bluuebunny/crossref_metadata_2025 huggingface dataset:
Antiviral activity of N-ω-Chloroacetyl-L-Ornithine on in vitro replication of Chikungunya virus
Authors: Luna-Rojas Lucero , Avila-Trejo Amanda M. , Alcántara-Farfán Verónica , Rodríguez-Páez Lorena I. , Pastor-Alonso Marvin Omar , Aguilar-Faisal J. Leopoldo
Published: August 2019

The infections causes by Chikungunya virus (CHIKV), family Togaviridae, genus Alfavirus, have become a health problem around the world, due to its widespread occurrence, the high morbidity rate and the absence of vaccines or antiviral treatments. We analyzed a competitive inhibitor of ornithine decarboxylase, enzyme key in the biosynthesis of Polyamines (PAs), N-ω-chloroacetyl-L-ornithine (NCAO), as a possible inhibitor of CHIKV replication because intracellular polyamines participate in the transcription andin vitrotranslation of CHIKV. NCAO does not have any cytotoxic effect on C6/36 cells even at a concentration of 1000μM at 72h after post-exposure but in Vero cells the cytotoxic effect was presented above 380μM at 48h post-exposure, which was considered when determining the inhibitory effect on viral replication. We demonstrate that NCAO inhibits the replication of CHIKV in Vero and C6/36 cells in a dose-dependent manner causing a decrease in the PFU/mL of at least 4-logarithm (p <0.01) in both cell lines. Viral yields were restored by the addition of exogenous polyamines, mainly putrescine. HPLC analyses it shown that NCAO decrease content of intracellular PAs even though in infected cells mainly decreased spermidine and spermine, so NCAO inhibits CHIKV replication, by depleting the intracellular polyamines in Vero and C6/36 cells, suggesting that this compound is a possible antiviral in CHIKV infections.

Importance

The infections caused by Chikungunya virus (CHIKV), genus Alfavirus, have become a worldwide health problem, due to its high morbidity rate and the absence of vaccines or antiviral treatments. It is known that CHIKV use intracellular poliamines during transcription and traduction process, so the depletion of intracellular putrescine, spermidine and spermine reduce the viral replication. N-ω-chloroacetyl-L-ornithine (NCAO) is known as a competitive inhibitor of ornithine decarboxylase, key enzyme in Polyamines biosynthesis, but no studies have proven its activity on the inhibition of polyamine-dependent viral replication. Here we demonstrate NCAO inhibits in vitro CHIKV replication, so we propose NCAO as an antiviral candidate.
Algal photosynthesis converts nitric oxide into nitrous oxide
Authors: Burlacot Adrien , Richaud Pierre , Gosset Arthur , Li-Beisson Yonghua , Peltier Gilles
Published: August 2019

Nitrous oxide (N2O), a potent greenhouse gas in the atmosphere, is produced mostly from aquatic ecosystems, to which algae substantially contribute. However, mechanisms of N2O production by photosynthetic organisms are poorly described. Here, we show that the green microalgaChlamydomonas reinhardtiireduces NO into N2O using the photosynthetic electron transport. Through the study ofC. reinhardtiimutants deficient in flavodiiron proteins (FLVs) or in a cytochrome p450 (CYP55), we show that FLVs contribute to NO reduction in the light, while CYP55 operates in the dark. Furthermore, NO reduction by both pathways is restricted to Chlorophytes, organisms particularly abundant in ocean N2O-producing hotspots. Our results provide a mechanistic understanding of N2O production in eukaryotic phototrophs and represent an important step toward a comprehensive assessment of greenhouse gas emission by aquatic ecosystems.

One sentence summary

Green microalgae produce N2O using flavodiiron proteins in the light and a cytochrome P450 NO reductase in the dark.
Gut Microbiome Biomarkers in Adolescent Obesity: a Regional Study
Authors: Gao Xuefeng , Wu Binbin , Pan Yonglong , Zhou Shaoming , Zhang Ming , Cai Yunpeng , Liang Yan
Published: August 2019

Purpose

This study aimed to characterize the gut microbiota in obese Shenzhen adolescents, and evaluate the influence of gender on BMI-related differences in the gut microbiome.

Methods

Physical examinations, blood pressure measurement, serological assay, and body composition evaluation were conducted on two-hundred and five adolescents from Shenzhen. Fecal microbiome composition was profiled via 16S rRNA gene sequencing. A Random Forest (RF) classifier model was built to distinguish the BMI categories based on the gut bacterial composition.

Results

Fifty-six taxa consisting mainly of Firmicutes were identified that having significant associations with BMI; two OTUs belonging to Ruminococcaceae and one belonging to Lachnospiraceae had relatively strong positive correlations with body fate rate, waistline, and most of serum biochemical parameters. Based on the 56 BMI-associated OTUs, the RF model showed a robust classification accuracy (AUC 0.96) for predicting the obese phenotype. Gender-specific differences in the gut microbiome composition was obtained, and a lower relative abundance of Odoribacter was particularly found in obese boys. Functional analysis revealed a deficiency in bacterial gene contents related to PPAR signaling pathway in obese subjects for both genders; significantly lower levels of adipocytokine signaling pathway and ethylbenzene degradation were particularly detected in obese girls.

Conclusions

This study revealed unique features of gut microbiome in terms of microbial composition and metabolic functions in obese Shenzhen adolescents. The effect of geographical location, age and gender on the gut microbiome should be carefully considered in case–control studies.
Modelling functional human neuromuscular junctions in a differentially-perturbable microfluidic environment, validated through recombinant monosynaptic pseudotyped ΔG-rabies virus tracing
Authors: Bauer Ulrich Stefan , van de Wijdeven Rosanne , Raveendran Rajeevkumar Nair , Fiskum Vegard , Kentros Clifford , Sandvig Ioanna , Sandvig Axel
Published: August 2019

Compartmentalized microfluidic culture systems provide new perspectives in in vitro disease modelling as they enable co-culture of different relevant cell types in interconnected but fluidically isolated microenvironments. Such systems are thus particularly interesting in the context of in vitro modelling of mechanistic aspects of neurodegenerative diseases such as amyotrophic lateral sclerosis, which progressively affect the function of neuromuscular junctions, as they enable the co-culture of motor neurons and muscle cells in separate, but interconnected compartments. In combination with cell reprogramming technologies for the generation of human (including patient-specific) motor neurons, microfluidic platforms can thus become important research tools in preclinical studies. In this study, we present the application of a microfluidic chip with a differentially-perturbable microenvironment as a platform for establishing functional neuromuscular junctions using human induced pluripotent stem cell derived motor neurons and human myotubes. As a novel approach, we demonstrate the functionality of the platform using a designer pseudotyped ΔG-rabies virus for retrograde monosynaptic tracing.

Graphical abstract

Functional neuromuscular junction in a microfluidic chip

(a) Overview of microfluidic chip. Human iPS cell-derived motor neuron aggregates (spheroids indicated by black arrows) are seeded in the three lateral compartments of the chip, while human myotubes (white arrows) are seeded in the middle compartment.

(b) Directed connectivity and retrograde virus tracing. Outgrowing axons (yellow arrow) from the motor neuron aggregate enter the directional axon tunnels (grey rectangles) and form connections with the myotubes (white arrow) within the opposite compartment. Addition of a designer monosynaptic pseudotyped ΔG-rabies virus to the myotube compartment, infects the myotubes (green) expressing an exogenous receptor (TVA) and rabies glycoprotein (G), subsequently making infectious viruses that are retrogradely transported through the motor neuron axons (green arrow) back to the neuronal cell bodies within the aggregate, validating neuromuscular junction functionality.
Assessing seasonal demographic covariation to understand environmental-change impacts on a hibernating mammal
Authors: Paniw Maria , Childs Dylan , Armitage Kenneth B , Blumstein Daniel T , Martin Julien , Oli Madan K. , Ozgul Arpat
Published: August 2019

Natural populations are exposed to seasonal variation in environmental factors that simultaneously affect several demographic rates (survival, development, reproduction). The resulting covariation in these rates determines population dynamics, but accounting for its numerous biotic and abiotic drivers is a significant challenge. Here, we use a factor-analytic approach to capture partially unobserved drivers of seasonal population dynamics. We use 40 years of individual-based demography from yellow-bellied marmots (Marmota flaviventer) to fit and project population models that account for seasonal demographic covariation using a latent variable. We show that this latent variable, by producing positive covariation among winter demographic rates, depicts a measure of environmental quality. Simultaneous, negative responses of winter survival and reproductive-status change to declining environmental quality result in a higher risk of population quasi-extinction, regardless of summer demography where recruitment takes place. We demonstrate how complex environmental processes can be summarized to understand population persistence in seasonal environments.
Evaluation of the impact of seasonal variations in photoperiod on the hepatic metabolism of medaka (Oryzias latipes)
Authors: Fujisawa Koichi , Takami Taro , Shintani Haruko , Sasai Nanami , Matsumoto Toshihiko , Yamamoto Naoki , Sakaida Isao
Published: August 2019

Organisms living in temperate regions are sensitive to seasonal variations in the environment; they are known to accumulate energy as fat in their livers during the winter when days are shorter, temperatures are lower, and food is scarce. However, the impact of variations in photoperiod alone on hepatic lipid metabolism has not been well-studied. Therefore, in this study, we analyzed lipid metabolism in the liver of medaka,Oryzias latipes, while varying the length of days at constant temperature. Larger amounts of fatty acids accumulated in the liver after 14 days under short-day conditions than under long-day conditions. Metabolome analysis showed no accumulation of the long-chain unsaturated fatty acids required at low temperatures, but showed a significant accumulation of long-chain saturated fatty acids. Short-day conditions induced decreased levels of succinate, fumarate, and malate in the tricarboxylic acid cycle, decreased expression of PPARα, and decreased accumulation of acylcarnitine, which suggested inhibition of lipolysis. In addition, when a high-fat diet was administered to transparent medaka under short-day conditions, larger amounts of fat accumulated and medaka with fatty liver were efficiently produced. Detailed analysis of the relationship between seasonal changes and hepatic steatosis will be important in the future as hepatic diseases become more prevalent in modern society; the findings obtained in our study will be useful for research studies pertaining to the relationship between photoperiod and disorders such as hepatic steatosis and non-alcoholic steatohepatitis.
Dynamic architecture and regulatory implications of the miRNA network underlying the response to stress in melon
Authors: Sanz-Carbonell Alejandro , Marques Maria Carmen , Martinez German , Gomez Gustavo
Published: August 2019

miRNAs are small RNAs that regulate mRNAs at both transcriptional and posttranscriptional level. In plants, miRNAs are involved in the regulation of different processes including development and stress-response. Elucidating how stress-responsive miRNAs are regulated is key to understand the global response to stress but also to develop efficient biotechnological tools that could help to cope with stress. Here, we describe a computational approach based on sRNA sequencing, transcript quantification and degradome data to analyze the accumulation, function and structural organization of melon miRNAs reactivated under seven biotic and abiotic stress conditions at two and four days post-treatment. Our pipeline allowed us to identify fourteen stress-responsive miRNAs (including evolutionary conserved such as miR156, miR166, miR172, miR319, miR398, miR399, miR894 and miR408) at both analyzed times. According to our analysis miRNAs were categorized in three groups showing a broad-, intermediate- or narrow- response range. miRNAs reactive to a broad range of environmental cues appear as central components in the stress-response network. The strictly coordinated response of miR398 and miR408 (broad response-range) to the seven stress treatments during the period analyzed here reinforces this notion. Although both, the amplitude and diversity of the miRNA-related response to stress changes during the exposition time, the architecture of the miRNA-network is conserved. This organization of miRNA response to stress is also conserved in rice and soybean supporting the conservation of miRNA-network organization in other crops. Overall, our work sheds light into how miRNA networks in plants organize and function during stress.
Quantitative Single-Cell Proteomics as a Tool to Characterize Cellular Hierarchies
Authors: Schoof Erwin M. , Furtwängler Benjamin , Üresin Nil , Rapin Nicolas , Savickas Simonas , Gentil Coline , Lechman Eric , auf dem Keller Ulrich , Dick John E. , Porse Bo T.
Published: August 2019

Large-scale single-cell analyses are of fundamental importance in order to capture biological heterogeneity within complex cell systems, but have largely been limited to RNA-based technologies. Here we present a comprehensive benchmarked experimental and computational workflow, which establishes global single-cell mass spectrometry-based proteomics as a tool for large-scale single-cell analyses.

By exploiting a primary leukemia model system, we demonstrate both through pre-enrichment of cell populations and through a non-enriched unbiased approach that our workflow enables the exploration of cellular heterogeneity within this aberrant developmental hierarchy. Our approach is capable of consistently quantifying approximately 1000 proteins per cell across thousands of individual cells using limited instrument time. Furthermore, we developed a computational workflow (SCeptre) that effectively normalizes the data, integrates available FACS data and facilitates downstream analysis. The approach presented here lays a solid foundation for implementing global single-cell proteomics studies across the world.
An Interpretable Performance Metric for Auditory Attention Decoding Algorithms in a Context of Neuro-Steered Gain Control
Authors: Geirnaert Simon , Francart Tom , Bertrand Alexander
Published: August 2019

In a multi-speaker scenario, a hearing aid lacks information on which speaker the user intends to attend, and therefore it often mistakenly treats the latter as noise while enhancing an interfering speaker. Recently, it has been shown that it is possible to decode the attended speaker from the brain activity, e.g., recorded by electroencephalography sensors. While numerous of these auditory attention decoding (AAD) algorithms appeared in the literature, their performance is generally evaluated in a non-uniform manner. Furthermore, AAD algorithms typically introduce a trade-off between the AAD accuracy and the time needed to make an AAD decision, which hampers an objective benchmarking as it remains unclear which point in each algorithm’s trade-off space is the optimal one in a context of neuro-steered gain control. To this end, we present an interpretable performance metric to evaluate AAD algorithms, based on an adaptive gain control system, steered by AAD decisions. Such a system can be modeled as a Markov chain, from which the minimal expected switch duration (MESD) can be calculated and interpreted as the expected time required to switch the operation of the hearing aid after an attention switch of the user, thereby resolving the trade-off between AAD accuracy and decision time. Furthermore, we show that the MESD calculation provides an automatic and theoretically founded procedure to optimize the number of gain levels and decision time in an AAD-based adaptive gain control system.
Extending the small molecule similarity principle to all levels of biology
Authors: Duran-Frigola Miquel , Pauls Eduardo , Guitart-Pla Oriol , Bertoni Martino , Alcalde Víctor , Amat David , Juan-Blanco Teresa , Aloy Patrick
Published: August 2019

We present the Chemical Checker (CC), a resource that provides processed, harmonized and integrated bioactivity data on 800,000 small molecules. The CC divides data into five levels of increasing complexity, ranging from the chemical properties of compounds to their clinical outcomes. In between, it considers targets, off-targets, perturbed biological networks and several cell-based assays such as gene expression, growth inhibition and morphological profilings. In the CC, bioactivity data are expressed in a vector format, which naturally extends the notion of chemical similarity between compounds to similarities between bioactivity signatures of different kinds. We show how CC signatures can boost the performance of drug discovery tasks that typically capitalize on chemical descriptors, including target identification and library characterization. Moreover, we demonstrate and experimentally validate that CC signatures can be used to reverse and mimic biological signatures of disease models and genetic perturbations, options that are otherwise impossible using chemical information alone.
Phase-based coordination of hippocampal and neocortical oscillations during human sleep
Authors: Cox Roy , Rüber Theodor , Staresina Bernhard P , Fell Juergen
Published: August 2019

During sleep, new memories undergo a gradual transfer from the hippocampus (HPC) to the neocortex (NC). Precisely timed neural oscillations interacting within and between these brain structures are thought to mediate this sleep-dependent memory consolidation, but exactly which sleep oscillations instantiate the HPC-NC dialog, and via what mechanisms, remains elusive. Employing invasive electroencephalography in ten neurosurgical patients across a full night of sleep, we identified three broad classes of phase-based HPC-NC communication. First, we observed interregional phase synchrony for non-rapid eye movement (NREM) spindles, N2 and rapid eye movement (REM) theta, and N3 beta activity. Second, and most intriguingly, we found asymmetrical N3 cross-frequency phase-amplitude coupling between HPC SOs and NC activity spanning the delta to high-gamma/ripple bands, but not in the opposite direction. Lastly, N2 theta and NREM spindle synchrony were themselves modulated by HPC SOs. These novel forms of phase-based interregional communication emphasize the role of HPC SOs in the HPC-NC dialog, and may offer a physiological basis for the sleep-dependent reorganization of mnemonic content.
Practicing one thing at a time: the secret to reward-based learning?
Authors: van der Kooij Katinka , van Mastrigt Nina M , Smeets Jeroen BJ
Published: August 2019

Binary reward feedback on movement success is sufficient for learning in some simple reaching tasks, but not in some more complex ones. It is unclear what the critical conditions for learning are. Here, we ask how reward-based sensorimotor learning depends on the number of factors that are task-relevant. In a task that involves two factors, we test whether learning improves by giving feedback on each factor in a separate phase of the learning. Participants learned to perform a 3D trajectory matching task on the basis of binary reward-feedback in three phases. In the first and second phase, the reward could be based on the produced slant, the produced length or the combination of the two. In the third phase, the feedback was always based on the combination of the two factors. The results showed that reward-based learning did not depend on the number of factors that were task-relevant. Consistently, providing feedback on a single factor in the first two phases did not improve motor learning in the third phase.
CRISPR-Cas9 mediated genome editing in vancomycin resistantEnterococcus faecium
Authors: de Maat Vincent , Stege Paul B. , Dedden Mark , Hamer Maud , van Pijkeren Jan-Peter , Willems Rob J.L. , van Schaik Willem
Published: August 2019

The Gram-positive bacteriumEnterococcus faeciumis becoming increasingly prevalent as a cause of hospital-acquired, antibiotic-resistant infections. There is thus an urgent need to mechanistically characterize the traits that contribute to the emergence ofE. faeciumas a multidrug resistant opportunistic pathogen. A fundamental part of research intoE. faeciumbiology relies on the ability to generate targeted mutants, but this process is currently labour-intensive and time-consuming, taking 4 to 5 weeks per mutant. In this report we describe a method relying on the high recombination rates ofE. faeciumand the application of the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Cas9 genome editing tool to more efficiently generate targeted mutants in theE. faeciumchromosome. Using this tool and the multi-drug resistant clinicalE. faeciumstrain E745, we generated a deletion mutant in thelacLgene, which encodes the large subunit of theE. faeciumβ-galactosidase. Blue/white screening using 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside (X-gal) could be used to distinguish between the wild-type andlacLdeletion mutant. We also inserted two copies ofgfpinto the intrinsicE. faeciummacrolide resistance genemsrCto generate stable green fluorescent cells. We conclude that CRISPR-Cas9 can be used to generate targeted genome modifications inE. faeciumin 3 weeks, with limited hands-on time. This method can potentially be implemented in other Gram-positive bacteria with high intrinsic recombination rates.
A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods
Authors: Moore Jill E. , Pratt Henry , Purcaro Michael , Weng Zhiping
Published: August 2019

Many genome-wide collections of candidate cis-regulatory elements (cCREs) have been defined using genomic and epigenomic data, but it remains a major challenge to connect these elements to their target genes. To facilitate the development of computational methods for predicting target genes, we developed a Benchmark of candidate Enhancer-Gene Interactions (BENGI) by integrating the Registry of cCREs we developed recently with experimentally-derived genomic interactions. We used BENGI to test several published computational methods for linking enhancers with genes, including signal correlation and the supervised learning methods TargetFinder and PEP. We found that while TargetFinder was the best performing method, it was modestly better than a baseline distance method for most benchmark datasets while trained and tested within the same cell type and that TargetFinder often did not outperform the distance method when applied across cell types. Our results suggest that current computational methods need to be improved and that BENGI presents a useful framework for method development and testing.
Rewards interact with explicit knowledge to enhance skilled motor performance
Authors: Anderson Sean P. , Adkins Tyler J. , Gary Bradley S. , Lee Taraz G.
Published: August 2019

From typing on a keyboard to playing the piano, many everyday skills require the ability to quickly and accurately perform sequential movements. It is well-known that the availability of rewards leads to increases in motivational vigor whereby people enhance both the speed and force of their movements. However, in the context of motor skills, it is unclear whether rewards also lead to more effective motor planning and action selection. Here, we trained human participants to perform four separate sequences in a skilled motor sequencing task. Two of these sequences were trained explicitly and performed with pre-cues that allow for the planning of movements, while the other two were trained implicitly. Immediately following the introduction of performance-contingent monetary incentives, participants improved their performance on all sequences consistent with enhancements in motivational vigor. However, there was a much larger performance boost for explicitly trained sequences. We replicated these results in a second, pre-registered experiment with an independent sample. We conclude from these experiments that rewards enhance both the planning of movements as well as motivational vigor.
Network models predict that pyramidal neuron hyperexcitability and synapse loss in the dlPFC lead to age-related spatial working memory impairment in rhesus monkeys
Authors: Ibañez Sara , Luebke Jennifer I. , Chang Wayne , Draguljić Danel , Weaver Christina M.
Published: August 2019

Behavioral studies have shown spatial working memory impairment with aging in several animal species, including humans. Persistent activity of layer 3 pyramidal dorsolateral prefrontal cortex (dlPFC) neurons during delay periods of working memory tasks is important for encoding memory of the stimulus. In vitro studies have shown that these neurons undergo significant age-related structural and functional changes, but the extent to which these changes affect neural mechanisms underlying spatial working memory is not understood fully. Here we confirm previous studies showing impairment on the Delayed Recognition Span Task in the spatial condition (DRSTsp), and increased in vitro action potential firing rates (hyperexcitability), across the adult life span of the rhesus monkey. We use a bump attractor model to predict how empirically observed changes in the aging dlPFC affect performance on the Delayed Response Task (DRT), and introduce a model of memory retention in the DRSTsp. Persistent activity—and, in turn, cognitive performance—in both models was affected much more by hyperexcitability of pyramidal neurons than by a loss of synapses. Our DRT simulations predict that additional changes to the network, such as increased firing of inhibitory interneurons, are needed to account for lower firing rates during the DRT with aging reported in vivo. Synaptic facilitation was an essential feature of the DRSTsp model, but it did not compensate fully for the effects of the other age-related changes on DRT performance. Modeling pyramidal neuron hyperexcitability and synapse loss simultaneously led to a partial recovery of function in both tasks, with the simulated level of DRSTsp impairment similar to that observed in aging monkeys. This modeling work integrates empirical data across multiple scales, from synapse counts to cognitive testing, to further our understanding of aging in non-human primates.
Nanoluciferase-based Method for Detecting Gene Expression inC. elegans
Authors: Sfarcic Ivana , Bui Theresa , Daniels Erin C. , Troemel Emily R.
Published: August 2019

Genetic reporters such as the green fluorescent protein (GFP) can facilitate measurement of promoter activity and gene expression. However, GFP and other fluorophores have limited sensitivity, particularly in tissues that autofluoresce like the intestine of the nematodeCaenorhabditis elegans. Here, we present a highly sensitive Nanoluciferase (NanoLuc)-based method in multi-well format to detect constitutive and inducible gene expression inC. elegans. We optimize detection of bioluminescent signal from NanoLuc inC. elegansand show that it can be detected at 400,000-fold over background in a population of 100 animals expressing intestinal NanoLuc driven by thevha-6promoter. We can reliably detect signal in singlevha-6p::Nanoluc-expressing worms from all developmental stages. Furthermore, we can detect signal from 1/100 dilution of lysate from a singlevha-6p::Nanoluc-expressing adult and from a singlevha-6p::Nanoluc-expressing adult “hidden” in a pool of 5,000 N2 wild-type animals. We also optimized various steps of this protocol, which involves a lysis step that can be performed in minutes. As a proof of concept, we used NanoLuc to monitor promoter activity of thepals-5stress/immune reporter and we were able to measure 300 and 50-fold increased NanoLuc activity after proteasome blockade and infection with microsporidia, respectively. Altogether, these results indicate that NanoLuc provides a highly sensitive genetic reporter for rapidly monitoring gene expression inC. elegans.
Different clones for different contexts: Hippocampal cognitive maps as higher-order graphs of a cloned HMM
Authors: Gothoskar Nishad , Guntupalli J. Swaroop , Rikhye Rajeev V. , Lázaro-Gredilla Miguel , George Dileep
Published: August 2019

Hippocampus encodes cognitive maps that support episodic memories, navigation, and planning. Under-standing the commonality among those maps as well as how those maps are structured, learned from experience, and used for inference and planning is an interesting but unsolved problem. We propose higher-order graphs as the general principle and present, as a plausible model, a cloned hidden Markov model (HMM) that can learn these graphs efficiently from experienced sequences. In our experiments, we use the cloned HMM for learning spatial and abstract representations. We show that inference and planning in the learned CHMM encapsulates many of the key properties of hippocampal cells observed in rodents and humans. Cloned HMM thus provides a new frame-work for understanding hippocampal function.
Automatic mutual information noise omission (AMINO): generating order parameters for molecular systems
Authors: Ravindra Pavan , Smith Zachary , Tiwary Pratyush
Published: August 2019

Molecular dynamics (MD) simulations generate valuable all-atom resolution trajectories of complex systems, but analyzing this high-dimensional data as well as reaching practical timescales even with powerful super-computers remain open problems. As such, many specialized sampling and reaction coordinate construction methods exist that alleviate these problems. However, these methods typically don’t work directly on all atomic coordinates, and still require previous knowledge of the important distinguishing features of the system, known as order parameters (OPs). Here we present AMINO, an automated method that generates such OPs by screening through a very large dictionary of OPs, such as all heavy atom contacts in a biomolecule. AMINO uses ideas from information theory and rate distortion theory. The OPs learnt from AMINO can then serve as an input for designing a reaction coordinate which can then be used in many enhanced sampling methods. Here we outline its key theoretical underpinnings, and apply it to systems of increasing complexity. Our applications include a problem of tremendous pharmaceutical and engineering relevance, namely, calculating the binding affinity of a protein-ligand system when all that is known is the structure of the bound system. Our calculations are performed in a human-free fashion, obtaining very accurate results compared to long unbiased MD simulations on the Anton supercomputer, but in orders of magnitude less computer time. We thus expect AMINO to be useful for the calculation of thermodynamics and kinetics in the study of diverse molecular systems.
Sexual antagonism leads to a mosaic of X–autosome conflict
Authors: Frank Steven A. , Patten Manus M.
Published: August 2019

Males and females have different optimal values for some traits, such as body size. When the same genes control these traits in both sexes, selection pushes in opposite directions in males and females. Alleles at autosomal loci spend equal amounts of time in males and females, suggesting that the sexually antagonistic selective forces may approximately balance between the opposing optima. Frank and Crespi noted that alleles on the X chromosome spend twice as much time in diploid females as in haploid males. That distinction between the sexes may tend to favor X-linked genes that push more strongly toward the female optimum than the male optimum. The female bias of X-linked genes conflicts with the intermediate optimum of autosomal genes, potentially creating an X-autosome conflict. Patten has recently argued that explicit genetic assumptions about dominance and the relative magnitude of allelic effects may lead X-linked genes to favor the male rather than the female optimum, contradicting Frank and Crespi. This article combines the insights of those prior analyses into a new, more general theory. We find some parameter combinations for X-linked loci that favor a female bias and other parameter combinations that favor a male bias. We conclude that the X likely contains a mosaic pattern of loci that conflict with autosomes over sexually antagonistic traits. The overall tendency for a female or male bias on the X depends on prior assumptions about the distribution of key parameters across X-linked loci. Those parameters include the dominance coefficient and the way in which ploidy influences the magnitude of allelic effects.
Effect of synaptic cell-to-cell transmission and recombination on the evolution of double mutants in HIV
Authors: Kreger Jesse , Komarova Natalia L. , Wodarz Dominik
Published: August 2019

Recombination in HIV infection can impact virus evolutionin vivoin complex ways, as has been shown both experimentally and mathematically. The effect of free virus versus synaptic, cell-to-cell transmission on the evolution of double mutants, however, has not been investigated. Here we do so by using a stochastic agent-based model. Consistent with data, we assume spatial constraints for synaptic but not for free-virus transmission. Two important effects of the viral spread mode are observed: (i) For disadvantageous mutants, synaptic transmission protects against detrimental effects of recombination on double mutant persistence. Under free virus transmission, recombination increases double mutant levels for negative epistasis, but reduces them for positive epistasis. This reduction for positive epistasis is much diminished under pre-dominantly synaptic transmission, and recombination can in fact lead to increased mutant levels. (ii) The mode of virus spread also directly influences the evolutionary fate of double mutants. For disadvantageous mutants, double mutant production is the predominant driving force, and hence synaptic transmission leads to highest double mutant levels due to increased transmission efficiency. For advantageous mutants, double mutant spread is the most important force, and hence free virus transmission leads to fastest invasion due to better mixing. For neutral mutants, both production and spread of double mutants are important, and hence an optimal mixture of free virus and synaptic transmission maximizes double mutant fractions. Therefore, both free virus and synaptic transmission can enhance or delay double mutant evolution. Implications for drug resistance in HIV are discussed.
Structural basis for EPC1-mediated recruitment of MBTD1 into the NuA4/TIP60 acetyltransferase complex
Authors: Zhang Heng , Devoucoux Maëva , Song Xiaosheng , Li Li , Ayaz Gamze , Cheng Harry , Tempel Wolfram , Dong Cheng , Loppnau Peter , Côté Jacques , Min Jinrong
Published: August 2019

MBTD1, a H4K20me reader, has recently been identified as a component of the NuA4/TIP60 acetyltransferase complex, regulating gene expression and DNA repair. NuA4/TIP60 inhibits 53BP1 binding to chromatin through recognition of the H4K20me mark by MBTD1 and acetylation of H2AK15, blocking the ubiquitination mark required for 53BP1 localization at DNA breaks. The NuA4/TIP60 non-catalytic subunit EPC1 enlists MBTD1 into the complex, but the detailed molecular mechanism remains incompletely explored. Here, we present the crystal structure of the MBTD1-EPC1 complex, revealing a hydrophobic C-terminal fragment of EPC1 engaging the MBT repeats of MBTD1 in a site distinct from the H4K20me binding site. Different cellular assays validate the physiological significance of the key residues involved in the MBTD1-EPC1 interaction. Our study provides a structural framework for understanding the mechanism by which MBTD1 recruits the NuA4/TIP60 acetyltransferase complex to influence transcription and DNA repair pathway choice.
Nf1deletion results in depletion of theLhx6transcription factor and a specific loss of parvalbumin+ cortical interneurons
Authors: Angara Kartik , Pai Emily Ling-Lin , Bilinovich Stephanie M , Stafford April M , Nguyen Julie T , Paul Anirban , Rubenstein John L , Vogt Daniel
Published: August 2019

Neurofibromatosis-1 (NF-1) is a monogenic disorder caused by mutations in theNF1gene, which encodes the protein, Neurofibromin, an inhibitor of Ras GTPase activity. While NF-1 is often characterized by café-au-lait skin spots and benign tumors, the mechanisms underlying cognitive changes in NF-1 are poorly understood. Cortical GABAergic interneurons (CINs) are implicated in NF-1 pathology but cellular and molecular changes to CINs are poorly understood. We deletedNf1from the medial ganglionic eminence (MGE), which gives rise to both oligodendrocytes and CINs that express somatostatin and parvalbumin. Loss ofNf1led to a persistence of immature oligodendrocytes that prevented later born oligodendrocytes from occupying the cortex. Moreover, PV+ CINs were uniquely lost, without changes in SST+ CINs. We discovered that loss ofNf1results in a graded decrease inLhx6expression, the transcription factor necessary to establish SST+ and PV+ CINs, revealing a mechanism wherebyNf1regulates a critical CIN developmental milestone.
PLD3 is a neuronal lysosomal phospholipase D associated with β-amyloid plaques and cognitive function in Alzheimer’s disease
Authors: Nackenoff Alex G. , Hohman Timothy J. , Neuner Sarah M. , Akers Carolyn S. , Weitzel Nicole C. , Shostak Alena , Ferguson Shawn , Bennett David A. , Schneider Julie A. , Jefferson Angela L. , Kaczorowski Catherine C. , Schrag Matthew S.
Published: August 2019

Phospholipase D3 (PLD3) is a protein of unclear function that structurally resembles other members of the phospholipase D superfamily. A coding variant in this gene confers increased risk for the development of Alzheimer’s disease (AD), although the magnitude of this effect has been controversial. Because of the potential significance of this obscure protein, we undertook a study to determine whether PLD3 is relevant to memory and cognition in sporadic AD, to observe its distribution in normal human brain and AD-affected brain, to describe its subcellular localization, and to evaluate its molecular function. PLD3 mRNA levels in the human pre-frontal cortex inversely correlated with β-amyloid pathology severity and rate of cognitive decline in 531 participants enrolled in the Religious Orders Study and Rush Memory and Aging Project. PLD3 levels across genetically diverse BXD mouse strains and strains crossed with 5xFAD mice correlated strongly with learning and memory performance in a fear conditioning task. In human neuropathological samples, PLD3 was primarily found within neurons and colocalized with lysosome markers (LAMP2, progranulin, and cathepsins D and B). This colocalization was also present in AD brain with prominent enrichment on lysosomal accumulations within dystrophic neurites surrounding β-amyloid plaques. This pattern of protein distribution was conserved in mouse brain in wild type and the 5xFAD mouse model of cerebral β-amyloidosis. We discovered PLD3 has phospholipase D activity in lysosomes. A coding variant in PLD3 reported to confer AD risk significantly reduced enzymatic activity compared to wild-type PLD3. In summary, this study identified a new functional mammalian phospholipase D isoform which is lysosomal and closely associated with both β-amyloid pathology and cognition.
The translation inhibitor cycloheximide affects ribosome profiling data in a species-specific manner
Authors: Sharma Puneet , Nilges Benedikt S. , Wu Jie , Leidel Sebastian A.
Published: August 2019

Ribosome profiling provides genome-wide snapshots of translation dynamics by determining ribosomal positions at sub-codon resolution. To maintain this positional information, the translation inhibitor cycloheximide (CHX) has been widely used to arrest translating ribosomes prior to library preparation. Several studies have reported CHX-induced biases in yeast data casting uncertainty about its continued use and questioning the accuracy of many ribosome profiling studies. However, the presence of these biases has not been investigated comprehensively in organisms other than Saccharomyces cerevisiae. Here, we use a highly standardized and optimized protocol to compare different CHX-treatment conditions in yeast and human cells. Our data suggest that unlike in S. cerevisiae, translating ribosomes in human cells are not susceptible to conformational restrictions by CHX. Furthermore, CHX-induced codon-specific effects on ribosome occupancy are not detectable in human cells nor in other model organisms including Schizosaccharomyces pombe and Candida albicans. In fact, we find that even in S. cerevisiae most biases can be avoided by omitting CHX pre-treatment, indicating that other parameters of library generation contribute to differences between ribosome profiling experiments. Together our findings provide a framework for researchers who plan their own ribosome profiling experiments or who analyze published datasets to draw judicious conclusions.
Introns Control Stochasticity in Metazoan Gene Expression
Authors: Sands Bryan , Yun Soo , Mendenhall Alexander R.
Published: August 2019

Introns are noncoding DNA elements found in between coding exons of most genes in most metazoans. Introns are known to both increase expression levels and provide means for making different protein products from the same gene via alternative splicing. It is thought that evolution has selected for these functions of introns. Here we present evidence for an additional reason why so many metazoan genes have introns, and why some do not. We found that introns control stochasticity in metazoan gene expression. They do this by controlling stochastic autosomal allele bias. We determined this by measuring the expression of differently colored reporter alleles with and without introns. We find that introns control stochastic autosomal allele biases using a 5’-position dependent mechanism. Intron control of allele expression noise provides an additional mechanism to consider when pondering why so many metazoan genes have introns and why some have lost them.
Herpes Simplex viral nucleoprotein creates a competitive transcriptional environment facilitating robust viral transcription and host shut off
Authors: Dremel Sarah E. , DeLuca Neal A.
Published: August 2019

Herpes simplex virus-1 (HSV-1) replicates within the nucleus coopting the host’s RNA Polymerase II (Pol II) machinery for production of viral mRNAs culminating in host transcriptional shut off. The mechanism behind this rapid reprogramming of the host transcriptional environment is largely unknown. We identified ICP4 as responsible for preferential recruitment of the Pol II machinery to the viral genome. ICP4 is a viral nucleoprotein which binds double stranded DNA. We determined ICP4 discriminately binds the viral genome due to the absence of cellular nucleosomes and high density of cognate binding sites. We posit that ICP4’s ability to recruit not just Pol II, but also more limiting essential components, such as TBP and Mediator create a competitive transcriptional environment. These distinguishing characteristics ultimately result in a rapid and efficient reprogramming of the host’s transcriptional machinery, which does not occur in the absence of ICP4.

Highlights

HSV-1 ICP4 coats the viral genome promoting robust recruitment of Pol II transcription machinery.

ICP4 prefers the viral genome due to the absence of nucleosomes and density of binding motifs.

At high concentrations ICP4 promiscuously binds DNA including euchromatic host promoters.

ICP4 is required for host transcriptional shut off, independent of genome replication.
Hormone Levels Are Related to Altered Functional Connectivity in Prolactinomas
Authors: Yao Shun , Cao Chenglong , Lin Pan , Juvekar Parikshit , Zhang Ru-Yuan , Vera Matthew , Zeng Ailiang , Golby Alexandra J. , Xu Guozheng , Tie Yanmei , Song Jian
Published: August 2019

Background and Objective

Prolactinomas may cause drastic hormone fluctuations throughout the body. It is not fully understood how endogenous hormone disorders such as prolactinomas reshape the patient’s brain. By employing the resting-state functional magnetic resonance imaging technique, we aimed to investigate the whole-brain functional connectivity (FC) and its relationship with hormone levels in patients with prolactinomas.

Methods

Using whole-brain and seed-based functional connectivity analyses, we compared FC metrics between 33 prolactinoma patients and 31 healthy controls matched with age, sex, and handedness. Then we performed partial correlation analysis to examine the relationship between FC metrics and hormone levels.

Results

Compared to healthy controls, we found that prolactinoma patients showed significantly increased thalamocortical (visual cortex) and cerebellar-cerebral connectivity. In addition, endogenous hormone levels were positively correlated with the increased FC, and the hormone-FC relationships showed sex difference in prolactinoma patients.

Conclusions

Our findings are the first to reveal the altered FC patterns and sex-dependent hormone-FC relationships in prolactinoma patients, indicating the important role of hormone levels in the neural mechanism of brain reorganization and hyperactive intrinsic connections in prolactinomas.
Complex symbiont-pathogen interactions inhibit intestinal repair
Authors: Fast David , Petkau Kristina , Ferguson Meghan , Shin Minjeong , Galenza Anthony , Kostiuk Benjamin , Pukatzki Stefan , Foley Edan
Published: August 2019

Pathogen-mediated damage to the intestinal epithelium activates compensatory growth and differentiation repair programs in progenitor cells. Accelerated progenitor growth replenishes damaged tissue and maintains barrier integrity. Despite the importance of epithelial renewal to intestinal homeostasis, we know little about the effects of pathogen-commensal interactions on progenitor growth. We found that the enteric pathogen Vibrio cholerae, blocks critical growth and differentiation pathways in Drosophila progenitors despite extensive damage to the epithelial tissue. We showed that inhibition of epithelial repair requires interactions of the Vibrio cholerae type six secretion system with a complex community of symbiotic bacteria, and that elimination of the gut microbiome is sufficient to restore homeostatic growth in infected intestines. Together, this work highlights the importance of pathogen-symbiont interactions on intestinal immune responses and outlines a previously undescribed impact of the type six secretion system on pathogenesis.