bluuebunny/crossref_metadata_2025 huggingface dataset:
Equine synovial fluid small non-coding RNA signatures in early osteoarthritis
Authors: Castanheira Catarina , Balaskas Panagiotis , Falls Charlotte , Ashraf-Kharaz Yalda , Clegg Peter , Burke Kim , Fang Yongxiang , Dyer Philip , Welting Tim JM , Peffers Mandy J
Published: May 2020

Background

Osteoarthritis remains one of the greatest causes of morbidity and mortality in the equine population. The inability to detect pre-clinical changes in osteoarthritis has been a significant impediment to the development of effective therapies against this disease. Synovial fluid represents a potential source of disease-specific small non-coding RNAs (sncRNAs) that could aid in the understanding of the pathogenesis of osteoarthritis. We hypothesised that early stages of osteoarthritis would alter the expression of sncRNAs, facilitating the understanding of the underlying pathogenesis and potentially provide early biomarkers.

Methods

Small RNA sequencing was performed using synovial fluid from the metacarpophalangeal joints of both control and early osteoarthritic non-Thoroughbred horses. A group of differentially expressed sncRNAs was selected for further validation through qRT-PCR using an independent cohort of synovial fluid samples from control and early osteoarthritic horses. Bioinformatic analysis was performed in order to identify putative targets of the differentially expressed microRNAs and to explore potential associations with specific biological processes.

Results

Results revealed 22 differentially expressed sncRNAs including 13 microRNAs; miR-10a, miR-223, let7a, miR-99a, miR-23b, miR-378, miR-143 (and six novel microRNAs), four small nuclear RNAs; U2, U5, U11, U12, three small nucleolar RNAs; U13, snoR38, snord96, and one small cajal body-specific RNA; scarna3. Five sncRNAs were validated; miR-223 was significantly reduced in early OA and miR-23b, let-7a-2, snord96A and snord13 were significantly upregulated. Significant cellular functions deduced by the differentially expressed microRNAs included apoptosis (P < 0.0003), necrosis (P < 0.0009), autophagy (P < 0.0007) and inflammation (P < 0.00001). A conservatively filtered list of 57 messenger RNA targets was obtained; the top biological processes associated were regulation of cell population proliferation (P < 0.000001), cellular response to chemical stimulus (P < 0.000001) and cell surface receptor signalling pathway (P < 0.000001).

Conclusions

Synovial fluid sncRNAs can be used as molecular biomarkers for early disease in equine osteoarthritic joints. The biological processes they regulate may play an important role in understanding early osteoarthritis pathogenesis. Characterising these dynamic molecular changes could provide novel insights on the process and mechanism of early osteoarthritis development and is critical for the development of new therapeutic approaches.
Artificially selecting microbial communities using propagule strategies
Authors: Chang Chang-Yu , Osborne Melisa L. , Bajic Djordje , Sanchez Alvaro
Published: May 2020

Artificial selection is a promising approach to manipulate the function of microbial communities. Here, we report the outcome of two artificial selection experiments at the microbial community level. Both experiments used “propagule” strategies, in which a set of the best-performing communities are used as the inocula to form a new generation of communities. In both cases, the selected communities are compared to a control treatment where communities are randomly selected. The first experiment used a defined set of strains as the starting inoculum, and the function under selection was the amylolytic activity of the consortia. The second experiment used a diverse set of natural communities as the inoculum, and the function under selection was the cross-feeding potential of the resulting communities towards a reference bacterial strain. In both experiments, the selected communities reached a higher mean and a higher maximum function than the control. In the first experiment this is caused by a decline in function of the control, rather than an improvement of the selected line. In the second experiment, the strong response of the mean is caused by the large initial variance in function across communities, and is the immediate consequence of the spread of the top-performing community in the starting group, whose function does not increase. Our results are in agreement with basic expectations of artificial selection theory, pointing out some of the limitations of community-level selection experiments which can inform the design of future studies.
Submodular sketches of single-cell RNA-seq measurements
Authors: Yang Wei , Schreiber Jacob , Bilmes Jeffrey , Noble William Stafford
Published: May 2020

Analyzing and sharing massive single-cell RNA-seq data sets can be facilitated by creating a “sketch” of the data—a selected subset of cells that accurately represent the full data set. Using an existing benchmark, we demonstrate the utility of submodular optimization in efficiently creating high quality sketches of scRNA-seq data.
Oxygen radicals and cytoplasm zoning in growing lily pollen tubes
Authors: Podolyan Alexandra , Luneva Oksana , Breygina Maria
Published: May 2020

Recently redox-regulation of tip growth has been extensively studied, but differential sensitivity of growing cells to particular ROS and their subcellular localization is still unclear. Here we used specific dyes to provide mapping of H2O2and O•2−in short and long pollen tubes. We found apical accumulation of H2O2and H2O2–producing organelles in the shank that were not colocalized with O•2−-producing mitochondria. Differential modulation of ROS content of the germination medium affected both growth speed and pollen tube morphology. Oxygen radicals affected ionic zoning: membrane potential and pH gradients. OH• caused depolarization all along the tube while O•2−provoked hyperpolarization and cytoplasm alkalinization. O•2−accelerated growth and reduced tube diameter, indicating that this ROS can be considered as pollen tube growth stimulator along with H2O2. Serious structural disturbances were observed upon exposure to OH• and H2O2and O•2−quencher MnTMPP: pollen tube growth slowed down and ballooned tips formed in both cases, but in the presence of OH• membrane transport and organelle distribution was affected as well. OH•, thus, can be considered as a negative influence on pollen tubes which, presumably, have mechanisms for leveling it. The assumption was confirmed by EPR spectroscopy: pollen tubes actively reduce OH• content in the incubation medium.
Transcriptomic expression patterns of two contrasting lowland rice varieties reveal high iron stress tolerance
Authors: Kar Saradia , Mai Hans-Jörg , Khalouf Hadeel , Ben Abdallah Heithem , Flachbart Samantha , Fink-Straube Claudia , Bräutigam Andrea , Xiong Guosheng , Shang Lianguang , Panda Sanjib Kumar , Bauer Petra
Published: May 2020

Iron (Fe) toxicity is a major challenge for plant cultivation in acidic water-logged soil environments, where lowland rice is a major staple food crop. Only few studies addressed the molecular characterization of excess Fe tolerance in rice, and these highlight different mechanisms for Fe tolerance in the studied varieties.

Here, we screened 16 lowland rice varieties for excess Fe stress growth responses to identify contrasting lines, Fe-tolerant Lachit and -susceptible Hacha. Hacha and Lachit differed in their physiological and morphological responses to excess Fe, including leaf growth, leaf rolling, reactive oxygen species generation, Fe and metal contents. These responses were mirrored by differential gene expression patterns, obtained through RNA-sequencing, and corresponding GO term enrichment in tolerant versus susceptible lines. From the comparative transcriptomic profiles between Lachit and Hacha in response to excess Fe stress, individual genes of the category metal homeostasis, mainly root-expressed, may contribute to the tolerance of Lachit. 22 out of these 35 metal homeostasis genes are present in selection sweep genomic regions, in breeding signatures and/or differentiated during rice domestication. These findings will serve to design targeted Fe tolerance breeding of rice crops.

Summary statement

Lowland rice varieties Hacha and Lachit were selected for contrasting abilities to cope with iron excess stress. Morphological and physiological phenotypes were mirrored by molecular transcriptome changes, indicating altered metal homeostasis in the root as an adaptive tolerance mechanism in Lachit.
Social play is critical for the development of prefrontal inhibitory synapses and cognitive flexibility in rats
Authors: Bijlsma Ate , Omrani Azar , Spoelder Marcia , Verharen Jeroen P.H. , Bauer Lisa , Cornelis Cosette , de Zwart Beleke , van Dorland René , Vanderschuren Louk J.M.J. , Wierenga Corette J.
Published: May 2020

Sensory driven activity during early life is critical for setting up the proper connectivity of the sensory cortices. Here we ask if social play behavior, a particular form of social interaction that is highly abundant during post-weaning development, is equally important for setting up connections in the developing prefrontal cortex (PFC). Young rats were deprived from social play with peers for 3 weeks during the period in life when social play behavior normally peaks (P21-42; SPD rats), followed by resocialization until adulthood. We recorded synaptic currents in L5 cells in slices from medial PFC of adult SPD and control rats and observed that inhibitory synaptic currents were reduced in SPD slices, while excitatory synaptic currents were unaffected. This was associated with a decrease in perisomatic inhibitory synapses from parvalbumin-positive GABAergic cells. In parallel experiments, adult SPD rats achieved more reversals in a probabilistic reversal learning task (PRL), which depends on the integrity of the PFC. They appeared to use a different cognitive strategy than controls. One hour of intense play during SPD did not prevent the decrease in inhibitory synaptic inputs and had only a limited effect on behavioral outcomes in the PRL. Our data demonstrate the importance of unrestricted social play for the development of inhibitory synapses in the PFC and cognitive skills in adulthood.
Kaleidoscope: A New Bioinformatics Pipeline Web Application for In Silico Hypothesis Exploration of Omics Signatures
Authors: Alganem Khaled , Shukla Rammohan , Eby Hunter , Abel Mackenzie , Zhang Xiaolu , McIntyre William Brett , Lee Jiwon , Au-Yeung Christy , Asgariroozbehani Roshanak , Panda Roshni , O’Donovan Sinead M , Funk Adam , Hahn Margaret , Meller Jarek , McCullumsmith Robert
Published: May 2020

Background

In silicodata exploration is a key first step of exploring a research question. There are many publicly available databases and tools that offer appealing features to help with such a task. However, many applications lack exposure or are constrained with unfriendly or outdated user interfaces. Thus, it follows that there are many resources that are relevant to investigation of medical disorders that are underutilized.

Results

We developed an R Shiny web application, called Kaleidoscope, to address this challenge. The application offers access to several omics databases and tools to let users explore research questionsin silico. The application is designed to be user- friendly with a unified user interface, while also scalable by offering the option of uploading user-defined datasets. We demonstrate the application features with a starting query of a single gene (Disrupted in schizophrenia 1, DISC1) to assess its protein-protein interactions network. We then explore expression levels of the gene network across tissues and cell types in the brain, as well as across 34 schizophrenia versus control differential gene expression datasets.

Conclusion

Kaleidoscope provides easy access to several databases and tools under a unified user interface to explore research questionsin silico. The web application is open-source and freely available athttps://kalganem.shinyapps.io/Kaleidoscope/. This application streamlines the process ofin silicodata exploration for users and expands the efficient use of these tools to stakeholders without specific bioinformatics expertise.
A Proposed Drought Response Equation Added to the Münch-Horwitz Theory of Phloem Transport
Authors: Goeschl John D. , Han Lifeng
Published: May 2020

Theoretical and experimental evidence for an effect of sieve tube turgor pressure on the mechanisms of phloem unloading near the root tips during moderate levels of drought stress is reviewed. An additional, simplified equation is proposed relating decreased turgor pressure to decreased rate kinetics of membrane bound transporters. The effect of such a mechanism would be to decrease phloem transport Speed, but increase Concentration and Pressure, and thus prevent or delay negative Pressure in the phloem. Experimental evidence shows this mechanism precedes and exceeds a reduction in stomatal conductance.
CoV-Seq: SARS-CoV-2 Genome Analysis and Visualization
Authors: Liu Boxiang , Liu Kaibo , Zhang He , Zhang Liang , Bian Yuchen , Huang Liang
Published: May 2020

COVID-19 has become a global pandemic not long after its inception in late 2019. SARS-CoV-2 genomes are being sequenced and shared on public repositories at a fast pace. To keep up with these updates, scientists need to frequently refresh and reclean datasets, which is ad hoc and labor-intensive. Further, scientists with limited bioinformatics or programming knowledge may find it difficult to analyze SARS-CoV-2 genomes. In order to address these challenges, we developed CoV-Seq, a webserver to enable simple and rapid analysis of SARS-CoV-2 genomes. Given a new sequence, CoV-Seq automatically predicts gene boundaries and identifies genetic variants, which are presented in an interactive genome visualizer and are downloadable for further analysis. A command-line interface is also available for high-throughput processing.

Availability and Implementation

CoV-Seq is implemented in Python and Javascript. The webserver is available athttp://covseq.baidu.com/and the source code is available fromhttps://github.com/boxiangliu/covseq.

Contact

jollier.liu@gmail.com

Supplementary information

Supplementary information are available atbioRxivonline.
Sex-dependent effects of chronic intermittent voluntary alcohol consumption on attentional, not motivational, measures during probabilistic learning and reversal
Authors: Aguirre Claudia G. , Stolyarova Alexandra , Das Kanak , Kolli Sriya , Marty Vincent , Ray Lara , Spigelman Igor , Izquierdo Alicia
Published: May 2020

Background

Forced alcohol (ethanol, EtOH) exposure has been shown to cause significant impairments on reversal learning, a widely-used assay of cognitive flexibility, specifically on fully-predictive, deterministic versions of this task. However, previous studies have not adequately considered voluntary EtOH consumption and sex effects on probabilistic reversal learning. The present study aimed to fill this gap in the literature.

Methods

Male and female Long-Evans rats underwent either 10 weeks of voluntary intermittent 20% EtOH access or water only (H2O) access. Rats were then pretrained to initiate trials and learn stimulus-reward associations via touchscreen response, and subsequently required to select between two visual stimuli, rewarded with probability 0.70 or 0.30. In the final phase, reinforcement contingencies were reversed.

Results

We found significant sex differences on several EtOH-drinking variables, with females reaching a higher maximum EtOH consumption, exhibiting more high-drinking days, and escalating their EtOH at a quicker rate compared to males. During early abstinence, EtOH drinkers made more initiation omissions and were slower to initiate trials than H2O drinking controls, particularly during pretraining. EtOH drinking females were most affected. A similar pattern in trial initiations was also observed in discrimination, but not in reversal learning. EtOH drinking rats were unaffected in their reward collection and stimulus response times, indicating intact motivation and motor responding. Although there were sex differences in discrimination and reversal phases, performance improved over time. We also observed sex-independent drinking group differences in win-stay and lose-shift strategies specific to the reversal phase.

Conclusions

Females exhibit increased vulnerability to EtOH effects in early learning: there were sex-dependent EtOH effects on attentional measures during pretraining and discrimination phases. We also found sexindependent EtOH effects on exploration strategies during reversal. Future studies should aim to uncover the neural mechanisms for changes in attention and exploration in both acute and prolonged EtOH withdrawal.
No evidence for transient transformation via pollen magnetofection in several monocot species
Authors: Vejlupkova Zuzana , Warman Cedar , Sharma Rita , Scheller Henrik Vibe , Mortimer Jenny C. , Fowler John E.
Published: May 2020

The development of rapid and efficient transformation methods for many plant species remains an obstacle in both the basic and applied plant sciences. A novel method described by Zhao et al. (2017) used magnetic nanoparticles to deliver DNA into pollen grains of several dicot species, and one monocot (lily), to achieve transformation (“pollen magnetofection”). Using the published protocol, extensive trials by two independent research groups showed no indication of transient transformation success with pollen from two monocots, maize and sorghum. To further address the feasibility of magnetofection, lily pollen was used for side-by-side trials of magnetofection with a proven methodology for transient transformation, biolistics. Using a Green Fluorescent Protein reporter plasmid, transformation efficiency with the biolistic approach averaged 0.7% over three trials. However, the same plasmid produced no recognizable transformants via magnetofection, despite screening >3500 individual pollen grains. We conclude that pollen magnetofection is not effective for transient transformation of pollen for at least three species of monocots, and suggest that efforts to replicate the magnetofection protocol in dicot species would be useful to fully assess its potential.

ARISING FROM Zhao et al.Nature Plantshttps://doi.org/10.1038/s41477-017-0063-z(2017)
The microbiota promotes social behavior by modulating microglial remodeling of forebrain neurons
Authors: Bruckner Joseph J. , Stednitz Sarah J. , Grice Max Z. , Zaidan Dana , Massaquoi Michelle S. , Larsch Johannes , Tallafuss Alexandra , Guillemin Karen , Washbourne Philip , Eisen Judith S.
Published: May 2020

Host-associated microbiotas guide the trajectory of developmental programs, and microbial dysbiosis is linked to neurodevelopmental conditions such as autism spectrum disorder. Recent work suggests that microbiotas modulate behavioral phenotypes associated with these disorders. We discovered that the zebrafish microbiota is required for normal social behavior, and reveal a molecular pathway linking the microbiota, microglial remodeling of neural circuits, and social behavior in this experimentally tractable model vertebrate. Examining neuronal correlates of behavior, we found that the microbiota restrains neurite complexity and targeting of forebrain neurons required for normal social behavior and is necessary for localization of forebrain microglia, brain resident phagocytes that remodel neuronal arbors. The microbiota also influences microglial molecular functions, including promoting expression of the remodeling factorc1q, which we find is required for normal forebrain neurite complexity. Several distinct bacterial taxa are individually sufficient for normal microglial and neuronal phenotypes, suggesting that host neuroimmune development is sensitive to a feature common among many bacteria. Our results demonstrate that the microbiota influences zebrafish social behavior by stimulating microglial remodeling of forebrain circuits during early neurodevelopment, and suggest pathways for new interventions in multiple neurodevelopmental disorders.
Iron Responsive Element (IRE)-mediated responses to iron dyshomeostasis in Alzheimer’s disease
Authors: Hin Nhi , Newman Morgan , Pederson Stephen , Lardelli Michael
Published: May 2020

Background

Iron trafficking and accumulation is associated with Alzheimer’s disease (AD) pathogenesis. However, the role of iron dyshomeostasis in early disease stages is uncertain. Currently, gene expression changes indicative of iron dyshomeostasis are not well characterized, making it difficult to explore these in existing datasets.

Objective

To identify sets of genes predicted to contain Iron Responsive Elements (IREs) and use these to explore possible iron dyshomeostasis-associated gene expression responses in AD.

Methods

Comprehensive sets of genes containing predicted IRE or IRE-like motifs in their 3’ or 5’ untranslated regions (UTRs) were identified in human, mouse, and zebrafish reference transcriptomes. Further analyses focusing on these genes were applied to a range of cultured cell, human, mouse, and zebrafish gene expression datasets.

Results

IRE gene sets are sufficiently sensitive to distinguish not only between iron overload and deficiency in cultured cells, but also between AD and other pathological brain conditions. Notably, changes in IRE transcript abundance are amongst the earliest observable changes in zebrafish familial AD (fAD)-like brains, preceding other AD-typical pathologies such as inflammatory changes. Unexpectedly, while some IREs in the 3’ untranslated regions of transcripts show significantly increased stability under iron deficiency in line with current assumptions, many such transcripts instead display decreased stability, indicating that this is not a generalizable paradigm.

Conclusion

Our results reveal IRE gene expression changes as early markers of the pathogenic process in fAD and are consistent with iron dyshomeostasis as an important driver of this disease. Our work demonstrates how differences in the stability of IRE- containing transcripts can be used to explore and compare iron dyshomeostasis-associated gene expression responses across different species, tissues, and conditions.
Arabidopsis SMN2/HEN2, Encoding DEAD-box RNA Helicase, Governs Proper Expression of the Resistance GeneSMN1/RPS6and Is Involved in Dwarf, Autoimmune Phenotypes ofmekk1andmpk4Mutants
Authors: Takagi Momoko , Iwamoto Naoki , Kubo Yuta , Morimoto Takayuki , Takagi Hiroki , Takahashi Fuminori , Nishiuchi Takumi , Tanaka Keisuke , Taji Teruaki , Kaminaka Hironori , Shinozaki Kazuo , Akimitsu Kazuya , Terauchi Ryohei , Shirasu Ken , Ichimura Kazuya
Published: May 2020

InArabidopsis thaliana, a mitogen-activated protein kinase pathway, MEKK1–MKK1/MKK2–MPK4, is important for basal resistance, and disruption of this pathway results in dwarf, autoimmune phenotypes. To elucidate the complex mechanisms activated by the disruption of this pathway, we have previously developed a mutant screening system based on a dwarf autoimmune line that overexpressed the N-terminal regulatory domain of MEKK1. Here, we report that the second group of mutants,smn2, had defects in theSMN2gene, encoding a DEAD-box RNA helicase.SMN2is identical toHEN2, whose function is vital for the nuclear RNA exosome because it provides non-ribosomal RNA specificity for RNA turnover, RNA quality control, and RNA processing. AberrantSMN1/RPS6transcripts were detected insmn2andhen2mutants. Disease resistance againstPseudomonas syringaepv.tomatoDC3000 (hopA1), which is conferred bySMN1/RPS6, was decreased insmn2mutants, suggesting a functional connection betweenSMN1/RPS6andSMN2/HEN2. We produced double mutantsmekk1smn2andmpk4smn2to determine whether thesmn2mutations suppress the dwarf, autoimmune phenotypes of themekk1andmpk4mutants, as thesmn1mutations do. As expected, themekk1andmpk4phenotypes were suppressed by thesmn2mutations. These results suggested thatSMN2is involved in proper function ofSMN1/RPS6. The GO enrichment analysis using RNA-seq data showed that defense genes were downregulated insmn2, suggesting positive contribution ofSMN2to genome-wide expression of defense-related genes. In conclusion, this study provides novel insight into plant immunity viaSMN2/HEN2, an essential component of the nuclear RNA exosome.
Comprehensive characterization of N- and O- glycosylation of SARS-CoV-2 human receptor angiotensin converting enzyme 2
Authors: Shajahan Asif , Archer-Hartmann Stephanie , Supekar Nitin T. , Gleinich Anne S. , Heiss Christian , Azadi Parastoo
Published: May 2020

The emergence of the COVID-19 pandemic caused by SARS-CoV-2 has created the need for development of new therapeutic strategies. Understanding the mode of viral attachment, entry and replication has become a key aspect of such interventions. The coronavirus surface features a trimeric spike (S) protein that is essential for viral attachment, entry and membrane fusion. The S protein of SARS-CoV-2 binds to human angiotensin converting enzyme 2 (hACE2) for entry. Herein, we describe glycomic and glycoproteomic analysis of hACE2 expressed in HEK293 human cells. We observed high glycan occupancy (73.2 to 100%) at all seven possible N-glycosylation sites and surprisingly detected one novel O-glycosylation site. To deduce the detailed structure of glycan epitopes on hACE2 that may be involved in viral binding, we have characterized the terminal sialic acid linkages, the presence of bisecting GlcNAc, and the pattern of N-glycan fucosylation. We have conducted extensive manual interpretation of each glycopeptide and glycan spectrum, in addition to using bioinformatics tools to validate the hACE2 glycosylation. Our elucidation of the site-specific glycosylation and its terminal orientations on the hACE2 receptor, along with the modeling of hACE2 glycosylation sites can aid in understanding the intriguing virus-receptor interactions and assist in the development of novel therapeutics to prevent viral entry. The relevance of studying the role of ACE2 is further increased due to some recent reports about the varying ACE2 dependent complications with regard to age, sex, race, and pre-existing conditions of COVID-19 patients.
Engineering the Compression of Sequencing Reads
Authors: Kowalski Tomasz , Grabowski Szymon
Published: May 2020

Motivation

FASTQ remains among the widely used formats for high-throughput sequencing data. Despite advances in specialized FASTQ compressors, they are still imperfect in terms of practical performance tradeoffs.

Results

We present a multi-threaded version of Pseudogenome-based Read Compressor (PgRC), an in-memory algorithm for compressing the DNA stream, based on the idea of building an approximation of the shortest common superstring over high-quality reads. The current version, v1.2, practically preserves the compression ratio and decompression speed of the previous one, reducing the compression time by a factor of about 4–5 on a 6-core/12-thread machine.

Availability

PgRC 1.2 can be downloaded fromhttps://github.com/kowallus/PgRC.

Contact

sgrabow@kis.p.lodz.pl
Estimating RNA dynamics using one time point for one sample in a single-pulse metabolic labeling experiment
Authors: Hersch Micha , Biasini Adriano , Marques Ana C. , Bergmann Sven
Published: May 2020

Over the past decade, experimental procedures such as metabolic labeling for determining RNA turnover rates at the transcriptome-wide scale have been widely adopted and are now turning to single cell measurements. Several computational methods to estimate RNA processing and degradation rates from such experiments have been suggested, but they all require several RNA sequencing samples. Here we present a method that can estimate RNA synthesis, processing and degradation rates from a single sample. Our method is computationally efficient and outputs rates that correlate well with previously published data sets. Using it on a single sample, we were able to reproduce the observation that dynamic biological processes tend to involve genes with higher metabolic rates, while stable processes involve genes with lower rates. This supports the hypothesis that cells control not only the mRNA steady-state abundance, but also its responsiveness, i.e., how fast steady-state is reached. In addition to saving experimental work and computational time, having a sample-based rate estimation has several advantages. It does not require an error-prone normalization across samples and enables the use of replicates to estimate uncertainty and perform quality control. Finally the method and theoretical results described here are general enough to be useful in other contexts such as nucleotide conversion methods and single cell metabolic labeling experiments.
Concomitant processing of choice and outcome in frontal corticostriatal ensembles correlates with performance of rats
Authors: Handa Takashi , Harukuni Rie , Fukai Tomoki
Published: May 2020

The frontal cortex-basal ganglia network plays a pivotal role in adaptive goal-directed behaviors. Medial frontal cortex (MFC) encodes information about choices and outcomes into sequential activation of neural population, or neural trajectory. While MFC projects to the dorsal striatum (DS), whether DS also displays temporally coordinated activity remains unknown. We studied this question by simultaneously recording neural ensembles in the MFC and DS of rodents performing an outcome-based alternative choice task. We found that the two regions exhibited highly parallel evolution of neural trajectories, transforming choice information into outcome-related information. When the two trajectories were highly correlated, spike synchrony was task-dependently modulated in some MFC-DS neuron pairs. Our results suggest that neural trajectories concomitantly process decision-relevant information in MFC and DS with increased spike synchrony between these regions.
Bottom-Illuminated Orbital Shaker for Microalgae Cultivation
Authors: Nedbal Jakub , Gao Lu , Suhling Klaus
Published: May 2020

A bottom-illuminated orbital shaker designed for the cultivation of microalgae suspensions is described in this open-source hardware report. The instrument agitates and illuminates microalgae suspensions grown inside flasks. It was optimized for low production cost, simplicity, low power consumption, design flexibility, consistent, and controllable growth light intensity.

The illuminated orbital shaker is especially well suited for low-resource research laboratories and education. It is an alternative to commercial instruments for microalgae cultivation. It improves on typical do-it-yourself microalgae growth systems by offering consistent and well characterized illumination light intensity. The illuminated growth area is 20 cm × 15 cm, which is suitable for three T75 tissue culture flasks or six 100 ml Erlenmeyer flasks. The photosynthetic photon flux density, is variable in eight steps (26 – 800 μmol · m−2· s−1) and programmable in a 24-hour light/dark cycle. The agitation speed is variable (0 – 210 RPM). The overall material cost is around £300, including an entry-level orbital shaker. The build takes two days, requiring electronics and mechanical assembly capabilities. The instrument build is documented in a set of open-source protocols, design files, and source code. The design can be readily modified, scaled, and adapted for other orbital shakers and specific experimental requirements.

The instrument function was validated by growing fresh-water microalgaeDesmodesmus quadricaudaandChlorella vulgaris. The cultivation protocols, microalgae growth curves, and doubling times are included in this report.

Specifications table
Structural and molecular determinants of CCS-mediated copper activation of MEK1/2
Authors: Grasso Michael , Bond Gavin J. , Kim Ye-Jin , Alwan Katherine B. , Boyd Stefanie , Dzebo Maria Matson , Valenzuela Sebastian , Tsang Tiffany , Schibrowsky Natalie A. , Matthews Megan L. , Burslem George M. , Wittung-Stafshede Pernilla , Winkler Duane D. , Blackburn Ninian J. , Marmorstein Ronen , Brady Donita C.
Published: May 2020

Normal physiology relies on the precise coordination of intracellular signal transduction pathways that respond to nutrient availability to balance cell growth and cell death. We recently established a critical mechanistic function for the redox-active micronutrient copper (Cu) in the canonical mitogen activated protein kinase (MAPK) pathway at the level of MEK1 and MEK2. Here we report the X-ray crystal structure of Cu-MEK1 and reveal active site chemical ligands and oxidation state specificity for MEK1 Cu coordination. Mechanistically, the Cu chaperone CCS selectively bound to and facilitated Cu transfer to MEK1. Mutations in MEK1 that disrupt Cu(I) affinity or a CCS small molecule inhibitor reduced Cu-stimulated MEK1 kinase activity. These atomic and molecular level data provide the first mechanistic insights of Cu kinase signaling and could be exploited for the development of novel MEK1/2 inhibitors that either target the Cu structural interface or blunt dedicated Cu delivery mechanisms via CCS.
Schizophrenia-associated variation atZNF804Acorrelates with altered experience-dependent dynamics of sleep slow-waves and spindles in healthy young adults
Authors: Bartsch Ullrich , Corbin Laura J , Hellmich Charlotte , Taylor Michelle , Easey Kayleigh E , Durant Claire , Marston Hugh M , Timpson Nicholas J , Jones Matthew W
Published: May 2020

Background

The rs1344706 polymorphism inZNF804Ais robustly associated with schizophrenia (SZ), yet brain and behavioral phenotypes related to this variant have not been extensively characterized. In turn, SZ is associated with abnormal non-rapid eye movement (NREM) sleep neurophysiology. To examine whether rs1344706 is associated with intermediate neurophysiological traits in the absence of disease, we assessed the relationship between genotype, sleep neurophysiology, and sleep-dependent memory consolidation in healthy participants.

Methods

We recruited healthy adult males, with no history of psychiatric disorder, from the Avon Longitudinal Study of Parents and Children (ALSPAC) birth cohort. Participants were homozygous for either the SZ-associated ‘A’ allele (N=25) or the alternative ‘C’ allele (N=22) at rs1344706. Actigraphy, polysomnography (PSG) and a motor sequencing task (MST) were used to characterize daily activity patterns, sleep neurophysiology and sleep-dependent memory consolidation.

Results

Average MST learning and sleep-dependent performance improvements were similar across genotype groups, but with increased variability in the AA group. CC participants showed increased slow-wave and spindle amplitudes, plus augmented coupling of slow-wave activity across recording electrodes after learning. Slow-waves and spindles in those with the AA genotype were insensitive to learning, whilst slow-wave coherence decreased following MST training.

Conclusion

We describe evidence that rs1344706 polymorphism inZNF804Ais associated with changes in experience- and sleep-dependent, local and distributed neural network activity that supports offline information processing during sleep in a healthy population. These findings highlight the utility of sleep neurophysiology in mapping the impacts of SZ-associated variants on neural circuit oscillations and function.
Compound 21, a two-edged sword with both DREADD-selective and off-target outcomes in rats
Authors: Goutaudier Raphaël , Coizet Véronique , Carcenac Carole , Carnicella Sebastien
Published: May 2020

Although Designer Receptors Exclusively Activated by Designer Drugs (DREADDs) represent a technical revolution in integrative neuroscience, the first ligands used were not as selective as expected. Compound 21 (C21) was recently proposed as an alternative, butin vivocharacterization of its properties is not sufficient yet. Here, we evaluated its potency to selectively modulate the activity of nigral dopaminergic (DA) neurons through the canonical DREADD receptor hM4Di using TH-Cre rats. In males, 1 mg.kg−1of C21 strongly increased nigral neurons activity in control animals, indicative of a significant off-target effect. Reducing the dose to 0.5 mg.kg−1circumvented this aspecific effect, while activated the inhibitory DREADDs and selectively reduced nigral neurons firing. In females, 0.5 mg.kg−1of C21 induced a transient and residual off-target effect that may mitigated the inhibitory DREADDs-mediated effect. This study raises up the necessity to test selectivity and efficacy of chosen ligands for each new experimental condition.
An integrated genomics approach towards deciphering human genome codes shaping HIV-1 proviral transcription and fate
Authors: Ruess Holly , Lee Jeon , Guzman Carlos , Malladi Venkat , D’Orso Iván
Published: May 2020

A large body of work has revealed fundamental principles of HIV-1 integration into the human genome. However, the effect of the integration site to proviral transcription activity has so far remained elusive. Here we combine open-source, large-scale datasets including epigenetics, transcriptome, and 3D genome architecture to interrogate the chromatin states, transcription activity landscape, and nuclear sub-compartments around HIV-1 integration sites in CD4+T cells to decipher human genome codes shaping the transcription of proviral classes defined based on their position and orientation in the genome. Using a Hidden Markov Model, we describe the importance of specific chromatin states and genome architecture in the control of HIV-1 transcription activity. Additionally, implementation of a machine-learning logistic regression model reveals upstream chromatin accessibility, transcription activity, and categorical nuclear sub-compartments as optimal features predicting HIV-1 transcriptional outcomes. We finally demonstrate clinical relevance by interrogating the positions of intact proviruses persisting in patients under suppressive therapy and provide a compass compatible with clinical decision-making.
Decreased investigatory head scanning during exploration in learning-impaired, aged rats
Authors: Rao Geeta , Lee Heekyung , Gallagher Michela , Knierim James J.
Published: May 2020

“Head scanning” is an investigatory behavior that has been linked to spatial exploration and the one-trial formation or strengthening of place cells in the hippocampus. Previous studies have demonstrated that a subset of aged rats with normal spatial learning performance show head scanning rates during a novel, local-global cue-mismatch manipulation that are similar to those of young rats. However, these aged rats demonstrated different patterns of expression of neural activity markers in brain regions associated with spatial learning, perhaps suggesting neural mechanisms that compensate for age-related brain changes. These prior studies did not investigate the head scanning properties of aged rats that had spatial learning impairments. The present study analyzed head scanning behavior in young, aged-unimpaired, and aged-impaired Long Evans rats. Aged-impaired rats performed the head scan behavior at a lower rate than the young rats. These results suggest that decreased attention to spatial landmarks may be a contributing factor to the spatial learning deficits shown by the aged-impaired rats.
Model for Deformation of Cells from External Electric Fields at or Near Resonant Frequencies
Authors: Martinez L. , Dhruv A. , Lin L. , Balaras E. , Keidar M.
Published: May 2020

This paper presents a numerical model to investigate the deformation of biological cells by applying external electric fields operating at or near cell resonant frequencies. Cells are represented as pseudo solids with high viscosity suspended in liquid media. The electric field source is an atmospheric plasma jet developed inhouse, for which the emitted energy distribution has been measured.

Viscoelastic response is resolved in the entire cell structure by solving a deformation matrix assuming an isotropic material with a prescribed modulus of elasticity. To investigate cell deformation at resonant frequencies, one mode of natural cell oscillation is considered in which the cell membrane is made to radially move about its eigenfrequency. An electromagnetic wave source interacts with the cell and induces oscillation and viscoelastic response. The source carries energy in the form of a distribution function which couples a range of oscillating frequencies with electric field amplitude.

Results show that cell response may be increased by the external electric field operating at or near resonance. In the elastic regime, response increases until a steady threshold value, and the structure moves as a damped oscillator. Generally, this response is a function of both frequency and magnitude of the source, with a maximum effect found at resonance. To understand the full effect of the source energy spectrum, the system is solved by considering five frequency-amplitude couplings. Results show that the total solution is a nonlinear combination of the individual solutions. Additionally, sources with different signal phases are simulated to determine the effect of initial conditions on the evolution of the system, and the result suggests that there may be multiple solutions within the same order of magnitude for elastic response and velocity. Cell rupture from electric stress may occur during application given a high energy source.

Significance

Cold atmospheric plasma jets (CAPJs) have been widely researched for their potential applications in cancer therapy. Existing research has focused mainly on the ability of CAPJs to deliver a mixture of reactive species which can be absorbed by cancer cells and induce cell death. The objective of our study is to investigate the mechanical effect of CAPJ electromagnetic (EM) waves on interacting cells. By coupling the EM waves associated with plasma frequency and cell viscoelastic response, we have developed a numerical tool to investigate cell damage either by mechanical or thermal loads. This work is motivated by the promise of EM waves to function as a sensitizing agent for cancer cells in preparation for chemotherapy.
Advancing the genetic utility of pre-clinical species through a high-quality assembly of the cynomolgus monkey (Macaca fascicularis) genome
Authors: Oziolor Elias , Sullivan Shawn , Mangelson Hayley , Eacker Stephen M. , Agostino Michael , Whiteley Laurence , Cook Jon , Koza-Taylor Petra
Published: May 2020

The cynomolgus macaque is a non-human primate model, heavily used in biomedical research, but with outdated genomic resources. Here we have used the latest long-read sequencing technologies in order to assemble a fully phased, chromosome-level assembly for the cynomolgus macaque. We have built a hybrid assembly with PacBio, 10x Genomics, and HiC technologies, resulting in a diploid assembly that spans a length of 5.1 Gb with a total of 16,741 contigs (N50 of 0.86Mb) contained in 370 scaffolds (N50 of 138 Mb) positioned on 42 chromosomes (21 homologous pairs). This assembly is highly homologous to former assemblies and identifies novel inversions and provides higher confidence in the genetic architecture of the cynomolgus macaque genome. A demographic estimation is also able to capture the recent genetic bottleneck in the Mauritius population, from which the sequenced individual originates. We offer this resource as an enablement for genetic tools to be built around this important model for biomedical research.
Serotonergic psychedelic drugs LSD and psilocybin reduce the hierarchical differentiation of unimodal and transmodal cortex
Authors: Girn Manesh , Roseman Leor , Bernhardt Boris , Smallwood Jonathan , Carhart-Harris Robin , Spreng R. Nathan
Published: May 2020

LSD and psilocybin are serotonergic psychedelic compounds with potential in the treatment of mental health disorders. Past neuroimaging investigations have revealed that both compounds can elicit significant changes to whole-brain functional organization and dynamics. A recent proposal linked past findings into a unified model and hypothesized reduced whole-brain hierarchical organization as a key mechanism underlying the psychedelic state, but this has yet to be directly tested. We applied a non-linear dimensionality reduction technique previously used to map hierarchical connectivity gradients to pharmacological resting-state fMRI data to assess cortical organization in the LSD and psilocybin state. Results supported our primary hypothesis: The principal gradient of cortical connectivity, describing a hierarchy from unimodal to transmodal cortex, was significantly flattened under both drugs relative to their respective placebo conditions. Between-condition contrasts revealed that this was driven by a reduction of functional differentiation at both hierarchical extremes – default and frontoparietal networks at the upper end, and somatomotor at the lower. Gradient-based connectivity mapping confirmed that this was underpinned by increased unimodal-transmodal crosstalk. In addition, LSD-dependent principal gradient changes tracked changes in self-reported ego-dissolution. Results involving the second and third gradient, which respectively represent axes of sensory and executive differentiation, also showed significant alterations across both drugs. These findings provide support for a recent mechanistic model of the psychedelic state relevant to therapeutic applications of psychedelics. More fundamentally, we provide the first evidence that macroscale connectivity gradients are sensitive to a pharmacological manipulation, specifically highlighting an important relationship between cortical organization and serotonergic modulation.
Mesenchymal ETV Transcription Factors Regulate Cochlear Length
Authors: Ebeid Michael , Huh Sung-Ho
Published: May 2020

Mammalian cochlear development encompasses a series of morphological and molecular events that results in the formation of a highly intricate structure responsible for hearing. One remarkable event occurs during development is the cochlear lengthening that starts with cochlear outgrowth around E11 and continues throughout development. Different mechanisms contribute to this process including cochlear progenitor proliferation and convergent extension. We previously identified that FGF9 and FGF20 promote cochlear lengthening by regulating auditory sensory epithelial proliferation through FGFR1 and FGFR2 in the periotic mesenchyme. Here, we provide evidence that ETS-domain transcription factors ETV4 and ETV5 are downstream of mesenchymal FGF signaling to control cochlear lengthening. Next generation RNA sequencing identified thatEtv1, Etv4andEtv5mRNAs are decreased in theFgf9andFgf20double mutant periotic mesenchyme. Deleting bothEtv4andEtv5in periotic mesenchyme resulted in shortening of cochlear length but maintaining normal patterning of organ of Corti and density of hair cells and supporting cells. This recapitulates phenotype of mesenchymal-specificFgfr1andFgfr2deleted inner ear. Furthermore, analysis ofEtv1/4/5triple conditional mutants revealed that ETV1 does not contribute in this process. Our study reveals that ETV4 and ETV5 function downstream of mesenchymal FGF signaling to promote cochlear lengthening.
Global, Highly Specific and Fast Filtering of Alignment Seeds
Authors: Ebel Matthis , Migliorelli Giovanna , Stanke Mario
Published: May 2020

An important initial phase of arguably most homology search and alignment methods such as required for genome alignments isseed finding. The seed finding step is crucial to curb the runtime as potential alignments are restricted to andanchored atthe sequence position pairs that constitute the seed. To identify seeds, it is good practice to use sets of spaced seed patterns, a method thatlocallycompares two sequences and requires exact matches at certain positions only.

We introduce a new method for filtering alignment seeds that we callgeometric hashing. Geometric hashing achieves a high specificity by combining non-local information from different seeds using a simple hash function that only requires a constant and small amount of additional time per spaced seed. Geometric hashing was tested on the task of finding homologous positions in the coding regions of human and mouse genome sequences. Thereby, the number of false positives was decreased about million-fold over sets of spaced seeds while maintaining a very high sensitivity.

An additional geometric hashing filtering phase could improve the run-time, accuracy or both of programs for various homology-search-and-align tasks.