bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimization and quantitative evaluation of fluorescence in situ hybridization chain reaction in clarified fresh-frozen brain tissues
Authors: Kumar Vivek , Krolewski David M , Hebda-Bauer Elaine K , Parsegian Aram , Martin Brian , Foltz Mathew , Akil Huda , Watson Stanley 
Published: September 2019

AbstractTranscript labelling in intact tissues using in situ hybridization chain reaction has potential to provide vital spatiotemporal information for molecular characterization of heterogeneous neuronal populations. However, it remains relatively unexplored in fresh-frozen brain which provides more flexible utilization than perfused tissue. In the present study, we optimized the combination of in situ hybridization chain reaction in fresh-frozen rodent brains and then evaluated the uniformity of neuronal labelling between two clearing methods, CLARITY and iDISCO+. We found that CLARITY yielded higher signal-to-noise ratios but more limited imaging depth and required longer clearing times, whereas, iDISCO+ resulted in better tissue clearing, greater imaging depth and a more uniform labelling of larger samples. Based on these results, we used iDISCO+-cleared fresh-frozen rodent brains to further validate this combination and map the expression of a few genes of interest pertaining to mood disorders. We then examined the potential of in situ hybridization chain reaction to label transcripts in cleared postmortem human brain tissues. The combination failed to produce adequate mRNA labelling in postmortem human cortical slices but produced visually adequate labeling in the cerebellum tissues. We next, investigated the multiplexing ability of in situ hybridization chain reaction in cleared tissues which revealed inconsistent fluorescence output depending upon the fluorophore conjugated to the hairpins. Finally, we applied our optimized protocol to assess the effect of glucocorticoid receptor overexpression on basal somatostatin expression in the mouse cortex. The constitutive glucocorticoid receptor overexpression resulted in lower number density of somatostatin-expressing neurons compared to wild type. Overall, the combination of in situ hybridization chain reaction with clearing methods especially iDISCO+ may find broad application in the transcript analysis in rodent studies but its limited use in postmortem human tissues can be improved by further optimizations.
Protein Tyrosine Phosphatase 1B Regulates MicroRNA-208b-Argonaute 2 Association and Thyroid Hormone Responsiveness in Cardiac Hypertrophy
Authors: Coulis Gérald , Shi Yanfen , Labbé David P. , Bergeron Alexandre , Sahmi Fatiha , Vinette Valérie , Karsenty Gérard , Allen Bruce G. , Tremblay Michel L. , Tardif Jean-Claude , Boivin Benoit 
Published: September 2019

ABSTRACTElevated reactive oxygen species (ROS) production plays an important role in the pathogenesis of several diseases, including cardiac hypertrophy. While the regulation of diverse sources of ROS is well characterized in the heart, the redox-sensitive targets that contribute to redox signaling remain largely undefined. We now report that protein tyrosine phosphatase 1B (PTP1B) is reversibly oxidized and inactivated in hearts undergoing hypertrophy and that gene deletion of PTP1B in mouse hearts cause an hypertrophic phenotype that is critically exacerbated in mice subjected to pressure overload. Furthermore, we show that PTP1B dephosphorylates Tyr393on argonaute 2, a key component of the RNA-induced silencing complex, and sustains gene silencing in the heart. Our results indicate that PTP1B inactivation and argonaute 2 Tyr393phosphorylation specifically prevents argonaute 2 from interacting with miR-208b. Phosphorylation and inactivation of argonaute 2 in PTP1B cKO mice revealed a mechanism by which defective miR-208b-mediated repression of thyroid hormone receptor-associated protein 1 (THRAP1/MED13) contributes to thyroid hormone-mediated cardiac hypertrophy. In support of this conclusion, inhibiting the synthesis of triiodothyronine (T3), using propylthiouracil, rescued TAC-induced hypertrophy and improved myocardial contractility and systolic function in PTP1B cKO mice. Together, our data illustrate that PTP1B activity exerts a cardioprotective effect in the heart and that redox signaling is tightly linked to thyroid hormone responsiveness and to microRNA-mediated gene silencing in pathological hypertrophy.
Secondary origin, hybridization and sexual reproduction in a diploid- tetraploid contact zone of the facultative apomictic orchidZygopetalum mackayi
Authors: de Moura Yohans Alves , Alves-Pereira Alessandro , Silva Carla Cristina , de Souza Lívia Moura , de Souza Anete Pereira , Koehler Samantha 
Published: September 2019

ABSTRACT>Mixed-cytotype populations are ideal to understand polyploid establishment and diversification. We used the orchidZygopetalum mackayito understand how facultative apomictic reproduction relates to polyploidy. Sexual diploids and facultative apomictic tetraploids occur under distinct niches, with a contact zone where triploids occur. We hypothesized that facultative apomictic reproduction increases the fitness of tetraploids through reproductive interference between cytotypes. We predict patterns of genetic diversity of allopatric tetraploid populations to be significantly different from contact zone populations as a result of dominant apomictic reproduction in the later. We also describe the contact nature of diploids and tetraploids and the role of the intermediate triploids based on patterns of genetic structure within and among pure and mixed-cytotype populations.>We designed eight microsatellite markers and genotyped 155 individuals from six populations resulting in 237 alleles. We described patterns of genetic diversity and structure within and among populations and cytotypes.>Genotypic diversity is similarly high among all populations and cytotypes. Each cytotype emerged as a genetically cluster, combining individuals from different populations. Triploids clustered in an intermediate position between diploids andtetraploids.>We rejected the hypothesis of reproductive interference between cytotypes ofZ. mackayi. Patterns of genetic diversity are incongruent with the occurrence of apomict reproduction in tetraploids. Mixed-cytotype populations originate from secondary contact and triploids are hybrids between diploids and tetraploids and act as a reproductive barrier. We suggest polyploidy rather than facultative apomixis explains higher fitness of tetraploids in this species and, therefore, eco-geographical patterns of distribution.
HELLS and PRDM9 form a Pioneer Complex to Open Chromatin at Meiotic Recombination Hotspots
Authors: Spruce Catrina , Dlamini Sibongakonke , Ananda Guruprasad , Bronkema Naomi , Tian Hui , Paigen Ken , Carter Gregory W. , Baker Christopher L 
Published: September 2019

SUMMARYChromatin barriers prevent spurious interactions between regulatory elements and DNA-binding proteins. One such barrier, whose mechanism for overcoming is poorly understood, is access to recombination hotspots during meiosis. Here we show that the chromatin remodeler HELLS and DNA-binding protein PRDM9 function together to open chromatin at hotspots and provide access for the DNA double-strand break (DSB) machinery. Recombination hotspots are decorated by a unique combination of histone modifications, not found at other regulatory elements. HELLS is recruited to hotspots by PRDM9, and is necessary for both histone modifications and DNA accessibility at hotspots. In male mice lacking HELLS, DSBs are retargeted to other sites of open chromatin, leading to germ cell death and sterility. Together, these data provide a model for hotspot activation where HELLS and PRDM9 function as a pioneer complex to create a unique epigenomic environment of open chromatin, permitting correct placement and repair of DSBs.
Direct-fit to nature: an evolutionary perspective on biological (and artificial) neural networks
Authors: Hasson Uri , Nastase Samuel A. , Goldstein Ariel 
Published: September 2019

AbstractEvolution is a blind fitting process by which organisms, over generations, adapt to the niches of an ever-changing environment. Does the mammalian brain use similar brute-force fitting processes to learn how to perceive and act upon the world? Recent advances in training deep neural networks has exposed the power of optimizing millions of synaptic weights to map millions of observations along ecologically relevant objective functions. This class of models has dramatically outstripped simpler, more intuitive models, operating robustly in real-life contexts spanning perception, language, and action coordination. These models do not learn an explicit, human-interpretable representation of the underlying structure of the data; rather, they use local computations to interpolate over task-relevant manifolds in a high-dimensional parameter space. Furthermore, counterintuitively, over-parameterized models, similarly to evolutionary processes, can be simple and parsimonious as they provide a versatile, robust solution for learning a diverse set of functions. In contrast to traditional scientific models, where the ultimate goal is interpretability, over-parameterized models eschew interpretability in favor of solving real-life problems or tasks. We contend that over-parameterized blind fitting presents a radical challenge to many of the underlying assumptions and practices in computational neuroscience and cognitive psychology. At the same time, this shift in perspective informs longstanding debates and establishes unexpected links with evolution, ecological psychology, and artificial life.
Refining the composition of the Arabidopsis thaliana 80S cytosolic ribosome
Authors: Salih Karzan Jalal , Duncan Owen , Li Lei , Troesch Josua , Millar A. Harvey 
Published: September 2019

AbstractThe cytosolic 80S ribosome is composed of protein and RNA molecules and its function in protein synthesis is modulated through interaction with other cytosolic components. Defining the role of each of the proteins associated with ribosomes in plants is a major challenge which is hampered by difficulties in attribution of different proteins to roles in ribosome biogenesis, the mature cytosolic ribosome (r-proteins) or to the broader translatome associated with functioning ribosomes. Here we refined the core r-protein composition in plants by determining the abundance of proteins in low, partially and highly purified ribosomal samples from Arabidopsis thaliana cell cultures. To characterise this list of proteins further we determined their degradation (KD) and synthesis (KS) rate by progressive labelling with 15N combined with peptide mass spectrometry analysis. The turnover rates of 55 r-proteins, including 26 r-proteins from the 40S subunit and 29 r-proteins from the 60S subunit could be determined. Overall, ribosome proteins showed very similar KD and KS rates suggesting that half of the ribosome population is replaced every 3-4 days. Three proteins showed significantly shorter half-lives; ribosomal protein P0D (RPP0D) with a half-life of 0.5 days and RACK1b and c with half-lives of 1-1.4 days. The ribosomal RPP0D protein is a homolog of the human Mrt4 protein, a trans-acting factor in the assembly of the pre-60S particle, while RACK1 has known regulatory roles in cell function beyond its role as a 40S subunit. Our experiments also identified 58 proteins that are not from r-protein families but co-purify with ribosomes and co-express with r-proteins in Arabidopsis. Of this set, 26 were enriched more than 10-fold during ribosome purification. A number have known roles in translation or ribosome-association while others are newly proposed ribosome-associated factors in plants. This analysis provides a more robust understanding of Arabidopsis ribosome content, shows that most r-proteins turnover in unison in vivo, identifies a novel set of potential plant translatome components, and reveals how protein turnover can identify r-proteins involved in ribosome biogenesis or regulation in plants. Data are available via ProteomeXchange with identifier PXD012839.
Excessive assimilation of ammonium by plastidic glutamine synthetase is a major cause of ammonium toxicity in Arabidopsis thaliana
Authors: Hachiya Takushi , Inaba Jun , Wakazaki Mayumi , Sato Mayuko , Toyooka Kiminori , Miyagi Atsuko , Kawai-Yamada Maki , Kiba Takatoshi , Gojon Alain , Sakakibara Hitoshi 
Published: September 2019

AbstractPlants use nitrate and ammonium in the soil as their main nitrogen sources. Recently, ammonium has attracted attention due to evidence suggesting that, in C3 species, an elevated CO2 environment inhibits nitrate assimilation. However, high concentrations of ammonium as the sole nitrogen source for plants causes impaired growth, i.e. ammonium toxicity. Although ammonium toxicity has been studied for a long time, the primary cause remains to be elucidated. Here, we show that ammonium assimilation in plastids rather than ammonium accumulation is a primary cause for toxicity. Our genetic screen of ammonium-tolerant Arabidopsis lines with enhanced shoot growth identified plastidic GLUTAMINE SYNTHETASE 2 (GLN2) as the causal gene. Our reciprocal grafting of wild-type and GLN2 or GLN1;2-deficient lines suggested that shoot GLN2 activity results in ammonium toxicity, whilst root GLN1;2 activity prevents it. With exposure to toxic levels of ammonium, the shoot GLN2 reaction produced an abundance of protons within cells, thereby elevating shoot acidity and stimulating expression of acidic stress-responsive genes. Application of an alkaline ammonia solution to the toxic ammonium medium efficiently alleviated the ammonium toxicity with a concomitant reduction in shoot acidity. Consequently, we conclude that a primary cause of ammonium toxicity is acidic stress in the shoot. This fundamental insight provides a framework for enhanced understanding of ammonium toxicity in plants.
cGMP dynamics underlie thermosensation in C. elegans
Authors: Aoki Ichiro , Shiota Makoto , Nakano Shunji , Mori Ikue 
Published: September 2019

AbstractAnimals sense ambient temperature so that they can adjust their behavior to the environment; they avoid noxious heat and coldness and stay within a survivable temperature range. C. elegans can sense temperature, memorize past cultivation temperature and navigate towards preferable temperature, for which a thermosensory neuron, AFD, is essential. AFD responds to temperature increase from the past cultivation temperature by increasing intracellular Ca2+ level. We aimed to reveal how AFD encodes and memorizes the information of temperature. Although cGMP synthesis is crucial for thermosensation by AFD, whether and how cGMP level temporally fluctuates in AFD remained elusive. We therefore monitored cGMP level in AFD and found that cGMP dynamically responded to temperature change in a manner dependent on past cultivation temperature. Given that cGMP dynamics is supposed to be upstream of Ca2+ dynamics, our results suggest that AFD’s memory is formed by simpler molecular mechanisms than previously expected from the Ca2+ dynamics. Moreover, we analyzed how guanylyl cyclases and phosphodiesterases, which synthesize and degrade cGMP, respectively, contributed to cGMP and Ca2+ dynamics and thermotaxis behavior.
Arabidopsis PPC2 is crucial for growth at low CO2 by involvement in photorespiratory metabolism and integration of ABI5
Authors: You Lei , Zhang Jumei , Li Long , Xiao Chuanlei , Feng Xinhua , Chen Shaoping , Guo Liang , Hu Honghong 
Published: September 2019

AbstractPhosphoenolpyruvate carboxylase (PEPC) is a pivotal enzyme that plays a key role in photosynthetic CO2 fixation in C4. However, the function of C3 PEPCs and their roles at environmental CO2 changes are still limited. Here, we report the role of PPC2 in seedling growth at low CO2 by linking photorespiratory metabolism with primary metabolism and involvement of ABA and ABI5. Mutation of PPC2 caused seedling growth arrest, with reduced Fv/Fm, photosynthetic carbohydrates and ABA biosynthesis at low CO2. PPC2 is induced by low CO2 and the PEPC activity was greatly reduced in ppc2 leaves. Moreover, metabolic analyses showed the photorespiratory intermediates, glycine and serine, were greatly increased and primary metabolites were reduced. Application of sucrose, malate and ABA greatly rescued the growth arrest phenotype of ppc2. The expression of glycine/serine synthesis and metabolism related photorespiratory enzyme genes were decreased in ppc2 and regulated by ABI5 at low CO2 conditions. ppc2 and abi5 mature plants exhibited reduced A-Ci curves at relatively low CO2, which could be recovered by non-photorespiratory low oxygen conditions. ABI5 expression greatly rescued the growth arrest and A-Ci curves of ppc2 at low CO2. Our findings demonstrate the important role of C3 PEPCs in carbon fixation and metabolism.
Induced RPB1 depletion reveals a direct gene-specific control of RNA Polymerase III function by RNA Polymerase II
Authors: Gerber Alan , Ito Keiichi , Chu Chi-Shuen , Roeder Robert G. 
Published: September 2019

SummaryIncreasing evidence suggests that tRNA levels are dynamically and specifically regulated in response to internal and external cues to modulate the cellular translational program. However, the molecular players and the mechanisms regulating the gene-specific expression of tRNAs are still unknown. Using an inducible auxin-degron system to rapidly deplete RPB1 (the largest subunit of RNA Pol II) in living cells, we identified Pol II as a direct gene-specific regulator of tRNA transcription. Our data suggest that Pol II transcription robustly interferes with Pol III function at specific tRNA genes. This activity was further found to be essential for MAF1-mediated repression of a large set of tRNA genes during serum starvation, indicating that repression of tRNA genes by Pol II is dynamically regulated. Hence, Pol II plays a direct and central role in the gene-specific regulation of tRNA expression.
Cell type specific novel lincRNAs and circRNAs in the BLUEPRINT haematopoietic transcriptomes atlas
Authors: Grassi Luigi , Izuogu Osagie G. , Jorge Natasha A.N. , Seyres Denis , Bustamante Mariona , Burden Frances , Farrow Samantha , Farahi Neda , Martin Fergal J. , Frankish Adam , Mudge Jonathan M. , Kostadima Myrto , Petersen Romina , Lambourne John J. , Rowlston Sophia , Martin-Rendon Enca , Clarke Laura , Downes Kate , Estivill Xavier , Flicek Paul , Martens Joost H.A. , Yaspo Marie-Laure , Stunnenberg Hendrik G. , Ouwehand Willem H. , Passetti Fabio , Turro Ernest , Frontini Mattia 
Published: September 2019

AbstractTranscriptional profiling of hematopoietic cell subpopulations has helped characterize the developmental stages of the hematopoietic system and the molecular basis of malignant and non-malignant blood diseases for the past three decades. The introduction of high-throughput RNA sequencing has increased knowledge of the full repertoire of RNA molecules in hematopoietic cells of different types, without relying on prior gene annotation. Here, we introduce the analysis of the BLUEPRINT consortium gene expression data for mature hematopoietic cells, comprising 90 total RNA and 32 small RNA sequencing experiments, from 27 different cell types. We used these data to describe the transcriptional profile of each we used guided transcriptome assembly to extend the annotation of the transcribed genome, which led to the identification of hundreds of novel non-coding RNA genes, which display a high degree of cell type specificity. We also characterized the expression of circular RNAs and found that these are also highly cell type specific. This resource refines the active transcriptional landscape of mature hematopoietic cells, highlights abundant genes and transcriptional isoforms for each cell type, and provides valuable data and visualisation tools for the scientific community working on hematological development and diseases.
Homeostatic maintenance and age-related functional decline in theDrosophilaear
Authors: Keder Alyona , Tardieu Camille , Malong Liza , Filia Anastasia , Kashkenbayeva Assel , Gale Jonathan E. , Lovett Mike , Jarman Andrew P. , Albert Joerg T. 
Published: September 2019

AbstractThe widespread loss of hearing is one of the major threats to future wellbeing in ageing human societies. Amongst its various forms, age-related hearing loss (ARHL) carries the vast bulk of the global disease burden. The causes for the terminal decline of auditory function, however, are as unknown as the mechanisms that maintain sensitive hearing before its breakdown. We here present an in-depth analysis of maintenance and ageing in the auditory system of the fruit flyDrosophila melanogaster. We show thatDrosophila, just like humans, display ARHL and that their auditory life span is homeostatically supported by a set of evolutionarily conserved transcription factors. The transcription factors Onecut (closest human orthologues: ONECUT2, ONECUT3), Optix (SIX3, SIX6), Worniu (SNAI2) and Amos (ATOH1, ATOH7, NEUROD1) emerged as key regulators acting upstream of core sensory genes, including components of the fly’s molecular machinery for auditory transduction and amplification.
Predicting intentional and unintentional task unrelated thought with EEG
Authors: Martel Adrien , Arvaneh Mahnaz , Robertson Ian , Dockree Paul 
Published: September 2019

AbstractOur attention seldom remains on a singular activity, instead veering off into thoughts unrelated to the task at hand. Studies adopting a component process view of off-task thought have begun to identify the underlying mechanisms and associated electrophysiological correlates underlying ongoing thought. In the present study, we developed subject-independent classification algorithms based on electroencephalographic (EEG) markers to discriminate on-task vs off-task as well as intentional vs unintentional off-task thought. To that end, spatio-temporal and spectral features extracted from EEG activity prior to reports of ongoing thought during a test of sustained attention were ranked according to their discriminative power. Using data collected from 26 participants, average classification accuracies of 83.4% and 71.6% were achieved using a regularized linear model for on-task vs off-task and intentional vs unintentional off-task thought, respectively. Our results identified gamma oscillations as the most discriminative feature to distinguish on-task from off-task states, and alpha synchronization as the most prominent feature when off-task states are engaged in deliberately rather than when experienced as arising spontaneously. Our work represents the first successful attempt at reliably discriminating the degree of intentionality experienced during task-unrelated thought and highlights the importance of recognizing the heterogeneous nature of off-task states.