bluuebunny/crossref_metadata_2025 huggingface dataset:
Natural bacterial assemblages inArabidopsis thalianatissues become more distinguishable and diverse during host development
Authors: Beilsmith Kathleen , Perisin Matthew , Bergelson Joy
Published: March 2020

To study the spatial and temporal dynamics of bacterial colonization under field conditions, we planted and sampledArabidopsis thalianaduring two years at two Michigan sites and surveyed colonists by sequencing 16S rRNA gene amplicons. Mosaic and dynamic assemblages revealed the plant as a patchwork of tissue habitats that differentiated with age. Although assemblages primarily varied between roots and shoots, amplicon sequence variants (ASVs) also differentiated phyllosphere tissues. Increasing assemblage diversity indicated that variants dispersed more widely over time, decreasing the importance of stochastic variation in early colonization relative to tissue differences. As tissues underwent developmental transitions, the root and phyllosphere assemblages became more distinct. This pattern was driven by common variants rather than those restricted to a particular tissue or transiently present at one developmental stage. Patterns also depended critically on fine phylogenetic resolution: when ASVs were grouped at coarse taxonomic levels, their associations with host tissue and age weakened. Thus, the observed spatial and temporal variation in colonization depended upon bacterial traits that were not broadly shared at the family level. Some colonists were consistently more successful at entering specific tissues, as evidenced by their repeatable spatial prevalence distributions across sites and years. However, these variants did not overtake plant assemblages, which instead became more even over time. Together, these results suggested that the increasing effect of tissue type was related to colonization bottlenecks for specific ASVs rather than to their ability to dominate other colonists once established.

Importance

Developing synthetic microbial communities that can increase plant yield or deter pathogens requires basic research on several fronts, including the efficiency with which microbes colonize plant tissues, how plant genes shape the microbiome, and the microbe-microbe interactions involved in community assembly. Findings on each of these fronts depend upon the spatial and temporal scales at which plant microbiomes are surveyed. In our study, phyllosphere tissues housed increasingly distinct microbial assemblages as plants aged, indicating that plants can be considered as collections of tissue habitats in which microbial colonists-- natural or synthetic-- establish with differing success. Relationships between host genes and community diversity might vary depending on when samples are collected, given that assemblages grew more diverse as plants aged. Both spatial and temporal trends weakened when colonists were grouped by family, suggesting that functional rather than taxonomic profiling will be necessary to understand the basis for differences in colonization success.
Metagenomic data reveal diverse fungal and algal communities associated with the lichen symbiosis
Authors: Smith Hayden , Dal Grande Francesco , Muggia Lucia , Keuler Rachel , Divakar Pradeep K. , Grewe Felix , Schmitt Imke , Lumbsch H. Thorsten , Leavitt Steven D.
Published: March 2020

Lichens have traditionally been considered the symbiotic phenotype from the interactions of a single fungal partner and one or few photosynthetic partners. However, the lichen symbiosis has been shown to be far more complex and may include a wide range of other interacting organisms, including non-photosynthetic bacteria, accessory fungi, and algae. In this study, we analyzed metagenomic shotgun sequences to better characterize lichen mycobiomes. Specifically, we inferred the range of fungi associated within lichen thalli from five groups of lichens – horsehair lichens (mycobiont=Bryoriaspp.), shadow lichens (taxa in Physciaceae), rock posies (Rhizoplacaspp.), rock tripes (Umbilicariaspp.), and green rock shields (Xanthoparmeliaspp.). Metagenomic reads from the multi-copy nuclear ribosomal internal transcribed spacer region, the standard DNA barcode region for fungi, were extracted, clustered, and used to infer taxonomic assignments. Our data revealed diverse lichen-associated mycobiomes, and closely related mycobionts tended to have more similar mycobiomes. Many of the members of the lichen-associated mycobiomes identified here have not previously been found in association with lichens. We found little evidence supporting the ubiquitous presence of Cystobasidiales yeasts in macrolichens, although reads representing this putative symbiotic partner were found in samples of horsehair lichens, albeit in low abundance. Our study further highlights the ecosystem-like features of lichens, with partners and interactions far from being completely understood. Future research is needed to more fully and accurately characterize lichen mycobiomes and how these fungi interact with the major lichen components – the photo- and mycobionts.
A TAL effector-like protein of symbioticMycetohabitansincreases stress tolerance and alters the transcriptome of the fungal hostRhizopus microsporus
Authors: Carter Morgan E. , Carpenter Sara C.D. , Dubrow Zoë E. , Sabol Mark R. , Rinaldi Fabio C. , Lastovestsky Olga A. , Mondo Stephen J. , Pawlowska Teresa E. , Bogdanove Adam J.
Published: March 2020

Symbioses of bacteria with fungi have only recently been described and are poorly understood. In the symbiosis ofMycetohabitans(formerlyBurkholderia)rhizoxinicawith the fungusRhizopus microsporus, bacterial type III (T3) secretion is known to be essential. Proteins resembling T3-secreted transcription activator-like (TAL) effectors of plant pathogenic bacteria are encoded in the three sequencedMycetohabitans spp.genomes. TAL effectors nuclear localize in plants, where they bind and activate genes important in disease. The Burkholderia TAL-like (Btl) proteins bind DNA but lack the N- and C-terminal regions in which TAL effectors harbor their T3 and nuclear localization signals, and activation domain. We characterized a Btl protein, Btl19-13, and found that, despite the structural differences, it can be T3-secreted and can nuclear localize. Abtl19-13gene knockout did not prevent the bacterium from infecting the fungus, but the fungus became less tolerant to cell membrane stress. Btl19-13 did not alter transcription in a plant-based reporter assay, but 15R. microsporusgenes were differentially expressed in comparisons both of the fungus infected with the wildtype bacterium vs the mutant and with the mutant vs. a complemented strain. Southern blotting revealedbtlgenes in 14 diverseMycetohabitansisolates. However, banding patterns and available sequences suggest variation, and thebtl19-13phenotype could not be rescued by abtlgene from a different strain. Our findings support the conclusion that Btl proteins are effectors that act on host DNA and play important but varied or possibly host-genotype-specific roles in theM. rhizoxinica-R. microsporussymbiosis.
Disentangling latent representations of single cell RNA-seq experiments
Authors: Kimmel Jacob C.
Published: March 2020

Single cell RNA sequencing (scRNA-seq) enables transcriptional profiling at the resolution of individual cells. These experiments measure features at the level of transcripts, but biological processes of interest often involve the complex coordination of many individual transcripts. It can therefore be difficult to extract interpretable insights directly from transcript-level cell profiles. Latent representations which capture biological variation in a smaller number of dimensions are therefore useful in interpreting many experiments. Variational autoencoders (VAEs) have emerged as a tool for scRNA-seq denoising and data harmonization, but the correspondence between latent dimensions in these models and generative factors remains unexplored. Here, we explore training VAEs with modifications to the objective function (i.e.β-VAE) to encourage disentanglement and make latent representations of single cell RNA-seq data more interpretable. Using simulated data, we find that VAE latent dimensions correspond more directly to data generative factors when using these modified objective functions. Applied to experimental data of stimulated peripheral blood mononuclear cells, we find better correspondence of latent dimensions to experimental factors and cell identity programs, but impaired performance on cell type clustering.

Publication Status

This pre-print represents the final output of a preliminary research direction and will not be updated or published in an archival journal. We are happy to discuss future directions we believe to be promising with any interested researchers.
Visual Biochemistry: modular microfluidics enables kinetic insight from time-resolved cryo-EM
Authors: Mäeots Märt-Erik , Lee Byungjin , Nans Andrea , Jeong Seung-Geun , Esfahani Mohammad M. N. , Smith Daniel J. , Lee Chang-Soo , Lee Sung Sik , Peter Matthias , Enchev Radoslav I.
Published: March 2020

Mechanistic understanding of biochemical reactions requires structural and kinetic characterization of the underlying chemical processes. However, no single experimental technique can provide this information in a broadly applicable manner and thus structural studies of static macromolecules are often complemented by biophysical analysis. Moreover, the common strategy of utilizing mutants or crosslinking probes to stabilize otherwise short-lived reaction intermediates is prone to trapping off-pathway artefacts and precludes determining the order of molecular events. To overcome these limitations and allow visualisation of biochemical processes at near-atomic spatial resolution and millisecond time scales, we developed a time-resolved sample preparation method for cryo-electron microscopy (trEM). We integrated a modular microfluidic device, featuring a 3D-mixing unit and a delay line of variable length, with a gas-assisted nozzle and motorised plunge-freeze set-up that enables automated, fast, and blot-free sample vitrification. This sample preparation not only preserves high-resolution structural detail but also substantially improves protein distribution across the vitreous ice. We validated the method by examining the formation of RecA filaments on single-stranded DNA. We could reliably visualise reaction intermediates of early filament growth across three orders of magnitude on sub-second timescales. Quantification of the trEM data allowed us to characterize the kinetics of RecA filament growth. The trEM method reported here is versatile, easy to reproduce and thus readily adaptable to a broad spectrum of fundamental questions in biology.
CYP154C5 Regioselectivity in Steroid Hydroxylation Explored by Substrate and Protein Engineering
Authors: Bracco Paula , Wijma Hein J. , Nicolai Bastian , Rodriguez Buitrago Jhon Alexander , Klünemann Thomas , Vila Agustina , Schrepfer Patrick , Blankenfeldt Wulf , Janssen Dick B. , Schallmey Anett
Published: March 2020

CYP154C5 fromNocardia farcinicais a P450 monooxygenase able to hydroxylate a range of steroids with high regio- and stereoselectivity at the 16α-position. Using protein and substrate engineering based on the crystal structure of CYP154C5, an altered regioselectivity of the enzyme in steroid hydroxylation could be achieved. Thus, conversion of progesterone by mutant CYP154C5 F92A resulted in formation of the corresponding 21-hydroxylated product 11-deoxycorticosterone in addition to 16α-hydroxylation. Using MD simulation, this altered regioselectivity appeared to result from an alternate binding mode of the steroid in the active site of mutant F92A. MD simulation further suggested that water entrance to the active site caused higher uncoupling in this mutant. Moreover, exclusive 15α-hydroxylation was observed for wild-type CYP154C5 in the conversion of 5α-androstan-3-one, lacking an oxy-functional group at C17. Overall, our data give valuable insight into the structure-function relationship of this cytochrome P450 monooxygenase for steroid hydroxylation.
Superabsorbent crosslinked bacterial cellulose biomaterials for chronic wound dressings
Authors: Ciecholewska-Juśko Daria , Żywicka Anna , Junka Adam , Drozd Radosław , Sobolewski Peter , Migdał Paweł , Kowalska Urszula , Toporkiewicz Monika , Fijałkowski Karol
Published: March 2020

In this work, we present novelex situmodification of bacterial cellulose (BC) polymer, that significantly improves its ability to absorb water after drying. The method involves a single inexpensive and easy-to-perform process of BC crosslinking, using citric acid along with catalysts, such as disodium phosphate, sodium bicarbonate, ammonium bicarbonate or their mixtures. In particular, the mixture of disodium phosphate and sodium bicarbonate was the most promising, yielding significantly greater water capacity (over 5 times higher as compared to the unmodified BC) and slower water release (over 6 times as compared to the unmodified BC). Further, our optimized crosslinked BC had over 1.5x higher water capacity than modern commercial dressings dedicated to highly exuding wounds, while exhibiting no cytotoxic effects against fibroblast cell line L929in vitro. Therefore, our novel BC biomaterial may find application in super-absorbent dressings, designed for chronic wounds with imbalanced moisture level.
The neuroplasticity of division of labor: worker polymorphism, compound eye structure and brain organization in the leafcutter ant Atta cephalotes
Authors: Arganda Sara , Hoadley Andrew P. , Razdan Evan S. , Muratore Isabella B. , Traniello James F. A.
Published: March 2020

Our understanding of how the design of peripheral sensory structures is coupled with neural processing capacity to adaptively support division of labor is limited. Workers of the remarkably polymorphic fungus-growing ant Atta cephalotes are behaviorally specialized by size: the smallest workers (minims) tend fungi in dark subterranean chambers while larger workers perform tasks mainly outside the nest. These strong differences in worksite light conditions are predicted to influence sensory and processing requirements for vision. We found that eye structure and visual neuropils have been be selected to maximize task performance according to light availability. Minim eyes had few ommatidia, large interommatidial angles and eye parameter values, suggesting selection for visual sensitivity over acuity. Large workers had larger eyes with disproportionally more and larger ommatidia, and smaller interommatidial angles and eye parameter values, reflecting peripheral sensory adaptation to ambient rainforest light. Additionally, optic lobe and mushroom body collar volumes were disproportionately small in minims, and within the optic lobe, lamina and lobula relative volumes increased with worker size whereas the medulla decreased. Visual system phenotypes thus correspond to task specializations in dark or light environments and reflect a functional neuroplasticity underpinning division of labor in this socially complex agricultural ant.
Aerobic scope does matter in temperature-size rule, but only under optimal conditions
Authors: Walczyńska Aleksandra , Labecka Anna Maria , Sobczyk Mateusz
Published: March 2020

We united the theoretical predictions on the factors responsible for the occurrence and evolutionary significance of the temperature-size rule. We tested the causal connection among them assuming that (i) the temperature-size rule is the response to temperature-dependent oxygenic conditions, (ii) body size decrease is a consequence of cell shrinkage in response to exposure to hypoxia, (iii) this response enables to keep the wide scope for aerobic performance, and (iv) it prevents the decrease in fitness. We conducted our tests on three clones of the rotiferLecane inermiswith different thermal preferences. These clones were exposed to three experimental regimes: mild hypoxia, severe hypoxia driven by a too high temperature, and severe hypoxia driven by an inadequate oxygen concentration. The results showed that our causative reasoning was generally correct, but only under mildly hypoxic conditions. In more stressful environments, rotifers had clone- and condition-specific responses, which in fact were equally successful in terms of the levels of fitness. Our results join for the first time all factors connecting the cause and effect in the temperature-size rule. They indicate the importance of the conditions under which it should be tested. The most important messages from this study were that (i) a decrease in the body size was one of but not the only option for preventing fitness reduction under hypoxia, and (ii) such a response to higher temperature enabled the maintenance of wide aerobic scope in clone-specific, thermally optimal conditions.
Resolving the dynamics of photosynthetically produced ROS by high-resolution monitoring of chloroplastic EGSHinArabidopsis
Authors: Haber Zachary , Rosenwasser Shilo
Published: March 2020

Plants are naturally subjected to fluctuations in light intensity, causing unbalanced photosynthetic electron fluxes and overproduction of reactive oxygen species (ROS). While high rates of ROS production are harmful, moderate levels play a signaling role, coordinating photosynthetic activity and downstream metabolism. Here, we explore the dynamics of light-dependent oxidant production by high-temporal-resolution monitoring of chloroplastic glutathione redox potential (chl-EGSH) using chloroplast-targeted-roGFP2-expressingArabidopsislines, over several days, under dynamic environmental conditions and in correlation with PSII operating efficiency. Peaks in chl-EGSHoxidation during light-darkness transitions, when light harvesting is not balanced with downstream metabolism, were observed. Increasing light intensities triggered a binary oxidation response, with a threshold around the light saturating point, pointing for two regulated oxidative states of the chl-EGSH. These patterns were not affected innpq1plants which are impaired in non-photochemical quenching. Frequency-dependent oscillations between the two oxidation states were observed under fluctuating light in WT andnpq1plants, but not inpgr5plants, suggesting a role for PSI photoinhibition in regulation of oxidant production. Remarkably,pgr5plants showed an increase in chl-EGSHoxidation during the nights following light stresses, linking between day photoinhibition and night redox metabolism. This work provides a comprehensive view on the balance between photosynthesis-dependent ROS production and antioxidant activity during light acclimation.
Expanding the Coverage of the Metabolic Landscape in Cultivated Rice with Integrated Computational Approaches
Authors: Li Xuetong , Zhou Hongxia , Xiao Ning , Wu Xueting , Shan Yuanhong , Chen Longxian , Wang Cuiting , Wang Zixuan , Huang Jirong , Li Aihong , Li Xuan
Published: March 2020

Genome-scale metabolomics analysis is increasingly used for pathway and function discovery in post-genomics era. The great potential offered by developed mass spectrometry (MS)-based technology has been hindered by the obstacle that only a small portion of detected metabolites were identifiable so far. To address the critical issue of low identification coverage in metabolomics, we adopted a deep metabolomics analysis strategy by integrating advanced algorithms and expanded reference databases. The experimental reference spectra, andin silicoreference spectra were adopted to facilitate the structural annotation. To further characterize the structure of metabolites, two approaches, structural motif search combined with neutral loss scanning, and metabolite association network were incorporated into our strategy. An untargeted metabolomics analysis was performed on 150 rice cultivars using Ultra Performance Liquid Chromatography (UPLC)-Quadrupole (Q)-Orbitrap mass spectrometer. 1939 of 4491 metabolite features in MS/MS spectral tag (MS2T) library were annotated, representing an extension of annotation coverage by an order of magnitude on rice. The differential accumulation patterns of flavonoids betweenindicaandjaponicacultivars were revealed, especially O-sulfated flavonoids. A series of closely-related flavonolignans were characterized, adding further evidence for the crucial role of tricin-oligolignols in lignification. Our study provides a great template in the exploration of phytochemical diversity for more plant species.
A Computational Design of a Programmable Biological Processor
Authors: Moškon Miha , Pušnik Žiga , Magdevska Lidija , Zimic Nikolaj , Mraz Miha
Published: March 2020

Basic synthetic information processing structures, such as logic gates, oscillators and flip-flops, have already been implemented in living organisms. Current implementations of these structures are, however, hardly scalable and are yet to be extended to more complex processing structures that would constitute a biological computer.

Herein, we make a step forward towards the construction of a biological computer. We describe a model-based computational design of a biological processor, composed of an instruction memory containing a biological program, a program counter that is used to address this memory and a biological oscillator that triggers the execution of the next instruction in the memory. The described processor uses transcription and translation resources of the host cell to perform its operations and is able to sequentially execute a set of instructions written within the so-called instruction memory implemented with non-volatile DNA sequences. The addressing of the instruction memory is achieved with a biological implementation of the Johnson counter, which increases its state after an instruction is executed. We additionally describe the implementation of a biological compiler that compiles a sequence of human-readable instructions into ordinary differential equations-based models. These models can be used to simulate the dynamics of the proposed processor.

The proposed implementation presents the first programmable biological processor that exploits cellular resources to execute the specified instructions. We demonstrate the application of the proposed processor on a set of simple yet scalable biological programs. Biological descriptions of these programs can be written manually or can be generated automatically with the employment of the provided compiler.
Co-occurrence, habitat use and activity pattern of carnivore species in a coastal area of Argentina
Authors: Caruso N.C. , Luengos Vidal E.M. , Manfredi M.C. , Araujo M.S. , Lucherini M. , Casanave E.B.
Published: March 2020

Land-sea interface is an ecotone where the intersection of marine and terrestrial ecosystems create unique ecological conditions for terrestrial mobile species and freshwater-adapted organisms to exploit marine-derived food resources. Mammalian carnivores play an important role in almost any ecosystem where they live due to their top-down (or trophic cascade) effects on prey species and primary producers, thus structuring ecosystems along varied food-web pathways. We use camera trapping to study the patterns of coexistence, habitat use and activity pattern of carnivores species in a coastal area in southern Buenos Aires province, Argentina. We were able to detect five of the seven species of Mammalian carnivores being the Pampas foxLycalopex gymnocercusand Geoffroy’s catLeopardus geoffroyithe two most common. Geoffroy’s cat seems to use more intensively those areas close to the shoreline, while we found little support of it for Pampas fox; which seems to use more inland areas. Congruently, we found evidence of a lack of spatial and, to a lower extent, temporal avoidance between the two most common carnivore species of our study area. Our findings support those previous studies indicating that the coastal dunes have an important role in the conservation of the biodiversity of Buenos Aires province. Wildlife conservation is compatible with carefully-designed ecotourism and limited infrastructure development and this may be a unique chance for the areas of Buenos Aires coast that have not been affected yet by poorly planned, conservation-unfriendly urbanization.
mrMLM v4.0: An R Platform for Multi-locus Genome-wide Association Studies
Authors: Zhang Ya-Wen , Tamba Cox Lwaka , Wen Yang-Jun , Li Pei , Ren Wen-Long , Ni Yuan-Li , Gao Jun , Zhang Yuan-Ming
Published: March 2020

Previous studies reported that some important loci are missed in single-locus genome-wide association studies (GWAS), especially because of the large phenotypic error in field experiments. To solve this issue, multi-locus GWAS methods have been recommended. However, only a few software packages are available. Therefore, an R software mrMLM, which includes our six multi-locus methods, was developed. mrMLM includes three components: dataset input, parameter setting and result output. The fread function in data.table is used to quickly read datasets, especially big datasets, and the doParallel package is used to conduct parallel computation using multiple CPUs. In addition, the graphical user interface software mrMLM.GUI v4.0, built upon Shiny, is also available. To confirm the correctness of the above programs, the same simulation datasets as used in previous studies, along with three real datasets, were re-analyzed by all the methods in mrMLM v4.0 and three widely-used methods. The results confirmed the advantages of our multi-locus methods over the current methods. The conclusion is also consistent with those in a Research Topic in Frontiers in Plant Science. Although a less stringent significance threshold is adopted, the false positive rates are effectively controlled. mrMLM is publicly available athttps://cran.r-project.org/web/packages/mrMLM/index.htmlorhttps://bigd.big.ac.cn/biocode/tools/BT007077as an open-source software.
Open Science Datasets from PREVENT-AD, a Longitudinal Cohort of Pre-symptomatic Alzheimer’s Disease
Authors: Tremblay-Mercier Jennifer , Madjar Cécile , Das Samir , Binette Alexa Pichet , Dyke Stephanie O.M. , Étienne Pierre , Lafaille-Magnan Marie-Elyse , Remz Jordana , Bellec Pierre , Collins D. Louis , Rajah M. Natasha , Bohbot Veronique , Leoutsakos Jeannie-Marie , Iturria-Medina Yasser , Kat Justin , Hoge Richard D. , Gauthier Serge , Tardif Christine L. , Chakravarty M. Mallar , Poline Jean-Baptiste , Rosa-Neto Pedro , Evans Alan C. , Villeneuve Sylvia , Poirier Judes , Breitner John C. S. ,   the PREVENT-AD Research Group
Published: March 2020

To move Alzheimer Disease (AD) research forward it is essential to collect data from large cohorts, but also make such data available to the global research community. We describe the creation of an open science dataset from the PREVENT-AD (PResymptomatic EValuation of Experimental or Novel Treatments for AD) cohort, composed of cognitively unimpaired older individuals with a parental or multiple-sibling history of AD. From 2011 to 2017, 386 participants were enrolled (mean age 63 years old ± 5) for sustained investigation among whom 349 have retrospectively agreed to share their data openly. Repositories are findable through the unified interface of the Canadian Open Neuroscience Platform (https://portal.conp.ca/) and contain up to five years of longitudinal imaging data, cerebral fluid biochemistry, neurosensory capacities, cognitive, genetic, and medical information. Imaging data can be accessed openly athttps://openpreventad.loris.cawhile most of the other information, sensitive by nature, is accessible by qualified researchers athttps://registeredpreventad.loris.ca. In addition to being a living resource for continued data acquisition, PREVENT-AD offers opportunities to facilitate understanding of AD pathogenesis.
Thalamic activity patterns unfolding over multiple time scales predict seizure onset in absence epilepsy
Authors: Sorokin Jordan Michael , Williams Alex , Ganguli Surya , Huguenard John
Published: March 2020

The brain has a remarkable, yet poorly understood, capacity to perform rapid dynamic switching between different cognitive states. Absence epilepsy, characterized by sudden transitions to and from highly synchronous thalamocortical oscillations, provides a unique window to investigate rapid state switching. Here we explored the transition into seizures in detail using simultaneous extracellular unit recordings from the thalamocortical circuit in the Scn8a mouse, a validated murine model of absence epilepsy. We find that trial-averaged neural firing in the thalamus, but not cortex, was transiently elevated several seconds prior to seizure onset. However, we observed large single-trial variability in pre-ictal dynamics both within and across subjects, suggesting possible heterogeneous transition dynamics into absence seizures. To quantify the single-trial amplitude and temporal variability, we developed a statistical model, which revealed that individual seizures are preceded by low dimensional neural dynamics that vary in amplitude and time across seizures. Interestingly, the single-trial pre-seizure amplitude modulation uncovered by the model showed strong periodicity over trials, suggesting that pre-ictal dynamics may co-modulate with arousal state. To our knowledge, our results are the first characterization of single-unit pre-ictal firing dynamics across the thalamocortical circuit in absence epilepsy. Our results argue that seizure-monitoring devices may be able to capitalize on seizure-by-seizure changes in pre-ictal activity to better predict seizure onset, and that the thalamus may be a source of clinically useful pre-ictal signatures.
Asymmetric second-generation genomic incompatibility in interspecific crosses betweenCiona robustaandCiona intestinalis
Authors: Ohta Naoyuki , Kaplan Nicole , Ng James Tyler , Gravez Basile Jules , Christiaen Lionel
Published: March 2020

Reproductive isolation is central to speciation, but interspecific crosses between two closely related species can produce viable and fertile hybrids. Two different species in the tunicate genusCiona,Ciona robustaandCiona intestinaliscan produce hybrids. However, wild sympatric populations display limited gene flow, suggesting the existence of obstacles to interspecific reproduction that remain unknown. Here, we took advantage of a closed inland culture system to crossC. robustawithC. intestinalisand established F1 and F2 hybrids. We monitored post-embryonic development, survival, and sexual maturation to further probe the physiological mechanisms underlying reproductive isolation. Partial viability of first and second generation hybrids indicated that both pre- and postzygotic mechanisms contributed to genomic incompatibilities in hybrids. Asymmetrical second generation inviability and infertility suggested that interspecific genomic incompatibilities involved interactions between the maternal, zygotic and mitochondrial genomes during development. This study paves the way to quantitative genetic approaches to study the mechanisms underlying genomic incompatibilities and other complex traits in the genome-enabledCionamodel.
Genome-wide alterations of uracil distribution patterns in human DNA upon chemotherapeutic treatments
Authors: Pálinkás Hajnalka L. , Békési Angéla , Róna Gergely , Pongor Lőrinc , Tihanyi Gergely , Holub Eszter , Póti Ádám , Gemma Carolina , Ali Simak , Morten Michael J. , Rothenberg Eli , Pagano Michele , Szüts Dávid , Győrffy Balázs , Vértessy Beáta G.
Published: March 2020

Numerous anti-cancer drugs perturb thymidylate biosynthesis and lead to genomic uracil incorporation contributing to their antiproliferative effect. Still, it is not yet characterized if uracil incorporations have any positional preference. Here, we aimed to uncover genome-wide alterations in uracil pattern upon drug-treatment in human cancer cell-line HCT116. We developed a straightforward U-DNA sequencing method (U-DNA-Seq) that was combined within situsuper-resolution imaging. Using a novel robust analysis pipeline, we found broad regions with elevated probability of uracil occurrence both in treated and non-treated cells. Correlation with chromatin markers and other genomic features shows that non-treated cells possess uracil in the late replicating constitutive heterochromatic regions, while drug treatment induced a shift of incorporated uracil towards more active/functional segments. Data were corroborated by colocalization studies via dSTORM microscopy. This approach can also be applied to study the dynamicspatio-temporalnature of genomic uracil.
Addition of new neurons and the emergence of a local neural circuit for precise timing
Authors: Tupikov Yevhen , Jin Dezhe Z.
Published: March 2020

During development, neurons arrive at local brain areas in extended period of time, but how they form local neural circuits is unknown. Here we computationally model the emergence of a network for precise timing in the premotor nucleus HVC in songbird. We show that new motor projection neurons, mostly added to HVC before and during song learning, are recruited to the end of a growing feedforward network. High spontaneous activity of new neurons makes them the prime targets for recruitment in a self-organized process via synaptic plasticity. Once recruited, the new neurons fire readily at precise times, and they become mature. Neurons that are not recruited become silent and replaced by new immature neurons. Our model incorporates realistic HVC features such as interneurons, spatial distributions of neurons, and distributed axonal delays. The model predicts that the birth order of the projection neurons correlates with their burst timing during the song.

Significance Statement

Functions of local neural circuits depend on their specific network structures, but how the networks are wired is unknown. We show that such structures can emerge during development through a self-organized process, during which the network is wired by neuron-by-neuron recruitment. This growth is facilitated by steady supply of immature neurons, which are highly excitable and plastic. We suggest that neuron maturation dynamics is an integral part of constructing local neural circuits.
Lysine63-linked ubiquitin chains earmark GPCRs for BBSome-mediated removal from cilia
Authors: Shinde Swapnil Rohidas , Nager Andrew R. , Nachury Maxence V.
Published: March 2020

Regulated trafficking of G-protein coupled receptors (GPCRs) controls cilium-based signaling pathways. β-arrestin, a molecular sensor of activated GPCRs, and the BBSome, a complex of Bardet-Biedl Syndrome (BBS) proteins, are required for the signal-dependent exit of ciliary GPCRs but the functional interplay between β-arrestin and the BBSome remains elusive. Here we find that, upon activation, ciliary GPCRs become tagged with K63-linked ubiquitin (K63Ub) chains in a β-arrestin-dependent manner prior to BBSome-mediated exit. Removal of ubiquitin acceptor residues from the somatostatin receptor 3 (SSTR3) and from the orphan GPCR GPR161 demonstrates that ubiquitination of ciliary GPCRs is required for their regulated exit from cilia. Furthermore, targeting a K63Ub-specific deubiquitinase to cilia blocks the exit of GPR161, SSTR3 and Smoothened (SMO) from cilia. Finally, ubiquitinated proteins accumulate in cilia of mammalian photoreceptors andChlamydomonascells when BBSome function is compromised. We conclude that K63Ub chains mark GPCRs and other unwanted ciliary proteins for recognition by the ciliary exit machinery.
Histidine-Triad Hydrolases Provide Resistance to Peptide-Nucleotide Antibiotics
Authors: Yagmurov Eldar , Tsibulskaya Darya , Livenskyi Alexey , Serebryakova Marina , Wolf Yury I. , Borukhov Sergei , Severinov Konstantin , Dubiley Svetlana
Published: March 2020

TheEscherichia colimicrocin C (McC) and related compounds are potent Trojan-horse peptide-nucleotide antibiotics. The peptide part facilitates transport into sensitive cells. Inside the cell, the peptide part is degraded by non-specific peptidases releasing an aspartamide-adenylate containing a phosphoramide bond. This non-hydrolyzable compound inhibits aspartyl-tRNA synthetase. In addition to the efficient export of McC outside of the producing cells, special mechanisms evolved to avoid self-toxicity caused by the degradation of the peptide part inside the producers. Here, we report that histidine triad (HIT) hydrolases encoded in biosynthetic clusters of some McC homologs or by stand-alone genes confer resistance to McC–like compounds by hydrolyzing the phosphoramide bond in toxic aspartamide-adenosine, rendering them inactive.

IMPORTANCE

Uncovering the mechanisms of resistance is a required step for countering the looming antibiotic resistance crisis. In this communication, we show how universally conserved histidine triad hydrolases provide resistance to microcin C – a potent inhibitor of bacterial protein synthesis.
Polar Gini Curve: a Technique to Discover Single-cell Biomarker Using 2D Visual Information
Authors: Nguyen Thanh Minh , Jeevan Jacob John , Xu Nuo , Chen Jake
Published: March 2020

In this work, we design the Polar Gini Curve (PGC) technique, which combines the gene expression and the 2D embedded visual information to detect biomarkers from single-cell data. Theoretically, a Polar Gini Curve characterizes the shape and ‘evenness’ of cell-point distribution of cell-point set. To quantify whether a gene could be a marker in a cell cluster, we can combine two Polar Gini Curves: one drawn upon the cell-points expressing the gene, and the other drawn upon all cell-points in the cluster. We hypothesize that the closers these two curves are, the more likely the gene would be cluster markers. We demonstrate the framework in several simulation case-studies. Applying our framework in analyzing neonatal mouse heart single-cell data, the detected biomarkers may characterize novel subtypes of cardiac muscle cells. The source code and data for PGC could be found athttps://figshare.com/projects/Polar_Gini_Curve/76749.
Solanaceae specialized metabolism in a non-model plant: trichome acylinositol biosynthesis
Authors: Leong Bryan J. , Hurney Steven M. , Fiesel Paul D. , Moghe Gaurav D. , Jones A. Daniel , Last Robert L.
Published: March 2020

Plants make hundreds of thousands of biologically active specialized metabolites varying widely in structure, biosynthesis and the processes that they influence. An increasing number of these compounds are documented to protect plants from harmful insects, pathogens, or herbivores, or mediate interactions with beneficial organisms including pollinators and nitrogen fixing microbes. Acylsugars – one class of protective compounds – are made in glandular trichomes of plants across the Solanaceae family. While most described acylsugars are acylsucroses, published examples also include acylsugars with hexose cores. The South American fruit cropSolanum quitoense(Naranjilla) produces acylsugars that contain amyo-inositol core. We identified an enzyme that acetylates triacylinositols, a function homologous to the last step in theSolanum lycopersicumacylsucrose biosynthetic pathway. Our analysis reveals parallels betweenS. lycopersicumacylsucrose andS. quitoenseacylinositol biosynthesis, suggesting a common evolutionary origin.

Material availability

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Robert L. Last (lastr@msu.edu).

One sentence summary

Evidence that the final step inSolanum quitoenseacylinositol biosynthesis evolved from an acylsucrose acetyltransferase enzyme.
Alt-RPL36 downregulates the PI3K-AKT-mTOR signaling pathway by interacting with TMEM24
Authors: Cao Xiongwen , Khitun Alexandra , Luo Yang , Na Zhenkun , Phoodokmai Thitima , Sappakhaw Khomkrit , Olatunji Elizabeth , Uttamapinant Chayasith , Slavoff Sarah A.
Published: March 2020

Thousands of previously unannotated small and alternative open reading frames (alt-ORFs) have recently been revealed in the human genome, and hundreds are now known to be required for cell proliferation. Many alt-ORFs are co-encoded with proteins of known function in multicistronic human genes, but the functions of only a handful are currently known in molecular detail. Using a proteomic strategy for discovery of unannotated short open reading frames in human cells, we report the detection of alt-RPL36, a 148-amino acid protein co-encoded with and overlapping human RPL36 (ribosomal protein L36). Alt-RPL36 partially localizes to the endoplasmic reticulum, where it interacts with TMEM24, which transports the phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] precursor phosphatidylinositol from the endoplasmic reticulum to the plasma membrane. Knock-out of alt-RPL36 in HEK 293T cells increases PI(4,5)P2levels in the plasma membrane, upregulates the PI3K-AKT-mTOR signaling pathway, and increases cell size. Four serine residues of alt-RPL36 are phosphorylated, and mutation of these four serines to alanine abolishes interaction with TMEM24 and, consequently, abolishes alt-RPL36 effects on PI3K signaling and cell size. These results implicate alt-RPL36 as a novel regulator of PI(4,5)P2synthesis upstream of the PI3K-AKT-mTOR signaling pathway. More broadly, these results show that the alt-RPL36 transcript can express two sequence-independent polypeptides from overlapping ORFs that regulate the same process – protein synthesis – via different molecular mechanisms (PI3K signaling and ribosome composition), expanding our knowledge of the mechanisms by which multicistronic human genes function.
Identifying loci with different allele frequencies among cases of eight psychiatric disorders using CC-GWAS
Authors: Peyrot Wouter J. , Price Alkes L.
Published: March 2020

Psychiatric disorders are highly genetically correlated, and many studies have focused on their shared genetic components. However, little research has been conducted on the genetic differences between psychiatric disorders, because case-case comparisons of allele frequencies among cases currently require individual-level data from cases of both disorders. We developed a new method (CC-GWAS) to test for differences in allele frequency among cases of two different disorders using summary statistics from the respective case-control GWAS; CC-GWAS relies on analytical assessments of the genetic distance between cases and controls of each disorder. Simulations and analytical computations confirm that CC-GWAS is well-powered and attains effective control of type I error. In particular, CC-GWAS identifies and discards false positive associations that can arise due to differential tagging of a shared causal SNP (with the same allele frequency in cases of both disorders), e.g. due to subtle differences in ancestry between the input case-control studies. We applied CC-GWAS to publicly available summary statistics for schizophrenia, bipolar disorder and major depressive disorder, and identified 116 independent genome-wide significant loci distinguishing these three disorders, including 21 CC-GWAS-specific loci that were not genome-wide significant in the input case-control summary statistics. Two of the CC-GWAS-specific loci implicate the genesKLF6andKLF16from the Kruppel-like family of transcription factors; these genes have been linked to neurite outgrowth and axon regeneration. We performed a broader set of case-case comparisons by additionally analyzing ADHD, anorexia nervosa, autism, obsessive-compulsive disorder and Tourette’s Syndrome, yielding a total of 196 independent loci distinguishing eight psychiatric disorders, including 72 CC-GWAS-specific loci. We confirmed that loci identified by CC-GWAS replicated convincingly in applications to data sets for which independent replication data were available. In conclusion, CC-GWAS robustly identifies loci with different allele frequencies among cases of different disorders using results from the respective case-control GWAS, providing new insights into the genetic differences between eight psychiatric disorders.
SCA4 locus-associated gene Ronin (Thap11) increases Ataxin-1 protein levels and induces cerebellar degeneration in a mouse model of ataxia
Authors: Zwaka Thomas P. , Richman Ronald , Dejosez Marion
Published: March 2020

Spinocerebellar ataxias (SCAs) are a group of genetically heterogeneous inherited neurodegenerative disorders characterized by progressive ataxia and cerebellar degeneration. Here, we tested if Ronin (Thap11), a polyglutamine-containing protein encoded in a region on human chromosome 16q22.1 that has been genetically linked to SCA4, can be connected with SCA disease in a mouse model. We report that transgenic expression ofRoninin mouse cerebellar Purkinje cells leads not only histopathologically to detrimental loss of Purkinje cells but also phenotypically to the development of severe ataxia as early as 10-12 weeks after birth. Mechanistically, we find that Ronin is part of a protein complex in the cerebellum that is distinct from the one previously found in embryonic stem cells. Importantly, ectopically expressedRoninraises the protein level of Ataxin-1 (Atxn1), the causative gene of the most common type of SCA, SCA1. Hence, our data provide evidence for a link between Ronin and SCAs, and also suggest that Ronin may be involved in the development of other neurodegenerative diseases.
Lipid membrane templated misfolding and self-assembly of intrinsically disordered tau protein
Authors: Majewski Jaroslaw , Jones Emmalee M. , Vander Zanden Crystal M. , Biernat Jacek , Mandelkow Eckhard , Chi Eva Y.
Published: March 2020

The aggregation of the intrinsically disordered tau protein into highly ordered β-sheet fibrils is implicated in many neurodegenerative disorders. Fibrillation mechanism remains unresolved, particularly early events that trigger tau misfolding and assembly. We investigated the role membrane plays in modulating aggregation of three tau variants, the largest isoform hTau40, the truncated construct K18, and a hyperphosphorylation mutant hTau40/3Epi. Despite being charged and soluble, tau proteins were also highly surface active and favorably interacted with anionic, but not zwitterionic, lipid monolayer at the air/water interface. Membrane binding induced macroscopic tau phase separation and β-sheet-rich tau oligomer formation. Concomitantly, membrane morphology and lipid packing became disrupted. Our findings support a general tau aggregation mechanism wherein tau’s inherent surface activity and favorable electrostatic interactions drive tau-membrane association, inducing tau phase separation that is accompanied by misfolding and self-assembly of disordered tau into β-sheet-rich oligomers, which subsequently seed fibrillation and deposition into diseased tissues.
Path integration error and adaptable search behaviors in a mantis shrimp
Authors: Patel Rickesh N. , Cronin Thomas W.
Published: March 2020

Mantis shrimp of the speciesNeogonodactylus oerstediioccupy small burrows in shallow waters throughout the Caribbean. These animals use path integration, a vector-based navigation strategy, to return to their homes while foraging. Here we report that path integration inN. oerstediiis prone to error accumulated during outward foraging paths and we describe the search behavior thatN. oerstediiemploys after it fails to locate its home following the route provided by its path integrator. This search behavior forms continuously expanding, non-oriented loops that are centered near the point of search initiation. The radius of this search is apparently scaled to the animal’s accumulated error during path integration, improving the effectiveness of the search. The search behaviors exhibited byN. oerstediibear a striking resemblance to search behaviors in other animals, offering potential avenues for the comparative examination of search behaviors and how they are optimized in disparate taxa.

Summary Statement

Mantis shrimp use path integration, an error-prone navigational strategy, when travelling home. When path integration fails, mantis shrimp employ a stereotyped yet flexible search pattern to locate their homes.