclear movement, supporting how the nucleus also regulates its oscillations. Our computationally automatized tool will be useful for the identification of new patterns of nuclear oscillations during gametogenesis.
Respiratory bacteria stabilize and promote airborne transmission of influenza A virus
Authors: Rowe Hannah M. , Livingston Brandi , Margolis Elisa , Davis Amy , Meliopoulos Victoria A. , Echlin Haley , Schultz-Cherry Stacey , Rosch Jason W
Published: July 2020

Influenza A virus (IAV) is a major pathogen of the human respiratory tract where the virus co-exists and interacts with bacterial populations comprising the respiratory microbiome. Synergies between IAV and respiratory bacterial pathogens promote enhanced inflammation and disease burden that exacerbate morbidity and mortality. We demonstrate that direct interactions between IAV and encapsulated bacteria commonly found in the respiratory tract promote environmental stability and infectivity of IAV. Antibiotic-mediated depletion of the respiratory bacterial flora abrogated IAV transmission in ferret models, indicating that these viral-bacterial interactions are operative for airborne transmission of IAV. Restoring IAV airborne transmission in antibiotic treated ferrets by co-infection withStreptococcus pneumoniaeconfirmed a role for specific members of the bacterial respiratory community in promoting IAV transmission. These results implicate a role for the bacterial respiratory flora in promoting airborne transmission of IAV.
Expression of the type III secretion system genes in epiphyticErwinia amylovoracells on apple stigmas benefits endophytic infection at the hypanthium
Authors: Cui Zhouqi , Huntley Regan B. , Schultes Neil P , Kakar Kaleem U. , Zeng Quan
Published: July 2020

Erwinia amylovoracauses fire blight on rosaceous plants. Flower surfaces are the primary location in the fire blight infection pathway. Here E. amylovora proliferates on stigmatic and hypanthium surfaces as epiphytic growth, followed by subsequent endophytic (intercellular) infection in the hypanthium. The type III secretion system (T3SS) is an important virulence factor inE. amylovora. Although the role of T3SS during the endophytic infection is well characterized, its expression during the epiphytic colonization and role in the subsequent infection is less understood. Here, we investigated the T3SS expression in epiphyticE. amylovoraon stigma and hypanthium of apple flowers, under different relative humidities (RH). On stigma surfaces, T3SS was expressed in a high percentage of E. amylovora cells, and its expression promotes epiphytic growth. On hypanthium surfaces however, T3SS was expressed in fewerE. amylovoracells than on the stigma, and displayed no correlation with epiphytic growth, even though T3SS expression is essential for infection.E. amylovoracells grown on stigmatic surfaces and then flushed down to the hypanthium displayed a higher level of T3SS expression than cells grown on the hypanthium surface alone. Furthermore, cells pre-cultured on stigma before inoculation on hypanthium caused more infections than cells pre-cultured in a T3SS-repressive medium then used as inoculum, suggesting that the T3SS induction during the stigmatic epiphytic colonization may be beneficial for the subsequent infection. Finally, the epiphytic expression of T3SS is influenced by RH. Higher percentage of stigmaticE. amylovoracells expressed T3SS under high RH than under low RH.
Ethoflow: computer vision and artificial intelligence-based software for automatic behavior analysis
Authors: Bernardes Rodrigo Cupertino , Lima Maria Augusta Pereira , Guedes Raul Narciso C. , Martins Gustavo Ferreira
Published: July 2020

Manual monitoring of animal behavior is time-consuming and prone to bias. An alternative to such limitations is the use of computational resources in behavioral assessments, such as a tracking system, to facilitate accurate and long-term evaluations. There is a demand for robust software that addresses analysis in heterogeneous environments (such as in field conditions) and evaluates multiple individuals in groups while maintaining their identities.

The Ethoflow software was developed using computer vision and artificial intelligence (AI) tools to automatically monitor various behavioral parameters. A state-of-the-art object detection algorithm based on instance segmentation was implemented, allowing behavior monitoring in the field under heterogeneous environments. Moreover, a convolutional neural network was implemented to assess complex behaviors, thus expanding the possibilities of animal behavior analyses.

The heuristics used to automatically generate training data for the AI models are described, and the models trained with these datasets exhibited high accuracy in detecting individuals in heterogeneous environments and assessing complex behavior. Ethoflow was employed for kinematic assessments and to detect trophallaxis in social bees. The software runs on the Linux, Microsoft Windows, and IOS operating systems with an intuitive graphical interface.

In the Ethoflow algorithm, the processing with AI is separate from the other modules, which facilitates kinematic measurements on an ordinary computer and the assessment of complex behavior on machines with graphics processing units (GPUs). Thus, Ethoflow is a useful support tool for applications in biology and related fields.
Synergid calcium ion oscillations define a new feature of pollen tube reception critical for blocking interspecific hybridization
Authors: Ponvert Nathaniel , Johnson Mark A.
Published: July 2020

Reproductive isolation leads to the evolution of distinct new species, however, the molecular mechanisms that promote and maintain reproductive barriers are elusive. In flowering plants sperm cells are immotile and are delivered to female gametes by the pollen grain which germinates a polarized extension, the pollen tube, into floral tissue. After growing via polar extension to the female gametophyte, the pollen tube signals with receptive female cells flanking the egg in two distinct steps. If signaling is successful, the pollen tube releases sperm cells for fusion with female gametes. To better understand cell-cell recognition during reproduction, we investigated calcium ion dynamics associated with interspecific cell signaling between mating partners. We observed that interspecific pollen tubes successfully complete initial cell-cell signaling, but fail during later phases of pollen tube reception. Our work refines our understanding of pollen tube reception as a critical block to interspecific hybridization. Our results also shed light on the functional significance of the two phases of pollen tube reception, and implicate the second step as being the stage during which the pollen tube presents its genetic identity.
On Rank Deficiency in Phenotypic Covariance Matrices
Authors: O’Keefe F. Robin , Meachen Julie A. , Polly P. David
Published: July 2020

This paper is concerned with rank deficiency in phenotypic covariance matrices: first to establish it is a problem by measuring it, and then proposing methods to treat for it. Significant rank deficiency can mislead current measures of whole-shape phenotypic integration, because they rely on eigenvalues of the covariance matrix, and highly rank deficient matrices will have a large percentage of meaningless eigenvalues. This paper has three goals. The first is to examine a typical geometric morphometric data set and establish that its covariance matrix is rank deficient. We employ the concept of information, or Shannon, entropy to demonstrate that a sample of dire wolf jaws is highly rank deficient. The different sources of rank deficiency are identified, and include the Generalized Procrustes analysis itself, use of the correlation matrix, insufficient sample size, and phenotypic covariance. Only the last of these is of biological interest.

Our second goal is to examine a test case where a change in integration is known, allowing us to document how rank deficiency affects two measures of whole shape integration (eigenvalue standard deviation and standardized generalized variance). This test case utilizes the dire wolf data set from Part 1, and introduces another population that is 5000 years older. Modularity models are generated and tested for both populations, showing that one population is more integrated than the other. We demonstrate that eigenvalue variance characterizes the integration change incorrectly, while the standardized generalized variance lacks sensitivity. Both metrics are impacted by the inclusion of many small eigenvalues arising from rank deficiency of the covariance matrix. We propose a modification of the standardized generalized variance, again based on information entropy, that considers only the eigenvalues carrying non-redundant information. We demonstrate that this metric is successful in identifying the integration change in the test case.

The third goal of this paper is to generalize the new metric to the case of arbitrary sample size. This is done by normalizing the new metric to the amount of information present in a permuted covariance matrix. We term the resulting metric the ‘relative dispersion’, and it is sample size corrected. As a proof of concept we us the new metric to compare the dire wolf data set from the first part of this paper to a third data set comprising jaws of Smilodon fatalis. We demonstrate that the Smilodon jaw is much more integrated than the dire wolf jaw. Finally, this information entropy-based measures of integration allows comparison of whole shape integration in dense semilandmark environments, allowing characterization of the information content of any given shape, a quantity we term ‘latent dispersion’.
Inferring the genetic basis of sex determination from the genome of a dioecious nightshade
Authors: Wu Meng , Anderson Gregory J. , Hahn Matthew W. , Moyle Leonie C. , Guerrero Rafael F.
Published: July 2020

Dissecting the genetic mechanisms underlying dioecy (i.e. separate female and male individuals) is critical for understanding the evolution of this pervasive reproductive strategy. Nonetheless, the genetic basis of sex determination remains unclear in many cases, especially in systems where dioecy has arisen recently. Within the economically important plant genusSolanum(∼2000 species), dioecy is thought to have evolved independently at least 4 times across roughly 20 species. Here, we generate the first genome sequence of a dioeciousSolanumand use it to ascertain the genetic basis of sex determination in this species. Wede novoassembled and annotated the genome ofS. appendiculatum(assembly size: ∼750 Mb; scaffold N50: 0.92 Mb; ∼35,000 genes), identified sex-specific sequences and their locations in the genome, and inferred that males in this species are the heterogametic sex. We also analyzed gene expression patterns in floral tissues of males and females, finding ∼100 genes that are differentially expressed between the sexes. These analyses, together with observed patterns of gene-family evolution specific toS. appendiculatum, consistently implicate a suite of genes from the regulatory network controlling pectin degradation and modification in the expression of sex. Furthermore, the genome of a species with a relatively young sex determination system provides the foundational resources for future studies on the independent evolution of dioecy in this speciose clade.
Bariatric surgery normalizes circulating glucocorticoid levels and lowers glucocorticoid action tissue-selectively in mice
Authors: Akalestou Elina , Lopez-Noriega Livia , Christakis Ioannis , Miras Alexander D. , Leclerc Isabelle , Rutter Guy A.
Published: July 2020

Background

Glucocorticoids produced by the adrenal cortex are essential for the maintenance of metabolic homeostasis. Glucocorticoid activation is catalyzed by 11β-hydroxysteroid dehydrogenase 1 (11β-HSD1) and signalling is achieved through the glucocorticoid receptor (GR), a ligand-dependent transcription factor. Excess glucocorticoids are associated with insulin resistance and hyperglycaemia. A small number of studies have investigated the effects of bariatric surgery, a gastrointestinal procedure known to improve insulin sensitivity, on glucocorticoid metabolism, but the hypothesised mechanism is assumed to be via weight loss.

Aim

To investigate the effect of bariatric surgery on glucocorticoid metabolism in lean and obese mice.

Methods

Lean mice and HFD mice underwent Vertical Sleeve Gastrectomy (VSG) or sham surgery. Glucose and insulin tolerance tests were performed at four and ten weeks post operatively and circulating corticosterone was measured. Liver and adipose tissues were harvested from fed mice and 11β-HSD1 and GR levels were measured by quantitative RT-PCR or Western (immuno-) blotting, respectively.

Results

VSG did not cause excess weight loss in lean mice when compared to sham operated mice. However, both lean and HFD VSG mice displayed significantly improved glucose clearance and insulin sensitivity. Remarkably, VSG restores physiological corticosterone production in HFD mice and reduces11β-HSD1 levels at four and ten weeks post-surgery. Additionally, lean mice displayed significantly lowered mRNA levels of 11β-HSD1 in subcutaneous adipose tissue and GR in liver.

Conclusions

Bariatric surgery improves insulin sensitivity and reduces glucocorticoid activation at tissular level, under physiological and pathophysiological (obesity) conditions, irrespective of weight loss. The reduction of glucocorticoid exposure may represent an additional contribution to the health benefits of bariatric surgery. These findings point towards a physiologically relevant gut-adrenal axis.
Balancing selection maintains hyper-divergent haplotypes inC. elegans
Authors: Lee Daehan , Zdraljevic Stefan , Stevens Lewis , Wang Ye , Tanny Robyn E. , Crombie Timothy A. , Cook Daniel E. , Webster Amy K. , Chirakar Rojin , Baugh L. Ryan , Sterken Mark G. , Braendle Christian , Félix Marie-Anne , Rockman Matthew V. , Andersen Erik C.
Published: July 2020

Across diverse taxa, selfing species have evolved independently from outcrossing species thousands of times. The transition from outcrossing to selfing significantly decreases the effective population size, effective recombination rate, and heterozygosity within a species. These changes lead to a reduction in genetic diversity, and therefore adaptive potential, by intensifying the effects of random genetic drift and linked selection. Within the nematode genusCaenorhabditis, selfing has evolved at least three times and all three species, including in the model organismCaenorhabditis elegans, show substantially reduced genetic diversity relative to outcrossing species. Selfing and outcrossingCaenorhabditisspecies are often found in the same niches, but we still do not know how selfing species with limited genetic diversity can adapt to these environments. Here, we examine the whole-genome sequences from 609 wildC. elegansstrains isolated worldwide and show that genetic variation is concentrated in punctuated hyper-divergent regions that cover 20% of theC. elegansreference genome. These regions are enriched in environmental response genes that mediate sensory perception, pathogen response, and xenobiotic stress response. Population genomic evidence suggests that genetic diversity in these regions has been maintained by long-term balancing selection. Using long-read genome assemblies for 15 wild strains, we show that hyper-divergent haplotypes contain unique sets of genes and show levels of divergence comparable to levels found betweenCaenorhabditisspecies that diverged millions of years ago. These results provide an example for how species can avoid the evolutionary “dead end” associated with selfing.
Dielectrophoretic separation of randomly shaped protein particles
Authors: Kwak Tae Joon , Jung Huihun , Allen Benjamin D , Demirel Melik C , Chang Woo-Jin
Published: July 2020

Recently, insoluble protein particles have been increasingly investigated for artificial drug delivery systems due to their favorable properties, including programmability for active drug targeting of diseases as well as their biocompatibility and biodegradability after administration. One of the biggest challenges is selectively collecting monodisperse particles in desirable morphologies and sizes to enable consistent levels and rates of drug loading and release. Therefore, technology that allows sorting of protein particles with respect to size and morphology will enhance the design and production of next-generation drug delivery materials. Here, we introduce a dielectrophoretic (DEP) separation technique to selectively isolate spherical protein particles from a mixture of randomly shaped particles. We tested this approach by applying it to a mixture of precipitated squid ring teeth inspired tandem repeat protein particles with diverse sizes and morphologies. The DEP trapping system enabled us to isolate specific-sized, spherical protein particles out of this mixture: after separation, the fraction of 2 μm and 4 μm spherical particles was increased from 28.64% of mixture to 80.53% and 74.02% with polydispersity indexes (PDIs) decreased from 0.93 of mixture to 0.19 and 0.09, respectively. The protein particles show high aqueous swelling capability (up to 74% by mass) that could enable delivery of drug solutions. This work is intended to inspire the future development of biocompatible drug-delivery systems.
Synergistic Effects of the DRD2/3 Antagonist ONC201 and Radiation in Glioblastoma
Authors: He Ling , Bhat Kruttika , Ioannidis Angeliki , Zhang Le , Nguyen Nhan T. , Allen Joshua E. , Nghiemphu Phioanh Leia , Cloughesy Timothy F. , Liau Linda M. , Kornblum Harley I. , Pajonk Frank
Published: July 2020

Background

Glioblastoma (GBM) is the deadliest of all brain cancers in adults. The current standard-of-care is surgery followed by radiotherapy and temozolomide, leading to a median survival time of only 15 months. GBM are organized hierarchically with a small number of glioma-initiating cells, responsible for therapy resistance and tumor recurrence, suggesting that targeting glioma-initiating cells could improve treatment response. ONC201 is a first-in-class anti-tumor agent with clinical efficacy in some forms of high-grade gliomas. Here we test its efficacy against GBM in combination with radiation.

Methods

Using patient-derived GBM lines and mouse models of GBM we test the effects of radiation and ONC201 on GBM self - renewalin vitroand survivalin vivo. A possible resistance mechanism is investigated using RNA-Sequencing.

Results

Treatment of GBM cells with ONC201 reduced self-renewal, clonogenicity and cell viabilityin vitro. ONC201 exhibited anti-tumor effects on radioresistant GBM cells indicated by reduced self-renewal in secondary and tertiary glioma spheres. Combined treatment with ONC201 and radiation prolonged survival in syngeneic and patient-derived orthotopic xenograft mouse models of GBM. Subsequent transcriptome analyses after combined treatment revealed shifts in gene expression signatures related to quiescent GBM populations, GBM plasticity, and GBM stem cells.

Conclusions

Our findings suggest that combined treatment with the DRD2/3 antagonist ONC201 and radiation improves the efficacy of radiation against GBMin vitroandin vivothrough suppression of GICs without increasing toxicity in mouse models of GBM. A clinical assessment of this novel combination therapy against GBM is further warranted.

Key points

- Combined treatment of ONC201 and radiation exhibit anti-tumor effects on cells from primary and recurrent GBM

- Combined treatment significantly prolongs survival in vivo

- Combined treatment potentially targets the quiescent GBM cell population

Importance of the Study

The survival rates for patients with GBM are unacceptably low and novel treatment approaches are needed. This study provides evidence that a combination of radiation and the dopamine receptor antagonist ONC201 significantly prolongs survival in mouse models of glioma.
Metabarcoding reveals different zooplankton communities in northern and southern areas of the North Sea
Authors: Macher Jan Niklas , van der Hoorn Berry B. , Peijnenburg Katja T. C. A. , van Walraven Lodewijk , Renema Willem
Published: July 2020

Zooplankton are key players in marine ecosystems, linking primary production to higher trophic levels. The high abundance and high taxonomic diversity renders zooplankton ideal for biodiversity monitoring. However, taxonomic identification of the zooplankton assemblage is challenging due to its high diversity, subtle morphological differences and the presence of many meroplanktonic species, especially in coastal seas. Molecular techniques such as metabarcoding can help with rapid processing and identification of taxa in complex samples, and are therefore promising tools for identifying zooplankton communities. In this study, we applied metabarcoding of the mitochondrial cytochrome c oxidase I gene to zooplankton samples collected along a latitudinal transect in the North Sea, a shelf sea of the Atlantic Ocean. Northern regions of the North Sea are influenced by inflow of oceanic Atlantic waters, whereas the southern parts are characterised by more coastal waters. Our metabarcoding results indicated strong differences in zooplankton community composition between northern and southern areas of the North Sea, particularly in the classes Copepoda, Actinopterygii (ray-finned fishes) and Polychaeta. We compared these results to the known distributions of species reported in previous studies, and by comparing the abundance of copepods to data obtained from the Continuous Plankton Recorder (CPR). We found that our metabarcoding results are mostly congruent with the reported distribution and abundance patterns of zooplankton species in the North Sea. Our results highlight the power of metabarcoding to rapidly assess complex zooplankton samples, and we suggest that the technique could be used in future monitoring campaigns and biodiversity assessments.

Highlights

Zooplankton communities are different in northern and southern areas of the North Sea

Metabarcoding results are consistent with known species distributions and abundance

Metabarcoding allows for fast identification of meroplanktonic species
PecanPy: a fast, efficient, and parallelized Python implementation ofnode2vec
Authors: Liu Renming , Krishnan Arjun
Published: July 2020

Learning low-dimensional representations (embeddings) of nodes in large graphs is key to applying machine learning on massive biological networks.Node2vecis the most widely used method for node embedding. However, its original Python and C++ implementations scale poorly with network density, failing for dense biological networks with hundreds of millions of edges. We have developed PecanPy, a new Python implementation ofnode2vecthat uses cache-optimized compact graph data structures and precomputing/parallelization to result in fast, high-quality node embeddings for biological networks of all sizes and densities. PecanPy software and documentation are available athttps://github.com/krishnanlab/pecanpy.
Podoplanin drives dedifferentiation and amoeboid invasion of melanoma
Authors: de Winde Charlotte M. , George Samantha L. , Arp Abbey B. , Benjamin Agnesska C. , Crosas-Molist Eva , Hari-Gupta Yukti , Carver Alexander , Imperatore Valerio , Martinez Victor G. , Sanz-Moreno Victoria , Acton Sophie E.
Published: July 2020

Melanoma is an aggressive skin cancer developing from melanocytes, frequently resulting in metastatic disease. Melanoma cells utilise amoeboid migration as mode of local invasion. Amoeboid invasion is characterized by rounded cell morphology and high actomyosin contractility driven by the RhoA signalling pathway. Migrastatic drugs targeting actin polymerization and contractility to inhibit invasion and metastasis are therefore a promising treatment option. To predict amoeboid invasion and metastatic potential, there is a need for biomarkers functionally linked to contractility pathways. The glycoprotein podoplanin drives actomyosin contractility in lymphoid fibroblasts, and is overexpressed in several cancer types. Here, we show that podoplanin enhances amoeboid invasion in melanoma. Expression of podoplanin in murine melanoma models drives rounded cell morphology, increasing motility and invasionin vivo. Podoplanin expression is upregulated in a subset of dedifferentiated human melanoma, andin vitrois sufficient to suppress melanogenesis and upregulate melanoma-associated markersMitfandPou3f2. Together, our data indicates that podoplanin is both a potential biomarker for dedifferentiated invasive melanoma and a promising migrastatic therapeutic target.