bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

ABSTRACTIn 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

ABSTRACTPyrimidine 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

ABSTRACTThe 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

AbstractThe 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

AbstractIsogenic 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

AbstractAnimal 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

AbstractAsymmetric 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

AbstractIt 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

ABSTRACTTermination 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

AbstractThe 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

AbstractThe 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.SummaryUnderstanding 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

AbstractObjectiveWe aimed to develop a system for people with amputation that non-invasively restores missing control and sensory information for an ankle-foot prosthesis.MethodsIn 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.ResultsBenchtop 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%).ConclusionWe 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.SignificanceThis 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

AbstractIn 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
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

AbstractHere 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.