bluuebunny/crossref_metadata_2025 huggingface dataset:
Loss of function from widely distributed, synonymous mutations at single codons
Authors: Gupta Kritika , Prabha Jyothi , Chandra Soumyanetra , Khare Shruti , Mohan Sonali Vishwa , Kohli Pehu , Asok Aparna , Gowda Harsha , Ramesh Arati , Varadarajan Raghavan
Published: July 2019

Mutational tolerance inferred from laboratory-based mutational studies is typically much higher than observed natural sequence variation. Using saturation mutagenesis, we show that the ccdA antitoxin component of the ccdAB toxin-antitoxin system is unusually sensitive to mutation with over 60% of mutations leading to loss of function. Multi-base synonymous mutations at a codon display enhanced propensity to show altered phenotypes, relative to single-base ones. Such mutations modulate RNA structure, leading to altered relative translation efficiencies of the two genes in the operon, and a CcdA:CcdB protein ratio below one. These insights were used to predict and experimentally validate synonymous mutations that lead to loss of function in the unrelated relBE operon as well as the lacZ gene. Thus, synonymous mutations can have significant phenotypic effects, in the absence of overexpression or extraneous reporters. More generally, proteins are likely more sensitive to mutation than inferred from previous saturation mutagenesis studies.
Loss of adaptive capacity in asthmatics revealed by biomarker fluctuation dynamics upon experimental rhinovirus challenge
Authors: Sinha Anirban , Lutter René , Xu Binbin , Dekker Tamara , Dierdorp Barbara , Sterk Peter J. , Frey Urs , Delgado-Eckert Edgar
Published: July 2019

Asthma is a dynamic disease, in which lung mechanical and inflammatory processes often interact in a complex, unpredictable manner. We hypothesize that this may be explained by respiratory disease-related systems instability and loss of adaptability to changing environmental conditions, resulting in highly fluctuating biomarkers and symptoms. Using time series of inflammatory (eosinophils, neutrophils, FeNO), clinical and lung function biomarkers (PEF, FVC, and FEV1), we estimated this loss of adaptive capacity (AC) during an experimental perturbation with a rhinovirus in 24 healthy and asthmatic volunteers. Loss of AC was estimated by comparing similarities between pre- and post-challenge time series. Unlike healthy participants, the asthmatic’s post-viral-challenge state resembled significantly more other rhinovirus-infected asthmatics than their own pre-viral-challenge state (hypergeometric-test: p=0.029). This reveals loss of AC, and supports the novel concept that not only single physiological mechanisms, but interacting dynamic disease properties are altered in asthma and contribute to a more vulnerable phenotype.
CNN explains tuning properties of anterior, but not middle, face-processing areas in macaque IT
Authors: Raman Rajani , Hosoya Haruo
Published: July 2019

Recent computational studies have emphasized layer-wise quantitative similarity between convolutional neural networks (CNNs) and the primate visual ventral stream. However, whether such similarity holds for the face-selective areas, a subsystem of the higher visual cortex, is not clear. Here, we extensively investigate whether CNNs exhibit tuning properties as previously observed in different macaque face areas. While simulating four past experiments on a variety of CNN models, we sought for the model layer that quantitatively matches the multiple tuning properties of each face area. Our results show that higher model layers explain reasonably well the properties of anterior areas, while no layer simultaneously explains the properties of middle areas, consistently across the model variation. Thus, some similarity may exist between CNNs and the primate face-processing system in the near-goal representation, but much less clearly in the intermediate stages, thus giving motivation for a more comprehensive model for understanding the entire system.
Cryptic role of tetrathionate in the sulfur cycle: A study from Arabian Sea oxygen minimum zone sediments
Authors: Mandal Subhrangshu , Bhattacharya Sabyasachi , Roy Chayan , Rameez Moidu Jameela , Sarkar Jagannath , Fernandes Svetlana , Mapder Tarunendu , Peketi Aditya , Mazumdar Aninda , Ghosh Wriddhiman
Published: July 2019

To explore the potential role of tetrathionate in the sulfur cycle of marine sediments, the population ecology of tetrathionate-forming, oxidizing, and respiring microorganisms was revealed at 15-30 cm resolution along two, ∼3-m-long, cores collected from 530- and 580-mbsl water-depths of Arabian Sea, off India’s west coast, within the oxygen minimum zone (OMZ). Metagenome analysis along the two sediment-cores revealed widespread occurrence of the structural genes that govern these metabolisms; high diversity and relative-abundance was also detected for the bacteria known to render these processes. Slurry-incubation of the sediment-samples, pure-culture isolation, and metatranscriptome analysis, corroborated thein situfunctionality of all the three metabolic-types. Geochemical analyses revealed thiosulfate (0-11.1 μM), pyrite (0.05-1.09 wt %), iron (9232-17234 ppm) and manganese (71-172 ppm) along the two sediment-cores. Pyrites (via abiotic reaction with MnO2) and thiosulfate (via oxidation by chemolithotrophic bacteria prevalentin situ) are apparently the main sources of tetrathionate in this ecosystem. Tetrathionate, in turn, can be either converted to sulfate (via oxidation by the chemolithotrophs present) or reduced back to thiosulfate (via respiration by native bacteria); 0-2.01 mM sulfide present in the sediment-cores may also reduce tetrathionate abiotically to thiosulfate and elemental sulfur. Notably tetrathionate was not detectedin situ- high microbiological and geochemical reactivity of this polythionate is apparently instrumental in the cryptic nature of its potential role as a central sulfur cycle intermediate. Biogeochemical roles of this polythionate, albeit revealed here in the context of OMZ sediments, may well extend to the sulfur cycles of other geomicrobiologically-distinct marine sediment horizons.
Deficiency in Bhlhe40 impairs resistance toH. polygyrus bakeriand reveals novel Csf2rb-dependent regulation of anti-helminth immunity
Authors: Jarjour Nicholas N. , Bradstreet Tara R. , Schwarzkopf Elizabeth A. , Cook Melissa E. , Lai Chin-Wen , Huang Stanley Ching-Cheng , Taneja Reshma , Stappenbeck Thaddeus S. , Van Dyken Steven J. , Urban Joseph F. , Edelson Brian T.
Published: July 2019

The cytokines GM-CSF and IL-5 are thought to possess largely divergent functions despite a shared dependence on the common beta (βC) chain to initiate signaling. Although IL-5 is part of the core type 2 cytokine signature and is required for protection against some helminths, it is dispensable for immunity to others, such asHeligmosomoides polygyrus bakeri(H. polygyrus). Whether this is due to compensatory mechanisms is unclear. The transcription factor Bhlhe40 has been shown to control GM-CSF production and is proposed to be a novel regulator of T helper type 2 cells. We have found that Bhlhe40 is required in T cells for a protective memory response to secondaryH. polygyrusinfection.H. polygyrusrechallenge elicited dramatic Bhlhe40-dependent changes in gene and cytokine expression by lamina propria CD4+T cells andin vitro-polarized TH2 cells, including induction of GM-CSF and maximal production of type 2 cytokines including IL-5. βCchain-deficient, but not GM-CSF-deficient, mice rechallenged withH. polygyrushad severely impaired protective immunity. Our results demonstrate that Bhlhe40 is an essential regulator of TH2 cell immunity during helminth infection and reveal unexpected redundancy of βCchain-dependent cytokines.
The environment selects: Modeling energy allocation in microbial communities under dynamic environments
Authors: da Silva Leonor Guedes , Tomás-Martínez Sergio , van Loosdrecht Mark C.M. , Wahl S. Aljoscha
Published: July 2019

What will be the best metabolic strategy in a competitive environment where oxygen is periodically unavailable? A few decades ago, an accidental, man-made cyclic anaerobic/aerobic environment selected for Polyphosphate Accumulating Organisms (PAOs) and this strategy is now widely used to allow for Enhanced Biological Phosphorus Removal (EBPR) of wastewater. But could it have been predicted? Here, a dynamic resource allocation modeling formalism was used to analyze the impact of selection pressures on metabolic function. With the same meta-network but modified selective pressures, different successful strategies can be predicted: Polyphosphate-AOs, Glycogen-AOs, Polyhydroxyalkanoate-AOs, and regular aerobic heterotrophs. The results demonstrate how storage metabolism allows for different trade-offs between growth yield, robustness, and competitiveness, and highlight how each metabolic function is an important determining factor for a selective advantage in a given environment. This can be seen as an example of when “Unity in biochemistry” by A.Kluyver meets “Everything is everywhere, but the environment selects” by B.Becking and how microbial ecosystems may be described by the energy allocation phenotype instead of a detailed description of each organism.
Oomycete small RNAs invade the plant RNA-induced silencing complex for virulence
Authors: Dunker Florian , Trutzenberg Adriana , Rothenpieler Jan Samuel , Kuhn Sarah , Pröls Reinhard , Schreiber Tom , Tissier Alain , Hückelhoven Ralph , Weiberg Arne
Published: July 2019

Fungal small RNAs (sRNAs) hijack the plant RNA silencing pathway to manipulate host gene expression, named cross-kingdom RNA interference (ckRNAi). It is currently unknown how conserved and significant ckRNAi is for microbial virulence. Here, we found for the first time that sRNAs of a pathogen representing the oomycete kingdom invade the host plant’s Argonaute (AGO)/RNA-induced silencing complex. To demonstrate the functionality of the plant-invading oomycete Hyaloperonospora arabidopsidis sRNAs (HpasRNAs), we designed a novel CRISPR endoribonuclease Csy4/GUS repressor reporter to visualize in situ pathogen-induced target suppression in Arabidopsis thaliana host plant. By using 5’ RACE-PCR we demonstrated HpasRNAs-directed cleavage of plant mRNAs. The significant role of HpasRNAs together with AtAGO1 in virulence was demonstrated by plant atago1 mutants and by transgenic Arabidopsis expressing a target mimic to block HpasRNAs, that both exhibited enhanced resistance. Individual HpasRNA plant targets contributed to host immunity, as Arabidopsis gene knockout or HpasRNA-resistant gene versions exhibited quantitative enhanced or reduced susceptibility, respectively. Together with previous reports, we found that ckRNAi is conserved among oomycete and fungal pathogens.
Effects of unilateral cortical resection of the visual cortex on bilateral human white matter
Authors: Maallo Anne Margarette S. , Freud Erez , Liu Tina Tong , Patterson Christina , Behrmann Marlene
Published: July 2019

Children with unilateral resections of ventral occipito-temporal cortex (VOTC) typically do not evince visual perceptual impairments, even when relatively large swathes of VOTC are resected. In search of possible explanations for this behavioral competence, we evaluated white matter microstructure and connectivity in eight pediatric epilepsy patients following unilateral cortical resection and 15 age-matched controls. To uncover both local and broader resection-induced effects, we analyzed tractography data using two complementary approaches. First, the microstructural properties were measured in the inferior longitudinal and the inferior fronto-occipital fasciculi, the major VOTC association tracts. Group differences were only evident in the ipsilesional, and not in the contralesional, hemisphere, and single-subject analyses revealed that these differences were limited to the site of the resection. Second, graph theory was used to characterize the connectivity of the contralesional occipito-temporal regions. There were no changes to the network properties in patients with left VOTC resections nor in patients with resections outside the VOTC, but altered network efficiency was observed in two cases with right VOTC resections. These results suggest that, in many, although perhaps not all, cases of unilateral VOTC resections in childhood, the white matter integrity in the preserved contralesional hemisphere along with residual neural activity might be sufficient for normal visual perception.

Highlights

There is well-circumscribed white matter damage in pediatric epilepsy after surgery

White matter pathways are normal distal as well as contralesional to the resection

Contralesional network properties differ after left or right hemisphere resection

Preserved cortex and white matter may be sufficient for normal perception
Dynamics and Topology of Human Transcribed Cis-regulatory Elements
Authors: Hirabayashi Shigeki , Bhagat Shruti , Matsuki Yu , Takegami Yujiro , Uehata Takuya , Kanemaru Ai , Itoh Masayoshi , Shirakawa Kotaro , Takaori-Kondo Akifumi , Takeuchi Osamu , Carninci Piero , Katayama Shintaro , Hayashizaki Yoshihide , Kere Juha , Kawaji Hideya , Murakawa Yasuhiro
Published: July 2019

Promoters and enhancers are key cis-regulatory elements, but how they orchestrate to generate cell-type-specific transcriptomes remains elusive. We developed a simple and robust approach to globally determine 5’-ends of nascent RNAs (NET-CAGE) in diverse cells and tissues, thereby sensitively detecting unstable transcripts including enhancer-derived RNAs. We studied RNA synthesis and degradation at the transcription start site level, uncovering the impact of differential promoter usage on transcript stability. We quantified transcription from cis-regulatory elements without influence of RNA turnover, and identified enhancer-promoter pairs which were simultaneously activated upon cellular stimulation. By integrating NET-CAGE data with chromatin interaction maps, we revealed that cis-regulatory elements are topologically connected according to their cell-type specificity. We discovered new enhancers with high sensitivity, and delineated primary locations of transcription within super-enhancers. Our collection of NET-CAGE data from human and mouse significantly expanded the FANTOM5 catalogue of transcribed enhancers, with broad applicability to biomedical research. (148 words)
Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models
Authors: Hadadi Noushin , Pandey Vikash , Chiappino-Pepe Anush , Morales Marian , Gallart-Ayala Hector , Mehl Florence , Ivanisevic Julijana , Sentchilo Vladimir , van der Meer Jan R.
Published: July 2019

Understanding the adaptive responses of individual bacterial strains is crucial for microbiome engineering approaches that introduce new functionalities into complex microbiomes, such as xenobiotic compound metabolism for soil bioremediation. Adaptation requires metabolic reprogramming of the cell, which can be captured by multi-omics, but this data remains formidably challenging to interpret and predict. Here we present a new approach that combines genome-scale metabolic modeling with transcriptomics and exometabolomics, both of which are common tools for studying dynamic population behavior. As a realistic demonstration, we developed a genome-scale model of Pseudomonas veronii 1YdBTEX2, a candidate bioaugmentation agent for accelerated metabolism of mono-aromatic compounds in soil microbiomes, while simultaneously collecting experimental data of P. veronii metabolism during growth phase transitions. Predictions of the P. veronii growth rates and specific metabolic processes from the integrated model closely matched experimental observations. We conclude that integrative and network-based analysis can help build predictive models that accurately capture bacterial adaptation responses. Further development and testing of such models may considerably improve the successful establishment of bacterial inoculants in more complex systems.
Meiotic drive reduces egg-to-adult viability in stalk-eyed flies
Authors: Finnegan Sam Ronan , White Nathan Joseph , Koh Dixon , Camus M. Florencia , Fowler Kevin , Pomiankowski Andrew
Published: July 2019

SR meiotic drive is a selfish genetic element located on the X chromosome in a number of species that causes dysfunction of Y-bearing sperm. SR is transmitted to up to 100% of offspring, causing extreme sex ratio bias. SR in several species is found in a stable polymorphism at a moderate frequency, suggesting there must be strong frequency-dependent selection resisting its spread. We investigate the effect of SR on female and male egg-to-adult viability in the Malaysian stalk-eyed fly,Teleopsis dalmanni. SR meiotic drive in this species is old, and appears to be broadly stable at a moderate (~20%) frequency. We use large-scale controlled crosses to estimate the strength of selection acting against SR in female and male carriers. We find that SR reduces the egg-to-adult viability of both sexes. In females, homozygous females experience greater reduction in viability (sf= 0.242) and the deleterious effects of SR are additive (ℎ = 0.511). The male deficit in viability (sm= 0.214) is not different from that in homozygous females. The evidence does not support the expectation that deleterious side-effects of SR are recessive or sex-limited. We discuss how these reductions in egg-to-adult survival, as well as other forms of selection acting on SR, act to maintain SR polymorphism in this species.
Stimulus-Locked Responses on Human Upper Limb Muscles and Corrective Reaches are Preferentially Evoked by Low Spatial Frequencies
Authors: Kozak Rebecca A. , Kreyenmeier Philipp , Gu Chao , Johnston Kevin , Corneil Brian D.
Published: July 2019

In situations requiring immediate action, humans can generate visually-guided responses at remarkably short latencies. Here, to better understand the visual attributes that best evoke such rapid responses, we recorded upper limb muscle activity while participants performed visually-guided reaches towards Gabor patches composed of differing spatial frequencies. We studied reaches initiated from a stable posture (experiment 1, a static condition), or during on-line reach corrections to an abruptly displaced target (experiment 2, a dynamic condition). In both experiments, we detail the latency and prevalence of stimulus-locked responses (SLRs), which are brief bursts of EMG activity that are time-locked to target presentation rather than movement onset. SLRs represent the first wave of EMG recruitment influenced by target presentation, and enable quantification of rapid visuomotor transformations. In both experiments, reach targets composed of low spatial frequencies elicited the shortest latency and most prevalent SLRs, with SLR latency increasing and SLR prevalence decreasing for reach targets composed of progressively higher spatial frequencies. SLRs could be evoked in either the static or dynamic condition, and when present in experiment 2, were associated with shorter latency and larger magnitude corrections. Furthermore, SLRs evolved at shorter latencies (~20 ms) when the arm was already in motion. These results demonstrate that stimuli composed of low spatial frequencies preferentially evoke the most rapid visuomotor responses which, in the context of rapidly correcting an on-going reaching movement, are associated with earlier and larger on-line reach corrections.

Significance Statement

Humans have a remarkable capacity to respond quickly to changes in our visual environment. Although our visual world is composed of a range of spatial frequencies, surprisingly little is known about which frequencies preferentially evoke rapid reaching responses. Here, we systematically varied the spatial frequency of peripheral reach targets while measuring EMG activity on an upper limb muscle. We found that visual stimuli composed of low-spatial frequencies elicit the most rapid and robust EMG responses and corrective reaches. Thus, when time is of the essence, low spatial frequencies preferentially drive fast visuomotor responses.
Molecular Profiling to Infer Neuronal Cell Identity: Lessons from small ganglia of the Crab Cancer borealis
Authors: Northcutt Adam J. , Kick Daniel R. , Otopalik Adriane G. , Goetz Benjamin M. , Harris Rayna M. , Santin Joseph M. , Hofmann Hans A. , Marder Eve , Schulz David J.
Published: July 2019

Understanding circuit organization depends on identification of cell types. Recent advances in transcriptional profiling methods have enabled classification of cell types by their gene expression. While exceptionally powerful and high throughput, the ground-truth validation of these methods is difficult: if cell type is unknown, how does one assess whether a given analysis accurately captures neuronal identity? To shed light on the capabilities and limitations of solely using transcriptional profiling for cell type classification, we performed two forms of transcriptional profiling – RNA-seq and quantitative RT-PCR, in single, unambiguously identified neurons from two small crustacean networks: the stomatogastric and cardiac ganglia. We then combined our knowledge of cell type with unbiased clustering analyses and supervised machine learning to determine how accurately functionally-defined neuron types can be classified by expression profile alone. Our results demonstrate that expression profile is able to capture neuronal identity most accurately when combined with multimodal information that allows for post-hoc grouping so analysis can proceed from a supervised perspective. Solely unsupervised clustering can lead to misidentification and an inability to distinguish between two or more cell types. Therefore, our study supports the general utility of cell identification by transcriptional profiling, but adds a caution: it is difficult or impossible to know under what conditions transcriptional profiling alone is capable of assigning cell identity. Only by combining multiple modalities of information such as physiology, morphology or innervation target can neuronal identity be unambiguously determined.

SIGNIFICANCE STATEMENT

Single cell transcriptional profiling has become a widespread tool in cell identification, particularly in the nervous system, based on the notion that genomic information determines cell identity. However, many cell type classification studies are unconstrained by other cellular attributes (e.g., morphology, physiology). Here, we systematically test how accurately transcriptional profiling can assign cell identity to well-studied anatomically- and functionally-identified neurons in two small neuronal networks. While these neurons clearly possess distinct patterns of gene expression across cell types, their expression profiles are not sufficient to unambiguously confirm their identity. We suggest that true cell identity can only be determined by combining gene expression data with other cellular attributes such as innervation pattern, morphology, or physiology.
Altitude and life-history shape the evolution ofHeliconiuswings
Authors: Montejo-Kovacevich Gabriela , Smith Jennifer E. , Meier Joana I. , Bacquet Caroline N. , Whiltshire-Romero Eva , Nadeau Nicola J. , Jiggins Chris D.
Published: July 2019

Phenotypic divergence between closely related species has long interested biologists. Taxa that inhabit a range of environments and have known and diverse, natural histories, can help understand how different selection pressures shape diverging traits. In butterflies, wing colour patterns have been extensively studied, whereas wing shape diversity is less well understood despite its importance for flight. Here we study a measure of wing shape, aspect ratio, and wing size in a large dataset of over 3200 individuals, representing 13Heliconiusspecies, from across the Neotropics. We assess the relative importance of phylogenetic relatedness, natural history and habitat in determining wing shape and size. We find that both larval and adult behavioural ecology affect patterns of adult size dimorphisms. On one hand, species with solitary larvae have larger adult males, in contrast to gregariousHeliconiusspecies, and indeed most Lepidoptera. On the other hand, species in the pupal-mating clade are smaller overall than those in the adult-mating clade. Interestingly, while controlling for phylogeny, sex ratios and allometry, we find that species inhabiting higher altitudes have rounder wings and, in one of the two majorHeliconiusclades, are also bigger in size than their lowland relatives. Thus, we reveal novel adaptive wing morphological divergence amongHeliconiusspecies beyond that imposed by natural selection on aposematic wing colouration. Our study highlights the value of phylogenetic comparative methods in study systems that have diverse and well-studied natural histories to disentangle the selection pressures shaping adaptive phenotypes.
Loss of cyclin A2 in murine colonic epithelial cells disrupts colon homeostasis by triggering DNA damage and dysplasia and high cyclin A2 expression is a good-prognosis factor in patients with colorectal cancer
Authors: Guo Yuchen , Gabola Monica , Lattanzio Rossano , Paul Conception , Pinet Valérie , Tang Ruizhi , Tulari Hulya , Bremond Julie , Maurizy Chloé , Da Costa Quentin , Finetti Pascal , Boissière-Michot Florence , Lemmers Céline , Garnier Séverine , Bertucci François , Azar Rania , Blanchard Jean-Marie , Sicinski Piotr , Mamessier Emilie , Lemmers Bénédicte , Hahne Michael
Published: July 2019

To clarify the function of cyclin A2 in colon homeostasis and colorectal cancer (CRC) we generated mice deficient for cyclin A2 in colonic epithelial cells (CEC). Colons of those mice displayed architectural changes in the mucosa, and signs of inflammation as well as an increased proliferation of CEC associated with the appearance of low- and high-grade dysplasia. The main initial events triggering those alterations in cyclin A2 deficient CEC appear to be abnormal mitoses and DNA damage. Cyclin A2 deletion in CEC promoted the development of dysplasia and adenocarcinomas in the murine colitis-associated cancer model. We next explored the status of cyclin A2 expression in clinical CRC samples at the mRNA and protein level and found higher expression in tumors of stage I and II patients compared to those of stage III and IV. A meta-analysis of 11 transcriptome datasets comprising 2,239 primary CRC tumors displayed differentCCNA2(the mRNA coding for cyclin A2) expression levels among the CRC tumor subtypes with highest in CMS1 and lowest in CMS4. Moreover, high expression ofCCNA2was found to be a good prognosis factor independently from other prognostic factors for the CMS1, CMS3 and CMS4 subtypes.
Histone H2AK119 Mono-Ubiquitination is Essential for Polycomb-Mediated Transcriptional Repression
Authors: Tamburri Simone , Lavarone Elisa , Fernández-Pérez Daniel , Zanotti Marika , Manganaro Daria , Conway Eric , Pasini Diego
Published: July 2019

The major function of Polycomb group proteins (PcG) is to maintain transcriptional repression to preserve cellular identity. This is exerted by two distinct repressive complexes, PRC1 and PRC2, that modify histones by depositing H2AK119ub1 and H3K27me3, respectively. Both complexes are essential for development and are deregulated in several types of human tumors. PRC1 and PRC2 exist in different variants and show a complex regulatory cross-talk. However, the contribution that H2AK119ub1 plays in mediating PcG repressive functions remains largely controversial. Coupling an inducible system with the expression of a fully catalytic inactive RING1B mutant, we demonstrated that H2AK119ub1 deposition is essential to maintain PcG-target genes repressed in ESC. Loss of H2AK119ub1 induced a rapid displacement of PRC2 activity and a loss of H3K27me3 deposition. This affected both PRC2.1 and PRC2.2 variants and further correlated with a strong displacement and destabilization of canonical PRC1. Finally, we find that variant PRC1 forms can sense H2AK119ub1 deposition, which contributes to their stabilization specifically at sites where this modification is highly enriched. Overall our data place H2AK119ub1 deposition as central hub that mount PcG repressive machineries to preserve cell transcriptional identity.
Leveraging genome-enabled growth models to study shoot growth responses to water deficit in rice
Authors: Campbell Malachy , Grondin Alexandre , Walia Harkamal , Morota Gota
Published: July 2019

Elucidating genotype-by-environment interactions (G×E) and partitioning its contribution to the phenotypic variation remains a long standing challenge for plant scientists. Recent quantitative genetic frameworks have improved predictions of G× E responses. However, these models do not explicitly consider the processes that give rise to G×E. To overcome this limitation, we propose a novel framework to elucidate the genetic basis of dynamic shoot growth trajectories under contrasting water regimes using genome-wide markers to model genotype-specific shoot growth trajectories as a function of soil water availability. A rice diversity panel was phenotyped daily over a period of twenty-one days during the early vegetative stage using an automated, high-throughput image-based, phenotyping platform that enabled us to estimate daily shoot biomass and soil water content. Using these data, we modeled shoot growth as a function of time and soil water content, and were able to determine the soil water content and/or time point where an inflection in the growth trajectory occurred. We found that larger, more vigorous plants tend to exhibit an earlier repression in growth compared to smaller, slow growing plants, indicating a potential trade off between early vigor and tolerance to prolonged water deficits. We integrated the growth model within a hierarchical Bayesian framework and used marker information to estimate model parameters and the associated loci through genome-wide association analysis. Genomic inference for model parameters and time of inflection (TOI) identified several candidate genes. Among them an aquaporin,OsPIP1;1was identified as a candidate for time of inflection under drought and showed significantly lower expression in accessions exhibiting later TOI in drought. This study is the first to utilize a genome-enabled growth model to study drought responses in rice, and presents a new approach to jointly model dynamic morpho-physiological responses and environmental covariates.
Generalist Eimeria species in rodents: multilocus analyses indicate inadequate resolution of established markers
Authors: Jarquín-Díaz Víctor Hugo , Balard Alice , Mácová Anna , Jost Jenny , Roth von Szepesbéla Tabea , Berktold Karin , Tank Steffen , Kvičerová Jana , Heitlinger Emanuel
Published: July 2019

Intracellular parasites of the genus Eimeria are described as tissue/host specific. Phylogenetic classification of rodent Eimeria suggested that some species have a broader host range than previously assumed. We explore if Eimeria spp. infecting house mice are misclassified by the most widely used molecular markers due to a lack of resolution, or if, instead, these parasite species are indeed infecting multiple host species.

With the commonly used markers (18S/COI), we recovered monophyletic clades of E. falciformis and E. vermiformis from Mus that included E. apionodes identified in other rodent host species (Apodemus spp., Myodes glareolus, and Microtus arvalis). A lack of internal resolution in these clades could suggest the existence of a species complex with a wide host range infecting murid and cricetid rodents. We question, however, the power of COI and 18S markers to provide adequate resolution for assessing host specificity. In addition to the rarely used marker ORF470 from the apicoplast genome, we present multilocus genotyping as an alternative approach. Phylogenetic analysis of 35 nuclear markers differentiated E. falciformis from house mice from isolates from Apodemus hosts. Isolates of E. vermiformis from Mus are still found in clusters interleaved with non-Mus isolates, even with this high resolution data.

In conclusion, we show that species-level resolution should not be assumed for COI and 18S markers in Coccidia. Host-parasite co-speciation at shallow phylogenetic nodes, as well as contemporary coccidian host ranges more generally, are still open questions that need to be addressed using novel genetic markers with higher resolution.
Steady-state responses in the somatosensory system interact with endogenous beta activity
Authors: Wälti Michel J. , Bächinger Marc , Ruddy Kathy L. , Wenderoth Nicole
Published: July 2019

Brain oscillations have been related to many aspects of human behavior. To understand a potential causal relationship, it is of great importance to develop methods for modulating ongoing neural activity. It has been shown that external rhythmic stimulation leads to an oscillatory brain response that follows the temporal structure of the presented stimulus and is assumed to reflect the synchronization of ongoing neural oscillations with the stimulation rhythm. This interaction between individual brain activity and so called steady-state evoked potentials (SSEPs) is the fundamental requirement of neural entrainment. Here, we investigate whether neural responses to rhythmic vibrotactile stimulation, measured with EEG, are dependent on ongoing individual brain oscillations, and therefore reflect entrained oscillatory activity. For this, we measured phase synchronization in response to rhythmic stimulation across various frequencies in the alpha and beta band. Three different stimulation intensities were applied for each frequency relative to the individual sensory threshold. We found that a higher stimulation intensity, compared to lower intensities, resulted in a more pronounced phase synchronization with the stimulation signal. Moreover, EEG responses to low stimulation frequencies closer to individual beta peak frequencies revealed a higher degree of entrainment, compared to stimulation conditions with frequencies that were more distant to endogenous oscillations. Our findings provide evidence that the efficacy of vibrotactile rhythmic beta stimulation to evoke a SSEPs is dependent on ongoing brain oscillations.
Phagocytic predation by the fungivorous amoebaProtostelium aurantiumtargets metal ion and redox homeostasis
Authors: Radosa Silvia , Sprague Jakob L. , Tóth Renáta , Wolf Thomas , Sprenger Marcel , Brunke Sascha , Panagiotou Gianni , Linde Jörg , Gácser Attila , Hillmann Falk
Published: July 2019

Predatory interactions among microbes are considered to be a major evolutionary driving force for biodiversity and the defense against phagocytic killing. The fungivorous amoebaProtostelium aurantiumhas a wide fungal food spectrum but strongly discriminates among major pathogenic members of theSaccharomycotina. WhileC. albicansis not recognized,C. glabratais rapidly internalized, but remains undigested. Phagocytic killing and feeding byP. aurantiumis highly effective for the third major fungal pathogen,C. parapsilosis.Here we show that the different prey patterns of the three yeasts were reflected by distinct transcriptional responses, indicating fungal copper and redox homeostasis as primary targets during intracellular killing ofC. parapsilosis. Gene deletions in this fungus for the highly expressed copper exporter Crp1 and the peroxiredoxin Prx1 confirmed their role in copper and redox homeostasis, respectively and identified methionine biosynthesis as a ROS sensitive metabolic target during predation. Both, intact Cu export and redox homeostasis contributed to the survival ofC. parapsilosisnot only when encounteringP. aurantium, but also in the presence of human macrophages. As both genes were found to be widely conserved within the entireCandidaclade, our results suggest that they could be part of a basic tool-kit to survive phagocytic attacks by environmental predators.
High-throughput transposon sequencing highlights the cell wall as an important barrier for osmotic stress in methicillin resistantStaphylococcus aureusand underlines a tailored response to different osmotic stressors
Authors: Schuster Christopher F. , Wiedemann David M. , Kirsebom Freja C. M. , Santiago Marina , Walker Suzanne , Gründling Angelika
Published: July 2019

Staphylococcus aureusis an opportunistic pathogen that can cause soft tissue infections but is also a frequent cause of foodborne illnesses. One contributing factor for this food association is its high salt tolerance allowing this organism to survive commonly used food preservation methods. How this resistance is mediated is poorly understood, particularly during long-term exposure. In this study, we used TN-seq to understand how the responses to osmotic stressors differ. Our results revealed distinctly different long-term responses to NaCl, KCl and sucrose stresses. In addition, we identified the DUF2538 domain containing geneSAUSA300_0957(gene957) as essential under salt stress. Interestingly, a957mutant was less susceptible to oxacillin and showed increased peptidoglycan crosslinking. The salt sensitivity phenotype could be suppressed by amino acid substitutions in the transglycosylase domain of the penicillin binding protein Pbp2, and these changes restored the peptidoglycan crosslinking to WT levels. These results indicate that increased crosslinking of the peptidoglycan polymer can be detrimental and highlight a critical role of the bacterial cell wall for osmotic stress resistance. This study will serve as a starting point for future research on osmotic stress response and help develop better strategies to tackle foodborne staphylococcal infections.
Genetic contributions to variation in human stature in prehistoric Europe
Authors: Cox Samantha L. , Ruff Christopher B. , Maier Robert M. , Mathieson Iain
Published: July 2019

The relative contributions of genetics and environment to temporal and geographic variation in human height remain largely unknown. Ancient DNA has identified changes in genetic ancestry over time, but it is not clear whether those changes in ancestry are associated with changes in height. Here, we directly test whether changes over the past 38,000 years in European height predicted using DNA from 1071 ancient individuals are consistent with changes observed in 1159 skeletal remains from comparable populations. We show that the observed decrease in height between the Early Upper Paleolithic and the Mesolithic is qualitatively predicted by genetics. Similarly, both skeletal and genetic height remained constant between the Mesolithic and Neolithic and increased between the Neolithic and Bronze Age. Sitting height changes much less than standing height–consistent with genetic predictions–although genetics predicts a small Bronze Age increase that is not observed in skeletal remains. Geographic variation in stature is also qualitatively consistent with genetic predictions, particularly with respect to latitude. Finally, we hypothesize that an observed decrease in genetic heel bone mineral density in the Neolithic reflects adaptation to the decreased mobility indicated by decreased femoral bending strength. This study provides a model for interpreting phenotypic changes predicted from ancient DNA and demonstrates how they can be combined with phenotypic measurements to understand the relative contribution of genetic and developmentally plastic responses to environmental change.

Significance

Measurements of prehistoric human skeletal remains provide a record of changes in height and other anthropometric traits, over time. Often, these changes are interpreted in terms of plastic developmental response to shifts in diet, climate or other environmental factors. These changes can also be genetic in origin but, until recently, it has been impossible to separate the effects of genetics and environment. Here we use ancient DNA to directly estimate genetic changes in phenotypes and to identify changes driven not by genetics, but by environment. We show that changes over the past 35,000 years are largely predicted by genetics, but also identify specific shifts that are more likely to be environmentally driven.
Developmental exposure to pesticide contaminated food impedes bumblebee brain growth predisposing adults to become poorer learners
Authors: Smith Dylan B. , Arce Andres N. , Rodrigues Ana Ramos , Bischoff Philipp H. , Burris Daisy , Ahmed Farah , Gill Richard J.
Published: July 2019

Understanding the risk to biodiversity from pesticide exposure is a global priority. For bees, an understudied step in evaluating pesticide risk is understanding how pesticide contaminated foraged food brought back to the colony can affect developing individuals. Provisioning bumblebee colonies with pesticide (neonicotinoid) treated food, we investigated how exposure during two key developmental phases (brood and/or early-adult), impacted brain growth and assessed the consequent effects on adult learning behaviour. Using micro-computed tomography (µCT) scanning and 3D image analysis, we compared brain development for multiple neuropils in workers 3 and 12-days post-emergence. Mushroom body calyces were the neuropils most affected by exposure during either of the developmental phases, with both age cohorts showing smaller structural volumes. Critically, reduced calyces’ growth in pesticide exposed workers was associated with lower responsiveness to a sucrose reward and impaired learning performance. Furthermore, the impact from brood exposure appeared irrecoverable despite no exposure during adulthood.
Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data
Authors: Blumberg Amit , Zhao Yixin , Huang Yi-Fei , Dukler Noah , Rice Edward J. , Chivu Alexandra G. , Krumholz Katie , Danko Charles G. , Siepel Adam
Published: July 2019

The rate at which RNA molecules decay is a key determinant of cellular RNA concentrations, yet current approaches for measuring RNA half-lives are generally labor-intensive, limited in sensitivity, and/or disruptive to normal cellular processes. Here we introduce a simple method for estimating relative RNA half-lives that is based on two standard and widely available high-throughput assays: Precision Run-On and sequencing (PRO-seq) and RNA sequencing (RNA-seq). Our method treats PRO-seq as a measure of transcription rate and RNA-seq as a measure of RNA concentration, and estimates the rate of RNA decay required for a steady-state equilibrium. We show that this approach can be used to assay relative RNA half-lives genome-wide, with good accuracy and sensitivity for both coding and noncoding transcription units. Using a structural equation model (SEM), we test several features of transcription units, nearby DNA sequences, and nearby epigenomic marks for associations with RNA stability after controlling for their effects on transcription. We find that RNA splicing-related features are positively correlated with RNA stability, whereas features related to miRNA binding, DNA methylation, and G+C-richness are negatively correlated with RNA stability. Furthermore, we find that a measure based on U1-binding and polyadenylation sites distinguishes between unstable noncoding and stable coding transcripts but is not predictive of relative stability within the mRNA or lincRNA classes. We also identify several histone modifications that are associated with RNA stability. Together, our estimation method and systematic analysis shed light on the pervasive impacts of RNA stability on cellular RNA concentrations.
Genomic selection analyses reveal tradeoff between chestnut blight tolerance and genome inheritance from American chestnut (Castanea dentata) in (C. dentataxC. mollissima) xC. dentatabackcross populations
Authors: Westbrook Jared W. , Zhang Qian , Mandal Mihir K. , Jenkins Eric V. , Barth Laura E. , Jenkins Jerry W. , Grimwood Jane , Schmutz Jeremy , Holliday Jason A.
Published: July 2019

American chestnut was once a foundation species of eastern North American forests, but was rendered functionally extinct in the early 20th century by an exotic fungal blight (Cryphonectria parasitica). Over the past 30 years, The American Chestnut Foundation (TACF) has pursued backcross breeding to generate hybrids that combine the timber-type form of American chestnut with the blight tolerance of Chinese chestnut. The backcross strategy has been implemented based on the hypothesis that blight tolerance is conferred by few major effect alleles. We tested this hypothesis by developing genomic prediction models for five presence/absence blight phenotypes of 1,230 BC3F2selection candidates and average canker severity of their BC3F3progeny. We also genotyped pure Chinese and American chestnut reference panels to estimate the proportion of BC3F2genomes inherited from parent species. We found that genomic prediction from a method that assumes an infinitesimal model of inheritance (HBLUP) has a similar predictive ability to a method that tends to perform well for traits controlled by major genes (Bayes C). Furthermore, the proportion of BC3F2trees’ genomes inherited from American chestnut was negatively correlated with the blight tolerance of BC3F2trees and their progeny. On average, selected BC3F2trees inherited 83% of their genome from American chestnut and have blight-tolerance that is intermediate between F1hybrids and American chestnut. Results suggest polygenic rather than major gene inheritance for blight tolerance. The blight-tolerance of restoration populations will be enhanced by advancing additional sources of blight-tolerance through fewer backcross generations and by potentially by breeding with transgenic blight-tolerant trees.
Early life maturation of human visual system white matter is altered by monocular enucleation
Authors: Dunkley Benjamin T. , Vandewouw Marlee , Chakraborty Arijit , Taylor Margot J. , Gallie Brenda , McCulloch Daphne L. , Thompson Benjamin
Published: July 2019

Monocular enucleation early in life and the resultant lack of binocular visual input during visual development results in functional and structural brain changes in adulthood, including alterations in white matter microstructure. However, the time courses of these neurodevelopmental changes are unknown. Here, we investigated whether structural brain changes were present at 8 to 12 years of age in a group of children with a history of monocular enucleation prior to 3 years of age (the ME group) relative to control participants with normal binocular vision (the BC group). Structural connectivity was measured using diffusion tensor imaging (DTI). Relative to the BC group, the ME group exhibited significantly increased radial and mean diffusivity in the optic radiation contralateral to the enucleated eye, the bidirectional interhemispheric V1 to V1 tracts and the V1 to MT tract ipsilateral to the enucleated eye. These changes indicate abnormal myelinization and reduced axonal density in subcortical and cortical visual pathway white matter structures following unilateral enucleation and loss of binocular vision. Our findings are broadly consistent with those recently reported for older uniocular individuals suggesting that these effects are present in childhood and persist into adulthood.