bluuebunny/crossref_metadata_2025_split huggingface dataset:
Highly diverse flavobacterial phages as mortality factor during North Sea spring blooms
Authors: Bartlau Nina , Wichels Antje , Krohne Georg , Adriaenssens Evelien M. , Heins Anneke , Fuchs Bernhard M. , Amann Rudolf , Moraru Cristina 
Published: May 2021

AbstractIt is generally recognized that phages have a modulating role in the marine environment. Therefore, we hypothesized that phages can be a mortality factor for the dense heterotrophic bacterial population succeeding in phytoplankton blooms. For the marine carbon cycle, spring phytoplankton blooms are important recurring events. In this study, we focused onFlavobacteriia, because they are main responders during these blooms and have an important role in the degradation of polysaccharides. A cultivation-based approach was used, obtaining 44 lytic flavobacterial phages (flavophages), representing twelve new species from two viral realms –DuplodnaviriaandMonodnaviria. Taxonomic analysis allowed us to delineate ten new phage genera and seven new families, from which nine and four, respectively, had no previously cultivated representatives. Genomic analysis predicted various life styles and genomic replication strategies. A likely eukaryote-associated host habitat was reflected in the gene content of some of the flavophages. Detection in cellular metagenomes and by direct-plating indicated that part of these phages were actively replicating in the environment during the 2018 spring bloom. Furthermore, CRISPR/Cas spacers and re-isolation during two consecutive years indicated that, at least part of the new flavophages are stable components of the microbial community in the North Sea. Together, our results indicate that these diverse flavophages have the potential to modulate their respective host populations.
Mapping the functional connectivity of ecosystem services supply across a regional landscape
Authors: Field Rachel D. , Parrott Lael 
Published: May 2021

AbstractSustainably managing multifunctional landscapes for production of multiple ecosystem services (ES) requires thorough understanding of the interactions between ES and the ecological processes that drive them. We build upon landscape connectivity theory to present a spatial approach for assessing functional connections between multiple ES at the landscape scale. We demonstrate application of the approach using existing ES supply mapping data for plant agriculture, waterflow regulation, and landscape aesthetics. The connections we observed between these three ES revealed high-value multifunctional linkages on the landscape that were not necessarily predictable from supply area mapping, nor from land use or land cover data. By providing spatial information on ES connectivity, our approach enables local and regional environmental planning and management that takes full consideration of the complex, multi-scale interactions between ecological processes, land use and land cover, and ecosystem service supply on a landscape.
Targeted deletion of the RNA-binding protein Caprin1 leads to progressive hearing loss and impairs recovery from noise exposure in mice
Authors: Nolan Lisa S. , Chen Jing , Cláudia Gonçalves Ana , Bullen Anwen , Steel Karen P. , Dawson Sally J. , Gale Jonathan E. 
Published: May 2021

AbstractCell cycle associated protein 1 (Caprin1) is an RNA-binding protein that can regulate the cellular post-transcriptional response to stress. It is a component of both stress granules and neuronal RNA granules and is implicated in neurodegenerative disease, synaptic plasticity and long-term memory formation. Our previous work suggested that Caprin1 also plays a role in the response of the cochlea to stress. Here, targeted inner ear-deletion of Caprin1 in mice leads to an early onset, progressive hearing loss. Auditory brainstem responses from Caprin1-deficient mice show reduced thresholds, with a significant reduction in wave-I amplitudes compared to wildtype. Whilst hair cell structure and numbers were normal, the inner hair cell-spiral ganglion neuron (IHC-SGN) synapse revealed abnormally large post-synaptic GluA2 receptor puncta, a defect consistent with the observed wave-I reduction. Unlike wildtype mice, mild-noise-induced hearing threshold shifts in Caprin1-deficient mice did not recover. Oxidative stress triggered TIA-1/HuR-positive stress granule formation in ex-vivo cochlear explants from Caprin1-deficient mice, showing that stress granules could still be induced. Taken together, these findings suggest that Caprin1 plays a key role in maintenance of auditory function, where it regulates the normal status of the IHC-SGN synapse.
DnaA and SspA Regulation of the iraD gene of E. coli: an alternative DNA damage response independent of LexA/RecA
Authors: Sass Thalia H. , Ferrazzoli Alexander E. , Lovett Susan T. 
Published: May 2021

ABSTRACTThe transcription factor RpoS (σS) of Escherichia coli controls a large number of genes important for tolerance of a variety of stress conditions. IraD promotes the post-translation stability of RpoS by inhibition of RssB, an adaptor protein for ClpXP degradation. We have previously documented DNA damage induction of iraD expression, independent of the SOS response. Both iraD and rpoS are required for tolerance to DNA damaging treatments such as H2O2 and the replication inhibitor azidothymidine in the log phase of growth. Using luciferase gene fusions to the 672 bp iraD upstream region, we show here that both promoters of iraD are induced by AZT. Genetic analysis suggests that both promoters are repressed by DnaA-ATP, partially dependent on a putative DnaA box at −81 bp, and regulated by RIDA (regulatory inactivation of DnaA), dependent on the DnaN processivity clamp. By electrophoretic mobility shift assays we show that purified DnaA protein binds to the iraD upstream region, so DnaA regulation of IraD is likely to be direct. DNA damage induction of iraD during log phase growth is abolished in the dnaA-T174P mutant, suggesting that DNA damage, in some way, relieves DnaA repression, possibly through the accumulation of replication clamps and enhanced RIDA. We demonstrate that the RNA-polymerase associated factor, SspA (stringent starvation protein A), induced by the accumulation of ppGpp, also affects IraD expression, with a positive effect on constitutive expression and a negative effect on AZT-induced expression, in a fashion independent of DnaA.SIGNIFICANCEDNA damage can lead to cell death or genomic instability. Cells have evolved transcriptional responses that sense DNA damage and up-regulate tolerance and repair factors; the LexA/RecA-regulated SOS response in E. coli was the first example of such a system. This work describes an alternative DNA damage response, controlled by DnaA and the IraD post-translational regulator of RpoS. The cellular signals for this response, we propose, are empty replication processivity (β) clamps that accumulate at replication blocks. IraD expression is also regulated by stringent starvation protein, SspA, induced by nutrient deprivation. This SOS-independent DNA damage response integrates a signal of incomplete replication with starvation to modulate expression of genes that promote the completion of replication.
Establishment of pan-Influenza A (H1-H18) and pan-Influenza B (pre-split, Vic/Yam) Pseudotype Libraries for efficient vaccine antigen selection
Authors: Del Rosario Joanne Marie M. , da Costa Kelly A.S. , Asbach Benedikt , Ferrara Francesca , Ferrari Matteo , Wells David A. , Mann Gurdip Singh , Ameh Veronica O. , Sabeta Claude T. , Banyard Ashley C. , Kinsley Rebecca , Scott Simon D. , Wagner Ralf , Heeney Jonathan L. , Carnell George W. , Temperton Nigel J. 
Published: May 2021

AbstractWe have developed an influenza hemagglutinin (HA) pseudotype library encompassing Influenza A subtypes HA1-18, and Influenza B subtypes (both lineages) to be employed in influenza pseudotype microneutralization (pMN) assays. The pMN is highly sensitive and specific for detecting virus-specific neutralizing antibodies against influenza viruses and can be used to assess antibody functionality in vitro. Here we show the production of these viral HA pseudotypes and their employment as substitutes for wildtype viruses in influenza serological and neutralization assays. We demonstrate its utility in detecting serum response to vaccination with the ability to evaluate cross-subtype neutralizing responses elicited by specific vaccinating antigens. Our findings may inform further pre-clinical studies involving immunization dosing regimens in mice and may help in the creation and selection of better antigens for vaccine design. These HA pseudotypes can be harnessed to meet strategic objectives that contribute to the strengthening of global influenza surveillance, expansion of seasonal influenza prevention and control policies, and strengthening pandemic preparedness and response.
Cortical VIP neurons locally control the gain but globally control the coherence of gamma band rhythms
Authors: Veit Julia , Handy Gregory , Mossing Daniel P. , Doiron Brent , Adesnik Hillel 
Published: May 2021

AbstractGamma band synchronization can facilitate local and long-range communication in neural circuits. In the primary visual cortex (V1) the strength of synchronization on the local level is strongly tuned to the contrast, size and center/surround orientation of grating stimuli. On the global level, the synchronization of gamma oscillations across the retinotopic map crucially depends on matched stimulus properties in the corresponding locations in the visual field. Although these features of V1 gamma rhythms are likely to be crucial for how they might support cortico-cortical communication and visual perception, their neural basis remains largely unknown. We hypothesized VIP disinhibitory interneurons, which shape other tuning properties in V1 by inhibiting SST neurons, may be responsible for tuning local gamma band power and global gamma synchronization. To test these ideas, we combined multi-electrode electrophysiology, cell-type specific optogenetic suppression of VIP neurons and computational modeling. Contrary to expectations, our data show that on the local level, VIP activity has no role in tuning gamma power to stimulus properties; rather, it scales the gain of gamma oscillations linearly across stimulus space and across behavioral state. Conversely, on the global level, VIP neurons specifically suppress gamma synchronization (as measured by spectral coherence) between spatially separated cortical ensembles when they are processing non-matched stimulus features. A straightforward computational model of V1 shows that like-to-like connectivity across retinotopic space, and specific, but powerful VIP➔SST inhibition are sufficient to capture these seemingly opposed effects. These data demonstrate how VIP neurons differentially impact local and global properties of gamma rhythms depending on the global statistics of the retinal image. VIP neurons may thus construct temporal filters in the gamma band for spatially continuous image features, such as contours, to facilitate the downstream generation of coherent visual percepts.
Capturing the songs of mice with an improved detection and classification method for ultrasonic vocalizations (BootSnap)
Authors: Abbasi Reyhaneh , Balazs Peter , Marconi Maria Adelaide , Nicolakis Doris , Zala Sarah M. , Penn Dustin J. 
Published: May 2021

AbstractHouse mice communicate through ultrasonic vocalizations (USVs), which are above the range of human hearing (>20 kHz), and several automated methods have been developed for USV detection and classification. Here we evaluate their advantages and disadvantages in a full, systematic comparison. We compared the performance of four detection methods, DeepSqueak (DSQ), MUPET, USVSEG, and the Automatic Mouse Ultrasound Detector (A-MUD). Moreover, we compared these to human-based manual detection (considered as ground truth), and evaluated the inter-observer reliability. All four methods had comparable rates of detection failure, though A-MUD outperformed the others in terms of true positive rates for recordings with low or high signal-to-noise ratios. We also did a systematic comparison of existing classification algorithms, where we found the need to develop a new method for automating the classification of USVs using supervised classification, bootstrapping on Gammatone Spectrograms, and Convolutional Neural Networks algorithms with Snapshot ensemble learning (BootSnap). It successfully classified calls into 12 types, including a new class of false positives used for detection refinement.BootSnapprovides enhanced performance compared to state-of-the-art tools, it has an improved generalizability, and it is freely available for scientific use.
Salt-dependent conformational changes of intrinsically disordered proteins
Authors: Wohl Samuel , Jakubowski Matthew , Zheng Wenwei 
Published: May 2021

AbstractThe flexible structure of an intrinsically disordered protein (IDP) is known to be perturbed by salt concentrations, which can be understood by electrostatic screening on charged amino acids. However, an IDP usually contains more uncharged residues which are influenced by the salting-out effect. Here we have parameterized the salting-out effect into a coarse-grained model using a set of Förster resonance energy transfer data and verified with experimental salt-dependent liquid-liquid phase separation (LLPS) of 17 proteins. The new model can correctly capture the behavior of 6 more sequences, resulting in a total of 13 when varying salt concentrations. Together with a survey of more than 500 IDP sequences, we conclude that the salting-out effect, which was considered to be secondary to electrostatic screening, is important for IDP sequences with moderate charged residues at physiological salt concentrations. The presented scheme is generally applicable to other computational models for capturing salt-dependent IDP conformations.Graphical TOC Entry
Simulating PIP2-induced gating transitions in Kir6.2 channels
Authors: Bründl Michael , Pellikan Sarala , Stary-Weinzinger Anna 
Published: May 2021

AbstractATP-sensitive potassium (KATP) channels consist of an inwardly rectifying K+ channel (Kir6.2) pore, to which four ATP-sensitive sulfonylurea receptor (SUR) domains are attached, thereby coupling K+ permeation directly to the metabolic state of the cell. Dysfunction is linked to neonatal diabetes and other diseases. K+ flux through these channels is controlled by conformational changes in the helix bundle region, which acts as a physical barrier for K+ flux. In addition, the G-loop, located in the cytoplasmic domain, and the selectivity filter might contribute to gating, as suggested by different disease-causing mutations. Gating of Kir channels is regulated by different ligands, like Gβγ, H+, Na+, adenosine nucleotides and the signaling lipid phosphatidyl-inositol 4,5-bisphosphate (PIP2), which is an essential activator for all eukaryotic Kir family members. Although molecular determinants of PIP2 activation of KATP channels have been investigated in functional studies, structural information of the binding site is still lacking as PIP2 could not be resolved in Kir6.2 cryo-EM structures. In this study, we used Molecular Dynamics (MD) simulations to examine the dynamics of residues associated with gating in Kir6.2. By combining this structural information with functional data, we investigated the mechanism underlying Kir6.2 channel regulation by PIP2.
The proportional recovery rule redux Arguments for its biological and predictive relevance
Authors: Goldsmith Jeff , Kitago Tomoko , de la Garza Angel Garcia , Kundert Robinson , Luft Andreas , Stinear Cathy , Byblow Winston D. , Kwakkel Gert , Krakauer John W. 
Published: May 2021

AbstractThe proportional recovery rule (PRR) posits that most stroke survivors can expect to reduce a fixed proportion of their motor impairment. As a statistical model, the PRR explicitly relates change scores to baseline values – an approach that has the potential to introduce artifacts and flawed conclusions. We describe approaches that can assess associations between baseline and changes from baseline while avoiding artifacts due either to mathematical coupling or regression to the mean due to measurement error. We also describe methods that can compare different biological models of recovery. Across several real datasets, we find evidence for non-artifactual associations between baseline and change, and support for the PRR compared to alternative models. We conclude that the PRR remains a biologically-relevant model of recovery, and also introduce a statistical perspective that can be used to assess future models.
A complex interplay between balancing selection and introgression maintains a genus-wide alternative life history strategy
Authors: Tunström Kalle , Woronik Alyssa , Hanly Joseph J. , Rastas Pasi , Chichvarkhin Anton , Warren Andrew D , Kawahara Akito , Schoville Sean D. , Ficarrotta Vincent , Porter Adam H. , Watt Ward B. , Martin Arnaud , Wheat Christopher W. 
Published: May 2021

AbstractAlternative life-history strategies (ALHS) are genetic polymorphisms generating phenotypes differing in life histories that generally arise due to metabolic resource allocation tradeoffs. Althouigh ALHS are often be limited to a single sex or populations of a species, they can, in rare cases, be found among several species across a genus. In the butterfly genus Colias, at least a third of the species have a female limited ALHS called Alba. While many females develop brightly pigmented wings, Alba females reallocate nitrogen resources used in pigment synthesis to reproductive development, producing white-winged, more fecund females. Whether this ALHS evolved once or many times, and whether it has moved among species via introgression or been maintained via long-term balancing selection, has not been established. Answering these questions presents an opportunity to investigate the genetic basis and evolutionary forces acting upon ALHS, which have rarely been studied at a genus level. Here we identify the genetic locus of Alba in a second Colias species, allowing us to compare this with previous results in a larger phylogenetic context. Our findings suggest Alba has a singular origin and has been maintained in Colias through a combination of balancing selection and introgression for nearly one million years and at least as many generations. Finally, using CRISPR/Cas9 deletions in the cis-regulatory region of the Alba allele, we demonstrate that the Alba allele is a modular enhancer for the BarH1 gene and is necessary for the induction of the ALHS, which potentially facilitates its long-term persistence in the genus.
Correction of a pathogenic mutation in iPSCs derived from a patient with Christianson syndrome using CRISPR/Cas9 genome editing
Authors: Ma Li , Wu Qing , Schmidt Michael , Morrow Eric M. 
Published: May 2021

AbstractSLC9A6 (also termed NHE6) encodes the endosomal Na+/H+ exchanger 6 (NHE6). Pathogenic, loss-of-function mutations in NHE6 cause the X-linked neurogenetic disorder Christianson syndrome (CS). We developed induced pluripotent stem cell (iPSC) lines derived from a patient with CS and from a biologically related control. The patient with CS contained the nonsense mutation c.1569G>A (p.(W523X)), which caused a significant reduction in NHE6 mRNA and a lack of detectable NHE6 protein in CS iPSCs in comparison to control iPSCs. To establish a cell model for study of CS with an isogenic control, we corrected the c.1569G>A mutation to the NHE6 reference genome sequence using CRISPR/Cas9-mediated homology directed repair knock-in methodology. Multiple subclonal lines were generated, and notably, NHE6 protein was expressed in all analyzed c.1569G>A (p.(W523X)) genome-corrected iPSC lines. This CS iPSC model together with the associated biologically related and isogenic control cell lines will serve as a valuable resource for both basic and translational studies in CS.
High resolution analysis of proteome dynamics during Bacillus subtilis sporulation
Authors: Tu Zhiwei , Dekker Henk L. , Roseboom Winfried , Swarge Bhagyashree N. , Setlow Peter , Brul Stanley , Kramer Gertjan 
Published: May 2021

AbstractBacillus subtilis vegetative cells switch to sporulation upon nutrient limitation. To investigate the proteome dynamics during sporulation, high resolution time-lapse proteomics was performed in a cell population that was induced to sporulate synchronously. Here, we are the first to comprehensively investigate the changeover of sporulation regulatory proteins, coat proteins and other proteins involved in sporulation and spore biogenesis. Protein co-expression analysis revealed four co-expressed modules (blue, brown, green and yellow). Modules brown and green are upregulated during sporulation and contain proteins associated with sporulation. Module blue, is negatively correlated with modules brown and green, and contained ribosomal and metabolic proteins. Finally, module yellow shows co-expression with the three other modules. Notably, several proteins not belonging to any of the known transcription regulons were identified as co-expressed with modules brown and green. We speculate that they may also play roles during sporulation. Finally, levels of some coat proteins, for example morphogenetic coat proteins, decreased late in sporulation. We speculate on their possible role in guiding or helping assembly of other coat proteins, after which they can be disposed of, but such a hypothesis remains to be experimentally addressed.
Loss of Acta2 in cardiac fibroblasts does not prevent the myofibroblast differentiation or affect the cardiac repair after myocardial infarction
Authors: Li Yuxia , Li Chaoyang , Liu Qianglin , Wang Leshan , Bao Adam X. , Jung Jangwook P. , Francis Joseph , Molkentin Jeffery D. , Fu Xing 
Published: May 2021

AbstractIn response to myocardial infarction (MI), quiescent cardiac fibroblasts differentiate into myofibroblasts mediating tissue repair in the infarcted area. One of the most widely accepted markers of myofibroblast differentiation is the expression of Acta2 which encodes smooth muscle alpha-actin (SMαA) that is assembled into stress fibers. However, the requirement of Acta2 in the myofibroblast differentiation of cardiac fibroblasts and its role in post-MI cardiac repair were still not known. To answer these questions, we generated a tamoxifen-inducible cardiac fibroblast-specific Acta2 knockout mouse line. Surprisingly, mice that lacked Acta2 in cardiac fibroblasts had a normal survival rate after MI. Moreover, Acta2 deletion did not affect the function or overall histology of infarcted hearts. No difference was detected in the proliferation, migration, or contractility between WT cardiac fibroblasts and Acta2-null cardiac myofibroblasts. Additional analysis identified that Acta2-null cardiac myofibroblasts had a normal total filamentous actin level and total actin level. Acta2 deletion caused a unique compensatory increase in the transcription level of Actg2 and a possible increase in the protein abundance of cytoplasmic actin isoforms. In conclusion, the deletion of Acta2 does not prevent the myofibroblast differentiation of cardiac fibroblasts or affect the post-MI cardiac repair, and the increase in the expression of non-SMαA actin isoforms and the functional redundancy between actin isoforms are likely able to compensate for the loss of Acta2 in cardiac myofibroblasts.