bluuebunny/crossref_metadata_2025 huggingface dataset:
A systems biology analysis of adrenergically stimulated adiponectin exocytosis in white adipocytes
Authors: Lövfors William , Simonsson Christian , Komai Ali M. , Nyman Elin , Olofsson Charlotta S. , Cedersund Gunnar
Published: July 2020

Circulating levels of the adipocyte hormone adiponectin are typically reduced in obesity and this deficiency has been linked to metabolic diseases. It is thus important to understand the mechanisms controlling adiponectin exocytosis. This understanding is hindered by the high complexity of the data and the underlying signaling network. To handle this complexity, we here analyze the data using systems biology mathematical modelling. Previously, we have developed a mathematical model for how different intracellular concentrations of Ca2+, cAMP and ATP affect adiponectin exocytosis (measured as increase in membrane capacitance). However, recent work has shown that adiponectin exocytosis is physiologically triggered via signaling pathways involving adrenergic β3 receptors (β3ARs). Therefore, we have herein developed a more comprehensive model that also includes adiponectin exocytosis stimulated by extracellularly applied epinephrine or the β3AR agonist CL 316,243. Our model can explain all previous patch-clamp data, as well as new data consisting of a combination of the intracellular mediators and extracellular adrenergic stimuli. Without changing the parameters, the model can accurately predict independent validation data with other combinations of patch-clamp pipette solutions and external stimuli. Finally, we use the model to perform newin silicoexperiments examining situations where corresponding wet lab experiments are difficult to perform. By this approach, we simulated adiponectin exocytosis in single cells, in response to the reduction of β3ARs that is observed in adipocytes from animals with obesity-induced diabetes. Our work brings us one step closer to understanding the intricate regulation of adiponectin exocytosis.
Stromal Heterogeneity in the Proliferative EndometrialFunctionalis- A single-cell approach
Authors: Queckbörner Suzanna , von Grothusen Carolina , Boggavarapu Nageswara , Davies Lindsay C. , Gemzell-Danielsson Kristina
Published: July 2020

The endometrium undergoes regular regeneration and stromal proliferation as part of the normal menstrual cycle. To better understand cellular interactions driving the mechanisms in endometrial regeneration we employed single-cell RNA sequencing. Endometrial samples were obtained during the proliferative phase of the menstrual cycle from healthy women aged 24–32 years. Within the stromal compartment multiple stromal populations were found, suggestive of specific stromal niches that control inflammation and extracellular matrix composition. Ten different stromal cell and two pericyte subsets were identified. Applying different R packages (Seurat, SingleR, Velocyto) we determined cell cluster diversity and cell lineage/trajectory while using external data to validate our findings. By understanding healthy regeneration in the described stromal compartments, we aim to identify points of intervention for novel therapy development in order to treat benign gynaecological disorders affecting endometrial regeneration and proliferation e.g. endometriosis and Asherman’s syndrome.
COVID-19 patients upregulate toll-like receptor 4-mediated inflammatory signaling that mimics bacterial sepsis
Authors: Sohn Kyung Mok , Lee Sung-Gwon , Kim Hyeon Ji , Cheon Shinhyea , Jeong Hyeongseok , Lee Jooyeon , Kim In Soo , Silwal Prashanta , Kim Young Jae , Park Chungoo , Kim Yeon-Sook , Jo Eun-Kyeong
Published: July 2020

Observational studies of the ongoing coronavirus disease 2019 (COVID-19) outbreak suggest that a cytokine storm is involved in the pathogenesis of severe illness. However, the molecular mechanisms underlying the altered pathological inflammation in COVID-19 are largely unknown. We report here that toll-like receptor (TLR) 4-mediated inflammatory signaling molecules are upregulated in peripheral blood mononuclear cells (PBMCs) from COVID-19 patients, compared with healthy controls. Among the most highly increased inflammatory mediators in severe/critically ill patients, S100A9, an alarmin and TLR4 ligand, was found as a noteworthy biomarker, because it inversely correlated with the serum albumin levels. These data support a link between TLR4 signaling and pathological inflammation during COVID-19 and contribute to develop therapeutic approaches through targeting TLR4-mediated inflammation.
A novel telencephalon-opto-hypothalamic morphogenetic domain produces most of the glutamatergic neurons of the medial extended amygdala
Authors: Morales Lorena , Castro-Robles Beatriz , Abellán Antonio , Desfilis Ester , Medina Loreta
Published: July 2020

Deficits in social cognition and behavior are a hallmark of many psychiatric disorders. The medial extended amygdala, including the medial amygdala and the medial bed nucleus of the stria terminalis, is a key component of functional networks involved in sociality. However, this nuclear complex is highly heterogeneous and contains numerous GABAergic and glutamatergic neuron subpopulations. Deciphering the connections of different neurons is essential in order to understand how this structure regulates different aspects of sociality, and it is necessary to evaluate their differential implication in distinct mental disorders. Developmental studies in different vertebrates are offering new venues to understand neuronal diversity of the medial extended amygdala, and are helping to establish a relation between the embryonic origin and molecular signature of distinct neurons with the functional subcircuits in which they are engaged. These studies have provided many details on the distinct GABAergic neurons of the medial extended amygdala, but information on the glutamatergic neurons is still scarce. Using an Otp-eGFP transgenic mouse and multiple fluorescent labeling, we show that most glutamatergic neurons of the medial extended amygdala originate in a novel telencephalo-opto-hypothalamic embryonic domain (TOH), located at the transition between telencephalon and hypothalamus, which produces Otp-lineage neurons expressing the telencephalic marker Foxg1 but not Nkx2.1 during development. These glutamatergic cells include a subpopulation of projection neurons of the medial amygdala, which activation has been previously shown to promote autistic-like behavior. Our data open new venues for studying the implication of this neuron subtype in neurodevelopmental disorders producing social deficits.
Increasing heart vascularisation after myocardial infarction using brain natriuretic peptide stimulation of endothelial and WT1+epicardium-derived cells
Authors: Li Na , Rignault-Clerc Stéphanie , Bielmann Christelle , Bon-Mathier Anne-Charlotte , Déglise Tamara , Carboni Alexia , Ducrest Mégane , Rosenblatt-Velin Nathalie
Published: July 2020

Brain natriuretic peptide (BNP) treatment increases heart function and decreases heart dilation after myocardial infarction. Here, we investigated whether part of the cardioprotective effect of BNP in infarcted hearts related to improved neovascularisation. Infarcted mice were treated with saline or BNP for 10 days. BNP treatment increased vascularisation and the number of endothelial cells in the infarct border and remote zones of infarcted hearts. Endothelial cell lineage tracing showed that BNP directly stimulated the proliferation of resident mature endothelial cells in both areas of the infarcted hearts, via NPR-A binding and p38 MAP kinase activation. BNP also stimulated the proliferation of WT1+epicardium-derived cells but only in the hypoxic area of infarcted hearts. Our results demonstrated that these immature cells have a natural capacity to differentiate into endothelial cells in infarcted hearts. BNP treatment increased their proliferation but not their differentiation capacity. We identified new roles for BNP and new therapeutic strategies to improve heart recovery in infarcted hearts.
Social chemical communication determines recovery from L1 arrest via DAF-16 activation
Authors: Mata-Cabana Alejandro , Gómez-Delgado Laura , Romero-Expósito Francisco Javier , Rodríguez-Palero María Jesús , Artal-Sanz Marta , Olmedo María
Published: July 2020

In a population, chemical communication determines the response of animals to changing environmental conditions, what leads to an enhanced resistance against stressors. In response to starvation, the nematodeCaenorhabditis elegansarrest post-embryonic development as L1 larva right after hatching. As arrested L1 larvae,C. elegansbecome more resistant to diverse stresses, allowing them to survive for several weeks expecting to encounter more favorable conditions. However, prolonged periods in L1 arrest lead to the accumulation of detrimental signs of aging, which ultimately provoke animal death. When arrested L1s feed, they undergo a recovery process to erase these harmful signs before resuming the developmental program. L1 arrested larvae secrete unidentified soluble compounds that improve survival to starvation. This protection is proportional to larval population density. Thus, animals arrested at high densities display an enhanced resistance to starvation. Here we show that this chemical communication also influences recovery after prolonged periods in L1 arrest. Animals at high density recovered faster than animals at low density. We found that the density effect on survival depends on the final effector of the insulin signaling pathway, the transcription factor DAF-16. Moreover, DAF-16 activation was higher at high density, consistent with a lower expression of the insulin-like peptide DAF-28 in the neurons. The improved recovery of animals after arrest at high density depended on soluble compounds present in the media of arrested L1s. In a try to find the nature of these compounds, we investigated the disaccharide trehalose as putative signaling molecule, since its production is enhanced during L1 arrest and it is able to activate DAF-16. We detected the presence of secreted trehalose in the medium of arrested L1 larvae at a low concentration. The addition of this concentration of trehalose to animals arrested at low density was enough to rescue DAF-28 production and DAF-16 activation to the levels of animals arrested at high density. However, despite activating DAF-16, trehalose was not capable of reversing survival and recovery phenotypes, suggesting the participation of additional signaling molecules. We finally identified GUR-3 as a possible trehalose receptor inC. elegans. With all, here we describe a molecular mechanism underlying social communication that allowsC. elegansto maintain arrested L1 larvae ready to quickly recover as soon as they encounter nutrient sources.
UMP inhibition and sequential firing in aspartate transcarbamoylase open ways to regulate plant growth
Authors: Bellin Leo , del Caño-Ochoa Francisco , Velázquez-Campoy Adrián , Möhlmann Torsten , Ramón-Maiques Santiago
Published: July 2020

Pyrimidine nucleotides are essential to plant development. We proved that Arabidopsis growth can be inhibited or enhanced by down- or upregulating aspartate transcarbamoylase (ATC), the first committed enzyme forde novobiosynthesis of pyrimidines in plants. To understand the unique mechanism of feedback inhibition of this enzyme by uridine 5-monophosphate (UMP), we determined the crystal structure of the Arabidopsis ATC trimer free and bound to UMP, demonstrating that the nucleotide binds and blocks the active site. The regulatory mechanism relies on a loop exclusively conserved in plants, and a single-point mutation (F161A) turns ATC insensitive to UMP. Moreover, the structures in complex with a transition-state analog or with carbamoyl phosphate proved a mechanism in plant ATCs for sequential firing of the active sites. The disclosure of the unique regulatory and catalytic properties suggests new strategies to modulate ATC activity and to controlde novopyrimidine synthesis and plant growth.
Y705 and S727 are required for mitochondrial import and transcriptional activities of STAT3 and regulate proliferation of embryonic and tissue stem cells
Authors: Peron Margherita , Meneghetti Giacomo , Dinarello Alberto , Martorano Laura , Betto Riccardo M. , Facchinello Nicola , Tesoriere Annachiara , Tiso Natascia , Martello Graziano , Argenton Francesco
Published: July 2020

The STAT3 transcription factor, acting both in the nucleus and mitochondria, maintains embryonic stem cell pluripotency and promotes their proliferation. In this work, using zebrafish, we determinedin vivothat mitochondrial STAT3 regulates mtDNA transcription in embryonic and larval stem cell niches and that this activity affects their proliferation rates. As a result, we demonstrated that STAT3 import inside mitochondria requires Y705 phosphorylation by Jak2, while its mitochondrial transcriptional activity, as well as its effect on proliferation, depends on the MAPK target S727. These data were confirmed using mouse embryonic stem cells: Y705 mutated STAT3 cannot enter the mitochondrion while the S727 mutation does not affect mitochondrial import of the protein. Surprisingly, STAT3-dependent increase of mitochondrial transcription seems independent from STAT3 binding to STAT3 responsive elements. Finally, loss of function experiments, with chemical inhibition of JAK/STAT3 pathway or genetic ablation ofstat3gene, demonstrated that STAT3 is also required for cell proliferation in the intestine of zebrafish.
Parthenogenesis in weevils of the tribe Naupactini (Coleoptera, Curculionidae): aWolbachia-density dependent trait?
Authors: Cruz Cabral Lucía da , Goya Lucía Fernandez , Piccinali Romina V. , Lanteri Analía A. , Confalonieri Viviana A. , Rodriguero Marcela S.
Published: July 2020

The intracellular bacteriaWolbachia pipientiscan manipulate host reproduction to enhance their vertical transmission. It has been reported an association between parthenogenesis andWolbachiainfection in weevils from the tribe Naupactini. A curing experiment suggested that a threshold density ofWolbachiais required for parthenogenesis to occur. The aim of this study was to analyzeWolbachiainfection status in the bisexual speciesNaupactus xanthographusandNaupactus dissimulator.

Wolbachiainfection was detected in both species from some geographic locations, not being fixed. In all positive cases, faint PCR bands were observed. Quantification through real time PCR confirmed thatWolbachialoads in bisexual species were significantly lower than in parthenogenetic ones; this strengthens the hypothesis of a threshold level. Strain typing showed that both species carrywNau1, the most frequent in parthenogenetic Naupactini weevils. These infections seem to be recently acquired by horizontal transfer.Wolbachiawas located throughout the whole body, which reinforce the idea of recent transmission. Moreover, we demonstrated that this strain carries the WO phage.

Finally, the analysis of eubacterial16S rRNAgene showed intense PCR bands for both bisexual species, suggesting –the presence of additional bacteria. Interspecific competition might explain why the parthenogenetic phenotype is not triggered.
Nutrient signaling, stress response, and interorganelle communication are non-canonical determinants of cell fate
Authors: Wood N Ezgi , Kositangool Piya , Hariri Hanaa , Marchand Ashley , Henne Mike
Published: July 2020

Isogenic cells can manifest distinct cellular fates for a single stress, however the nongenetic mechanisms driving such fates remain poorly understood. Here, we implement a robust multi-channel live-cell imaging approach to uncover noncanonical factors governing cell fate. We show that in response to acute glucose removal (AGR), budding yeast undergo distinct fates becoming either quiescent or senescent. Senescent cells fail to resume mitotic cycles following glucose replenishment but remain responsive to nutrient stimuli. Whereas quiescent cells manifest starvation-induced adaptation, senescent cells display perturbed endomembrane trafficking and defective nucleus-vacuole junction (NVJ) expansion. Surprisingly, we also show senescence occurs in the absence of lipid droplets. Importantly, we identify the nutrient-sensing linked kinase Rim15 as a key biomarker that predicts cell fates before AGR stress. We propose that isogenic yeast challenged with acute nutrient shortage contain determinants that influence their post-stress fate, and demonstrate that specific nutrient signaling, stress-response, endomembrane trafficking, and inter-organelle tether biomarkers are early indicators for long-term fate outcomes.
A neuromechanical model forDrosophilalarval crawling based on physical measurements
Authors: Sun Xiyang , Liu Yingtao , Liu Chang , Mayumi Koichi , Ito Kohzo , Nose Akinao , Kohsaka Hiroshi
Published: July 2020

Animal locomotion requires dynamic interactions between neural circuits, muscles, and surrounding environments. In contrast to intensive studies on neural circuits, the neuromechanical basis for animal behaviour remains unclear due to the lack of information on the physical properties of animals. Here, we proposed an integrated neuromechanical model based on physical measurements by takingDrosophilalarvae as a model of soft- bodied animals. The biomechanical parameters of fly larvae were measured by the stress- relaxation test. By optimizing parameters in the neural circuit, our neuromechanical model succeeded in quantitatively reproducing the kinematics of larval locomotion that were obtained experimentally. This model could reproduce the observation of optogenetic studies reported previously. The model predicted that peristaltic locomotion could be exhibited in a low friction condition. Analysis of floating larvae provided results consistent with this prediction. Furthermore, the model predicted a significant contribution of intersegmental connections in the central nervous system, which contrasts with a previous study. This hypothesis allowed us to make a testable prediction for the variability in intersegmental connection in sister species of the genusDrosophila. Our model based on physical measurement provides a new foundation to study locomotion in soft-bodied animals and soft robot engineering.
Co-translational targeting of transcripts to endosomes
Authors: Popovic Doris , Nijenhuis Wilco , Kapitein Lukas C. , Pelkmans Lucas
Published: July 2020

Asymmetric localization and translation of mRNAs is used by single cells to sense their environment and integrate extrinsic cues with the appropriate cellular response. Here we investigate the extent to which endosomes impact subcellular patterning of transcripts and provide a platform for localized translation. Using image-based transcriptomics, indirect immunofluorescence, and RNAseq of isolated organelles, we discover mRNAs that associate with early endosomes in a translation-dependent and -independent manner. We explore this in more detail for the mRNA of a major endosomal tethering factor and fusogen, Early Endosomal Antigen 1,EEA1, which localizes to early endosomes in a puromycin-sensitive manner. By reconstituting EEA1 knock-out cells with either the coding sequence or 3’UTR of EEA1, we show that the coding region is sufficient for endosomal localization of mRNA. Finally, we use quantitative proteomics to discover proteins associated withEEA1mRNA and identify CSRP1 as a factor that controls EEA1 translational efficiency. Our findings reveal that multiple transcripts associate with early endosomes in a translation-dependent manner and identify mRNA-binding proteins that may participate in controlling endosome-localized translation.
Linking scales of life-history variation with population structure in Atlantic cod
Authors: Wright P.J. , Doyle A. , Taggart J.B. , Davie A
Published: July 2020

It is increasing recognised that sustainable exploitation of marine fish requires the consideration of population diversity and associated productivity. This study used a combination of genotypic screening and phenotypic traits to define the scale of population structuring in Atlantic cod inhabiting the northern North Sea (ICES 4a) and Scottish west coast (6a). The genetic analysis indicated an isolation by distance pattern with an even finer scale structuring than previously reported, that persisted over a decade and between feeding and spawning seasons. Spatial variation in phenotypic traits reflected genetic variation with cod maturing later and at a larger size near the Viking Bank in 4a. The identified population structuring provides an explanation for differences in historic changes in maturation schedules and the temperature exposure recorded in previous electronic tagging studies. The study also highlights how the mismatch between stock divisions and population units is leading to a misunderstanding about stock recovery.
Integrator is a genome-wide attenuator of non-productive transcription
Authors: Lykke-Andersen Søren , Žumer Kristina , Molska Ewa Šmidová , Wu Guifen , Rouvière Jérôme O. , Demel Carina , Schwalb Björn , Schmid Manfred , Cramer Patrick , Jensen Torben Heick
Published: July 2020

Termination of RNA polymerase II (RNAPII) transcription in metazoans relies largely on the Cleavage and Polyadenylation (CPA) and Integrator (INT) complexes originally found to act at the ends of protein-coding and snRNA genes, respectively. Here we monitor CPA- and INT-dependent termination activities genome-wide, including over 8000 previously unannotated transcription units (TUs), that produce unstable RNA. We verify the global activity of CPA, that occurs at pA sites indiscriminately of their positioning relative to the TU promoter. We also identify a global activity of INT, which is, however, largely sequence-independent and restricted to a ~3 kb promoter-proximal region. Our analyses suggest two functions of genome-wide INT activity; it dampens transcriptional output from weak promoters and it provides quality-control of RNAPII complexes, that are unfavorably configured for transcriptional elongation. We suggest that the function of INT in stable snRNA production is an exception from its general cellular role, attenuation of non-productive transcription.
Active Time-Restricted Feeding Protects the Blood Pressure Circadian Rhythm in Diabetic Mice
Authors: Hou Tianfei , Su Wen , Duncan Marilyn J. , Olga Vsevolozhskaya A. , Guo Zhenheng , Gong Ming C.
Published: July 2020

The quantity and quality of food intake have been considered crucial for peoples’ wellness. Only recently has it become appreciated that the timing of food intake, independent of total calorie consumption, is also critical. The involvement and contribution of the timing of food intake in nondipping blood pressure (BP), the most common disruption of the BP circadian rhythm in diabetes, however, remains uncertain. Here, we demonstrate that the loss of diurnal rhythm in food intake coincided with nondipping BP in type 2 diabeticdb/dbmice, and imposing a food intake diurnal rhythm by active time-restricted feeding (ATRF) remarkably preventeddb/dbmice from the development of nondipping BP. Moreover, ATRF, independent of calorie restriction, also effectively restored the already disrupted BP circadian rhythm indb/dbmice. Mechanistically, ATRF reduced the sympathetic vascular tone and BP during the light phase via fasting, thus protecting the BP circadian rhythm indb/dbmice. Moreover, we identified BMAL1, an obligatory core clock gene, as a potentially key molecule that links ATRF, sympathetic vascular tone, and BP circadian rhythm. Collectively, these data reveal an important but previously unrecognized role of the timing of food intake in the onset, prevention, and treatment of nondipping BP in diabetes.
Probabilistic Ranking Of Microbiomes Plus Taxa Selection to discover and validate microbiome function models for multiple litter decomposition studies
Authors: Thompson Jaron , Lubbers Nicholas , Kroeger Marie E. , DeVan Rae , Johansen Renee , Dunbar John , Munsky Brian
Published: July 2020

The overwhelming complexity of microbiomes makes it difficult to decipher functional relationships between specific microbes and ecosystem properties. While machine learning analyses have demonstrated an impressive ability to correlate microbial community composition with macroscopic functions, mechanisms that dictate model predictions are often unknown, and predictions often lack an assigned metric of uncertainty. In this study, we apply Bayesian networks to build on prior feature selection analyses and construct easy-to-interpret probabilistic models, which accurately predict levels of dissolved organic carbon (DOC) from the relative abundance of soil bacteria (16S rRNA gene profiles). In addition to standard cross-validation, we show that a Bayesian network model trained using samples from a pine litter decomposition study accurately predicts DOC of samples from an independent oak litter decomposition study, suggesting that mechanisms driving variation in soil carbon storage may be conserved across different types of decomposing plant litter. Furthermore, the structure of the resulting Bayesian network model defines a minimal set of highly informative taxa, whose abundances directly constrain the probability of high or low DOC conditions. Significant accuracy of the Bayesian network model with independent data sets supports the validity of the identified relationships between taxa abundance and DOC.

Understanding the interplay between microbiomes and the environments they inhabit is a daunting task. While recent advances in gene sequencing technology provide a means of profiling the relative abundance of microbial species, the resulting data are noisy, sparse, and limited to small sample sizes. Despite these challenges, machine learning approaches have demonstrated a promising ability to discover patterns linking the microbiome with macroscopic behavior. However, most machine learning models applied to microbiome data do not estimate prediction uncertainty and provide little insight regarding how predictions are made. In this study, we couple machine learning approaches for feature reduction with Bayesian networks to model the relationship between the soil microbiome and dissolved organic carbon (DOC). We show that Bayesian networks are accurate and provide a transparent link between microbial abundance and DOC. To validate Bayesian networks, we demonstrate accurate predictions for held-out testing data and with data from independent decomposition experiments.
Teleoperation of an ankle-foot prosthesis with a wrist exoskeleton
Authors: Welker Cara G. , Chiu Vincent L. , Voloshina Alexandra S. , Collins Steven H. , Okamura Allison M.
Published: July 2020

Objective

We aimed to develop a system for people with amputation that non-invasively restores missing control and sensory information for an ankle-foot prosthesis.

Methods

In our approach, a wrist exoskeleton allows people with amputation to control and receive feedback from their prosthetic ankle via teleoperation. We implemented two control schemes: position control with haptic feedback of ankle torque at the wrist; and torque control that allows the user to modify a baseline torque profile by moving their wrist against a virtual spring. We measured tracking error and frequency response for the ankle-foot prosthesis and the wrist exoskeleton. To demonstrate feasibility and evaluate system performance, we conducted an experiment in which one participant with a transtibial amputation tracked desired wrist trajectories during walking, while we measured wrist and ankle response.

Results

Benchtop testing demonstrated that for relevant walking frequencies, system error was below human perceptual error. During the walking experiment, the participant was able to voluntarily follow different wrist trajectories with an average RMS error of 1.55° after training. The ankle was also able to track desired trajectories below human perceptual error for both position control (RMSE = 0.8°) and torque control (RMSE = 8.4%).

Conclusion

We present a system that allows a user with amputation to control an ankle-foot prosthesis and receive feedback about its state using a wrist exoskeleton, with accuracy comparable to biological neuromotor control.

Significance

This bilateral teleoperation system enables novel prosthesis control and feedback strategies that could improve prosthesis control and aid motor learning.
ReSeq simulates realistic Illumina high-throughput sequencing data
Authors: Schmeing Stephan , Robinson Mark D.
Published: July 2020

In high-throughput sequencing data, performance comparisons between computational tools are essential for making informed decisions in the data processing from raw data to the scientific result. Simulations are a critical part of method comparisons, but for standard Illumina sequencing of genomic DNA, they are often oversimplified, which leads to optimistic results for most tools.

ReSeq improves the authenticity of synthetic data by extracting and reproducing key components from real data. Major advancements are the inclusion of systematic errors, a fragment-based coverage model and sampling-matrix estimates based on two-dimensional margins. These improvements lead to a better representation of the original k-mer spectrum and more faithful performance evaluations. ReSeq and all of its code are available at:https://github.com/schmeing/ReSeq
Targeted Genome Editing of Bacteria Within Microbial Communities
Authors: Rubin Benjamin E. , Diamond Spencer , Cress Brady F. , Crits-Christoph Alexander , He Christine , Xu Michael , Zhou Zeyi , Smock Dylan C. , Tang Kimberly , Owens Trenton K. , Krishnappa Netravathi , Sachdeva Rohan , Deutschbauer Adam M. , Banfield Jillian F. , Doudna Jennifer A.
Published: July 2020

Knowledge of microbial gene functions comes from manipulating the DNA of individual species in isolation from their natural communities. While this approach to microbial genetics has been foundational, its requirement for culturable microorganisms has left the majority of microbes and their interactions genetically unexplored. Here we describe a generalizable methodology for editing the genomes of specific organisms within a complex microbial community. First, we identified genetically tractable bacteria within a community using a new approach, Environmental Transformation Sequencing (ET-Seq), in which non-targeted transposon integrations were mapped and quantified following community delivery. ET-Seq was repeated with multiple delivery strategies for both a nine-member synthetic bacterial community and a ~200-member microbial bioremediation community. We achieved insertions in 10 species not previously isolated and identified natural competence for foreign DNA integration that depends on the presence of the community. Second, we developed and used DNA-editing All-in-one RNA-guided CRISPR-Cas Transposase (DART) systems for targeted DNA insertion into organisms identified as tractable by ET-Seq, enabling organism- and locus-specific genetic manipulation within the community context. These results demonstrate a strategy for targeted genome editing of specific organisms within microbial communities, establishing a new paradigm for microbial manipulation relevant to research and applications in human, environmental, and industrial microbiomes.
The Argo: A 65,536 channel recording system for high density neural recordingin vivo
Authors: Sahasrabuddhe Kunal , Khan Aamir A. , Singh Aditya P. , Stern Tyler M. , Ng Yeena , Tadić Aleksandar , Orel Peter , LaReau Chris , Pouzzner Daniel , Nishimura Kurtis , Boergens Kevin M. , Shivakumar Sashank , Hopper Matthew S. , Kerr Bryan , Hanna Mina-Elraheb S. , Edgington Robert J. , McNamara Ingrid , Fell Devin , Gao Peng , Babaie-Fishani Amir , Veijalainen Sampsa , Klekachev Alexander V. , Stuckey Alison M. , Luyssaert Bert , Kozai Takashi D. Y. , Xie Chong , Gilja Vikash , Dierickx Bart , Kong Yifan , Straka Malgorzata , Sohal Harbaljit S. , Angle Matthew R.
Published: July 2020

Here we demonstrate the Argo System, a massively parallel neural recording system based on platinum-iridium microwire electrode arrays bonded to a CMOS voltage amplifier array. The Argo system is the highest channel count in vivo neural recording system built to date, supporting simultaneous recording from 65,536 channels, sampled at over 32 kHz and 12-bit resolution. This system is designed for cortical recordings, compatible with both penetrating and surface microelectrodes. We have validated this system by recording spiking activity from 791 neurons in rats and cortical surface Local Field Potential (LFP) activity from over 30,000 channels in sheep. While currently adapted for head-fixed recording, the microwire-CMOS architecture is well suited for clinical translation. Thus, this demonstration helps pave the way for a future high data rate intracortical implant.
Biased orientation representations can be explained by experience with non-uniform training set statistics
Authors: Henderson Margaret , Serences John
Published: July 2020

Visual acuity is better for vertical and horizontal compared to other orientations. This cross-species phenomenon is often explained by “efficient coding”, whereby more neurons show sharper tuning for the orientations most common in natural vision. However, it is unclear if experience alone can account for such biases. Here, we measured orientation representations in a convolutional neural network, VGG-16, trained on modified versions of ImageNet (rotated by 0°, 22.5°, or 45° counter-clockwise of upright). Discriminability for each model was highest near the orientations that were most common in the network’s training set. Furthermore, there was an over-representation of narrowly tuned units selective for the most common orientations. These effects emerged in middle layers and increased with depth in the network. Biases emerged early in training, consistent with the possibility that non-uniform representations may play a functional role in the network’s task performance. Together, our results suggest that biased orientation representations can emerge through experience with a non-uniform distribution of orientations, supporting the efficient coding hypothesis.
Improved protein structure refinement guided by deep learning based accuracy estimation
Authors: Hiranuma Naozumi , Park Hahnbeom , Baek Minkyung , Anishchanka Ivan , Dauparas Justas , Baker David
Published: July 2020

We develop a deep learning framework (DeepAccNet) that estimates per-residue accuracy and residue-residue distance signed error in protein models and uses these predictions to guide Rosetta protein structure refinement. The network uses 3D convolutions to evaluate local atomic environments followed by 2D convolutions to provide their global contexts and outperforms other methods that similarly predict the accuracy of protein structure models. Overall accuracy predictions for X-ray and cryoEM structures in the PDB correlate with their resolution, and the network should be broadly useful for assessing the accuracy of both predicted structure models and experimentally determined structures and identifying specific regions likely to be in error. Incorporation of the accuracy predictions at multiple stages in the Rosetta refinement protocol considerably increased the accuracy of the resulting protein structure models, illustrating how deep learning can improve search for global energy minima of biomolecules.
Ecological load and balancing selection in circumboreal barnacles
Authors: Nunez Joaquin C. B. , Rong Stephen , Damian-Serrano Alejandro , Burley John T. , Elyanow Rebecca G. , Ferranti David A. , Neil Kimberly B. , Glenner Henrik , Rosenblad Magnus Alm , Blomberg Anders , Johannesson Kerstin , Rand David M.
Published: July 2020

Acorn barnacle adults experience environmental heterogeneity at various spatial scales of their circumboreal habitat, raising the question of how adaptation to high environmental variability is maintained in the face of strong juvenile dispersal and mortality. Here we show that 4% of genes in the barnacle genome experience balancing selection across the entire range of the species. Many of these genes harbor mutations maintained across 2 million years of evolution between the Pacific and Atlantic oceans. These genes are involved in ion regulation, pain reception, and heat tolerance, functions which are essential in highly variable ecosystems. The data also reveal complex population structure within and between basins, driven by the trans-Arctic interchange and the last glaciation. Divergence between Atlantic and Pacific populations is high, foreshadowing the onset of allopatric speciation, and suggesting that balancing selection is strong enough to maintain functional variation for millions of years in the face of complex demography.
Basolateral amygdala CB1 receptors modulate HPA axis activation and context-cocaine memory strength during reconsolidation
Authors: Higginbotham Jessica A. , Jones Nicole M. , Wang Rong , McLaughlin Ryan J. , Fuchs Rita A.
Published: July 2020

Re-exposure to a cocaine-associated context triggers craving and relapse through the retrieval of salient context-drug memories. Upon retrieval, context-drug memories become labile and temporarily sensitive to modification before they are reconsolidated into long-term memory stores. Cannabinoid type 1 receptor (CB1R) signaling is necessary for cocaine-memory reconsolidation and associated glutamatergic plasticity in the basolateral amygdala (BLA); however, it remains unclear whether CB1Rs in the BLA mediate this phenomenon. To investigate this question, we examined whether CB1R antagonist or agonist administration into the BLA immediately after cocaine-memory retrieval (i.e., during memory reconsolidation) alters cocaine-memory strength and subsequent drug context-induced cocaine-seeking behavior in an instrumental rodent model of cocaine relapse. Intra-BLA administration of the CB1R antagonist, AM251 (0.3 µg/hemisphere) – during, but not after, memory reconsolidation – increased drug context-induced cocaine-seeking behavior three days later, while the CB1R agonist, WIN55,212-2 (0.5 µg/hemisphere) failed to alter this behavior. Furthermore, AM251 administration into the posterior caudate putamen (anatomical control region) during memory reconsolidation did not alter subsequent context-induced cocaine-seeking behavior. In a follow-up experiment, cocaine-memory retrieval elicited robust hypothalamic-pituitary-adrenal axis activation, as indicated by an increase in blood serum corticosterone concentration, and this response was selectively extended by intra-BLA AM251 administration during the putative time of memory reconsolidation relative to all control conditions. Together, these findings suggest that CB1R populations in the BLA gate memory strength or interfere with memory maintenance, possibly by diminishing the impact of cue-induced arousal on the integrity of the reconsolidating memory trace or on the efficiency of the memory reconsolidation process.
Comparative transcriptomics identifiesBotrytis cinereainduced conserved defences across different tissues ofFragaria vesca
Authors: Badmi Raghuram
Published: July 2020

Grey mould is one of the most devastating plant diseases that causes huge losses to the agricultural sector worldwide.Botrytis cinerea, the causal pathogen of grey mould, is a generalist necrotrophic fungus with the ability to infect over 1000 species and influence a broad array of host’s physiological responses.B. cinereais capable of infecting a wide variety of tissues such as leaves, stem, flowers and fruits that adds to the already complex problem in controlling its spread. Understanding the pathogen induced transcriptional reprogramming in different tissues is important to identify key genes for targeted gene modifications. Identifying the genes that are common between different tissue infections will reveal similarities and differences between these pathogen-tissue pairs. In this study, the transcriptomic datasets of Botrytis infected white berries ofFragaria vesca(WhiteBc) and Botrytis infected red berries ofF. vesca(RedBc) were (re)mapped to the latestF. vescatranscriptome to enable direct comparisons with the Botrytis infectedF. vescaleaves (LeafBc). The genes involved in MAP kinase signalling, pathogenesis-related, allergens, cell-wall defences, detoxification and secondary metabolites wereCommonResponsive andUpregulated (CoReUp) betweenLeafBc,WhiteBcandRedBc, suggesting their important roles againstB. cinereainfection in all three tissues. These insights maybe helpful for generatingB. cinerearesistant varieties of strawberry.
An autocrine Vitamin D-driven Th1 shutdown program can be exploited for COVID-19
Authors: McGregor Reuben , Chauss Daniel , Freiwald Tilo , Yan Bingyu , Wang Luopin , Nova-Lamperti Estefania , Zhang Zonghao , Teague Heather , West Erin E , Bibby Jack , Kelly Audrey , Malik Amna , Freeman Alexandra F , Schwartz Daniella , Portilla Didier , John Susan , Lavender Paul , Lionakis Michail S , Mehta Nehal N , Kemper Claudia , Cooper Nichola , Lombardi Giovanna , Laurence Arian , Kazemian Majid , Afzali Behdad
Published: July 2020

Pro-inflammatory immune responses are necessary for effective pathogen clearance, but cause severe tissue damage if not shut down in a timely manner1,2. Excessive complement and IFN-γ-associated responses are known drivers of immunopathogenesis3and are among the most highly induced immune programs in hyper-inflammatory SARS-CoV2 lung infection4. The molecular mechanisms that govern orderly shutdown and retraction of these responses remain poorly understood. Here, we show that complement triggers contraction of IFN-γ producing CD4+T helper (Th) 1 cell responses by inducing expression of the vitamin D (VitD) receptor (VDR) and CYP27B1, the enzyme that activates VitD, permitting T cells to both activate and respond to VitD. VitD then initiates the transition from pro-inflammatory IFN-γ+Th1 cells to suppressive IL-10+Th1 cells. This process is primed by dynamic changes in the epigenetic landscape of CD4+T cells, generating superenhancers and recruiting c-JUN and BACH2, a key immunoregulatory transcription factor5–7. Accordingly, cells in psoriatic skin treated with VitD increased BACH2 expression, and BACH2 haplo-insufficient CD4+T cells were defective in IL-10 production. As proof-of-concept, we show that CD4+T cells in the bronchoalveolar lavage fluid (BALF) of patients with COVID-19 are Th1-skewed and that VDR is among the top regulators of genes induced by SARS-CoV2. Importantly, genes normally down-regulated by VitD were de-repressed in CD4+BALF T cells of COVID-19, indicating that the VitD-driven shutdown program is impaired in this setting. The active metabolite of VitD, alfacalcidol, and cortico-steroids were among the top predicted pharmaceuticals that could normalize SARS-CoV2 induced genes. These data indicate that adjunct therapy with VitD in the context of other immunomodulatory drugs may be a beneficial strategy to dampen hyperinflammation in severe COVID-19.
Generation of ordered protein assemblies using rigid three-body fusion
Authors: Vulovic Ivan , Yao Qing , Park Young-Jun , Courbet Alexis , Norris Andrew , Busch Florian , Sahasrabuddhe Aniruddha , Merten Hannes , Sahtoe Danny D. , Ueda George , Fallas Jorge A. , Weaver Sara J. , Hsia Yang , Langan Robert A. , Plückthun Andreas , Wysocki Vicki H. , Veesler David , Jensen Grant J. , Baker David
Published: July 2020

Protein nanomaterial design is an emerging discipline with applications in medicine and beyond. A longstanding design approach uses genetic fusion to join protein homo-oligomer subunits via α-helical linkers to form more complex symmetric assemblies, but this method is hampered by linker flexibility and a dearth of geometric solutions. Here, we describe a general computational method that performs rigid three-body fusion of homo-oligomer and spacer building blocks to generate user-defined architectures, while at the same time significantly increasing the number of geometric solutions over typical symmetric fusion. The fusion junctions are then optimized using Rosetta to minimize flexibility. We apply this method to design and test 92 dihedral symmetric protein assemblies from a set of designed homo-dimers and repeat protein building blocks. Experimental validation by native mass spectrometry, small angle X-ray scattering, and negative-stain single-particle electron microscopy confirms the assembly states for 11 designs. Most of these assemblies are constructed from DARPins (designed ankyrin repeat proteins), anchored on one end by α-helical fusion and on the other by a designed homo-dimer interface, and we explored their use for cryo-EM structure determination by incorporating DARPin variants selected to bind targets of interest. Although the target resolution was limited by preferred orientation effects, small scaffold size, and the low-order symmetry of these dihedral scaffolds, we found that the dual anchoring strategy reduced the flexibility of the target-DARPIN complex with respect to the overall assembly, suggesting that multipoint anchoring of binding domains could contribute to cryo-EM structure determination of small proteins.
Structure and function of the nervous system in nectophores of the siphonophoreNanomia bijuga
Authors: Norekian Tigran P. , Meech Robert W.
Published: July 2020

AlthoughNanomianectophores are specialized for locomotion, their cellular elements and complex nerve structures suggest they have multiple subsidiary functions.

The main nerve complex is a nerve ring, an adjacent columnar-shaped matrix plus two associated nerve projections. An upper nerve tract appears to provide a sensory input while a lower nerve tract connects with the rest of the colony.

The nerve cell cluster that gives rise to the lower nerve tract may relay information from the colony stem.

The structure of the extensively innervated “flask cells” located around the bell margin suggests a secretory function. They are ideally placed to release chemical messengers or toxins into the jet of water that leaves the nectophore during each swim.

The numerous nematocytes present on exposed nectophore ridges appear to have an entangling rather than a penetrating role.

Movements of the velum, produced by contraction of the Claus’ muscle system during backwards swimming, can be elicited by electrical stimulation of the surface epithelium even when the major nerve tracts serving the nerve ring have been destroyed (confirming Mackie, 1964).

Epithelial impulses generated by electrical stimulation elicit synaptic potentials in Claus’ muscle fibres. Their amplitude suggests a neural input in the vicinity of the Claus’ muscle system. The synaptic delay is <1.3 ms (Temperature 11.5 to 15° C).

During backward swimming radial muscle fibres in the endoderm contract isometrically providing the Claus’ fibres with a firm foundation.

Summary Statement

Nanomia colonies have specialized swimming bells capable of backwards swimming; thrust is redirected by an epithelial signal that leads to muscle contraction via a synaptic rather than an electrotonic event.