bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic gain decomposition reveals functional effects of dendrites, ion channels and input statistics in population coding
Authors: Zhang Chenfei , Revah Omer , Wolf Fred , Neef Andreas 
Published: February 2022

AbstractModern, high-density neuronal recordings reveal at ever higher precision how information is represented by neural populations. Still, we lack the tools to understand these processes bottom-up, emerging from the biophysical properties of neurons, synapses, and network structure. The concept of the dynamic gain function, a spectrally resolved approximation of a population’s coding capability, has the potential to link cell-level properties to network-level performance. However, the concept is not only useful but also very complex because the dynamic gain’s shape is co-determined by axonal and somatodendritic parameters and the population’s operating regime. Previously, this complexity precluded an understanding of any individual parameter’s impact. Here, we decomposed the dynamic gain function into three components corresponding to separate signal transformations. This allowed attribution of network-level encoding features to specific cell-level parameters. Applying the method to data from real neurons and biophysically plausible models, we found: 1. The encoding bandwidth of real neurons, approximately 400 Hz, is constrained by the voltage dependence of axonal currents during early action potential initiation. 2. State-of-the-art models only achieve encoding bandwidths around 100 Hz and are limited mainly by subthreshold processes instead. 3. Large dendrites and low-threshold potassium currents modulate the bandwidth by shaping the subthreshold stimulus-to-voltage transformation. Our decomposition provides physiological interpretations when the dynamic gain curve changes, for instance during spectrinopathies and neurodegeneration. By pinpointing shortcomings of current models, it also guides inference of neuron models best suited for large-scale network simulations.Significant StatementThe dynamic gain function quantifies how neurons can engage in collective, network-level activity, shape brain rhythms and information encoding. Its shape results from a complex interaction between properties of different molecules (ion channels) and cell compartments (morphology, resistance), and is so far only understood for the simplest neuron models. Here we provide an interpretable analysis, decomposing the dynamic gain based on the stimulus transformation steps in individual neurons. We apply the decomposition to data from real neurons and complex models, and attribute changes of the dynamic gain to specific sub- and suprathreshold processes. Using this decomposition method, we reveal the relevance of subthreshold potassium channels for ultrafast information encoding and expose the shortcomings of even the state-of-the-art neuron models.
Minimal RNA replicons for targeted gene silencing based on an asymptomatic viroid
Authors: Marquez-Molins Joan , Urrutia-Perez María , Hernandez-Azurdia Andrea Gabriela , Pallas Vicente , Gomez Gustavo 
Published: February 2022

AbstractGene silencing for functional studies in plants has been largely facilitated by manipulating viral genomes with inserts from host genes to trigger virus induced gene silencing (VIGS) against the corresponding mRNAs. However, viral genomes encode multiple proteins and disrupt plant homeostasis by interfering with endogenous cell mechanisms. To circumvent this issue, we have developed a silencing method based on the minimal autonomously-infectious nucleic acids currently known: viroids. In particular,Eggplant latent viroid(ELVd), an asymptomatic viroid, was manipulated with insertions between 21 to 42 nucleotides and our results show that larger insertions are tolerated but secondary structure is critical for their stability. Additionally, these ELVd constructs are able of local and systemic spread and can silence a target gene in eggplant. Inspired by the design of artificial microRNAs, we have developed a standardized procedure to generate stable insertions into the ELVd genome capable of silencing the desired target gene. Analogously to VIGS, we have termed our approach Viroid Induced Gene Silencing (VdIGS) and demonstrate that is a promising tool for dissecting gene functions in eggplant. Overall, this represents the use of minimal circular replicating RNAs able to spread systemically combined with the production of a tailored sRNA for targeted silencing.
Chimeric a-subunit isoforms generate functional yeast V-ATPases with altered regulatory properties in vitro and in vivo
Authors: Tuli Farzana , Kane Patricia M. 
Published: February 2022

ABSTRACTV-ATPases are highly regulated, multi-subunit proton pumps that acidify organelles. The V-ATPase a-subunit is a two-domain protein containing a C-terminal transmembrane domain that participates in proton transport and a N-terminal cytosolic domain (aNT) that acts as a regulatory hub, integrating environmental inputs to regulate assembly, localization, and V-ATPase activity. Tissue- and organelle-specific a-subunit isoforms exist in most organisms, but how regulatory inputs are decoded by aNT isoforms is unknown. The yeast S. cerevisiae encodes only two organelle-specific a-isoforms, Stv1 in the Golgi and Vph1 in the vacuole. Based on recent structures, we designed chimeric yeast aNTs in which the globular proximal and distal ends are exchanged. The Vph1 proximal-Stv1 distal (VPSD) aNT chimera binds to the glucose-responsive RAVE assembly factor in vitro but exhibits little binding to phosphoinositide lipids that activate V-ATPases. The Stv1 proximal-Vph1 distal (SPVD) aNT lacks RAVE binding but binds more tightly to phosphoinositides than Vph1 or Stv1. When attached to the Vph1 C-terminal domain in vivo, both chimeras complement growth defects of a vph1Δ mutant, but only the SPVD chimera exhibits wild-type V-ATPase activity. Cells containing the SPVD chimera adapt more slowly to a poor carbon source than wild-type cells but grow more rapidly than wild-type after a shift to alkaline pH. This is the first example of a “redesigned” V-ATPase with altered regulatory properties and adaptation to specific stresses.
Targeted nanocarriers coopting pulmonary leukocytes for drug delivery to the injured brain
Authors: Glassman Patrick M. , Nong Jia , Myerson Jacob W. , Zuluaga-Ramirez Viviana , Rodriguez-Garcia Alba , Mukalel Alvin , Omo-Lamai Serena , Walsh Landis R. , Kiseleva Raisa Y. , Villa Carlos H. , Greineder Colin F. , Kasner Scott E. , Weissman Drew , Mitchell Michael J. , Muro Silvia , Persidsky Yuri , Brenner Jacob S. , Muzykantov Vladimir R. , Marcos-Contreras Oscar A. 
Published: February 2022

ABSTRACTSelective drug delivery to injured regions of the brain is an elusive, but biomedically important, goal. It is tempting to co-opt migrating white blood cells (WBC) to carry drugs to the injured brain, using natural WBC tropism. Current approaches to load cargoes to WBC have limited utility, particularly in acute conditions, due to the need for time consuming ex vivo manipulation and loading of cells. Physiological, in vivo loading of WBC may be advantageous in this scenario. Here we devised such a strategy, capitalizing on the unique features of the direct blood exchange between brain and lungs. Mediators emanating from the injured brain directly travel to the pulmonary vasculature via venous flow. In response to these mediators, WBCs, transiently residing in the pulmonary microvascular lumen, disembark and flow with arterial blood to the brain microvasculature, where they adhere and transmigrate to the brain parenchyma via the local chemoattractant gradient. We posited that direct in vivo targeting of cargoes to the pulmonary WBC pool may provide drug transfer to brain via this natural mechanism. To test this, we intravenously injected agents targeted to intercellular adhesion molecule 1 (ICAM) in mice with acute brain inflammation caused by direct injection of tumor necrosis factor alpha (TNF-α). We found that: A) At 2 hours, >20% of ICAM/NP accumulated in lungs, predominantly in WBCs; B) At 6 and 22 hours, ICAM/NP pulmonary uptake markedly decreased; C) In contrast, ICAM/NP uptake in brain increased ~5-fold in this time interval, concomitantly with migration of WBCs to the brain. Cranial window fluorescent microscopy confirmed WBC transport of ICAM/NP to the brain in TNF-α-challenged mice beyond the BBB. Importantly, demonstrating the pharmacologic relevance of this strategy, dexamethasone-loaded ICAM/liposomes abrogated brain edema in this model. In sum, coopting the natural homing of WBC from the lungs via ICAM-targeting to injured brain is an attractive strategy for precise interventions for treatment of acute brain injuries.VISUAL ABSTRACT
Interactions between evolved pesticide resistance and pesticide exposure influence immunity against pathogens
Authors: Birnbaum Stephanie S.L. , Schulz Nora K.E. , Tate Ann T. 
Published: February 2022

AbstractPesticide resistance readily evolves in natural insect populations and often coopts the same stress, detoxification, and immune pathways involved in physiological responses against primary pathogen and pesticide exposure. As a result, resistance evolution can alter antagonism or facilitation among chemical and biological pest control strategies in directions that remain difficult to predict. To investigate the interactive effects of chemical pesticide resistance, exposure, and bacterial infection on insect phenotypes, we experimentally evolved resistance to two different classes of pesticides (organophosphates and pyrethroids) in the red flour beetle,Tribolium castaneum. We exposed pesticide susceptible and resistant lines to pesticides, the entomopathogen and biocontrol agentBacillus thuringiensis(Bt), or both. Pesticide resistance and Bt exposure were individually associated with slower development, indicating sub-lethal fitness costs of resistance and infection, respectively. After organophosphate exposure, however, beetles developed more quickly and were more likely to survive if also exposed to Bt. We used RNAseq to examine the interactive effects of pesticide resistance, pesticide exposure, and Bt exposure on gene expression. Pyrethroid-resistant insects exhibited dampened immune responses to Bt infection relative to susceptible ones. In a similar vein, simultaneous exposure to organophosphates and Bt resulted in muted stress-associated transcriptional responses compared to exposure with only one factor. Our results suggest that direct and host-mediated indirect interactions among pathogens and pesticides may buffer the cost of exposure to host fitness-associated traits within generations but exacerbate trade-offs over evolutionary time.
Oligomerization processes limit photoactivation and recovery of the Orange Carotenoid Protein
Authors: Andreeva Elena A. , Nizinski Stanislaw , Wilson Adjélé , Levantino Matteo , De Zitter Elke , Munro Rory , Muzzopappa Fernando , Thureau Aurélien , Zala Ninon , Burdzinski Gotard , Sliwa Michel , Kirilovsky Diana , Schirò Giorgio , Colletier Jacques-Philippe 
Published: February 2022

AbstractThe Orange Carotenoid Protein (OCP) is a photoactive protein involved in cyanobacterial photoprotection, by quenching of the excess of light harvested energy. The photoactivation mechanism remains elusive, in part due to absence of data pertaining to the timescales over which protein structural changes take place. It also remains unclear whether or not oligomerization of the dark-adapted and light-adapted OCP could play a role in the regulation of its energy quenching activity. Here, we probed photo-induced structural changes in OCP by a combination of static and time-resolved X-ray scattering and steady-state and transient optical spectroscopy in the visible range. Our results suggest that oligomerization partakes in regulation of the OCP photocycle, with different oligomers slowing down the overall thermal recovery of the dark-adapted state of OCP. They furthermore reveal that upon non-photoproductive excitation, a numbed-state forms, which remains in a non-photoexcitable structural state for at least ∼0.5 µs after absorption of a first photon.Significance StatementThe orange carotenoid protein (OCP) is a photoactivatable protein involved in cyanobacterial photoprotection. Upon photoactivation, OCP becomes able to quench the excess of energy uptaken by the light-harvesting antennae, thereby evading damage to the cells. It remains unclear, however, what is the exact OCP photoactivation mechanism, and whether or not oligomerization partakes in the regulation of the OCP function. Here, we investigated these issues by combining static and time-resolved (TR) X-ray scattering and optical spectroscopy. Our results show that OCP oligomerizes in both the dark-adapted inactive and light-adapted active states, suggesting a functional role for oligomerization. TR scattering data furthermore reveal that the first large-scale conformational changes associated with OCP photoactivation take place on the µs time scale.
Tau forms dynamic hot spots that are resistant to microtubule perturbations and cholesterol depletion
Authors: Padmanabhan Pranesh , Kneynsberg Andrew , Gonzalez Esteban Cruz , Amor Rumelo , Sibarita Jean-Baptiste , Götz Jürgen 
Published: February 2022

ABSTRACTAccumulation of Tau aggregates is a pathological hallmark of Alzheimer’s disease, but little is known about where these aggregates assemble and how stable these assemblies are. Using quantitative, single-molecule imaging, we show that Tau exhibits spatial and kinetic heterogeneity near the plasma membrane, resulting in the formation of nanometer-sized hot spots smaller than the diffraction limit. The hot spots lasted tens of seconds, much longer than the short dwell time (~40 ms) of Tau on microtubules. Pharmacological and biochemical disruption of Tau/microtubule interactions did not affect hot spot formation, suggesting that these are different from the reported Tau condensation on microtubules. Although cholesterol removal has been shown to reduce Tau pathology, its depletion did not affect Tau hot spot dynamics. Our study identifies an intrinsic dynamic property of Tau near the plasma membrane that may facilitate the formation of assembly sites for Tau to assume its physiological and pathological functions.
Progerin triggers a phenotypic switch in vascular smooth muscle cells that causes replication stress and an aging-associated secretory signature
Authors: Coll-Bonfill Nuria , Mahajan Urvashi , Lin Chien-Jung , Mecham Robert P. , Gonzalo Susana 
Published: February 2022

ABSTRACTHutchinson Gilford Progeria Syndrome is a premature aging disease caused byLMNAgene mutation and the production of a truncated lamin A protein “progerin” that elicits cellular and organismal toxicity. Progerin accumulates in the vasculature, being especially toxic for vascular smooth muscle cells (VSMC). Patients’ autopsies show that vessel stiffening, and aortic atherosclerosis is accompanied by VSMC depletion in the medial layer, altered extracellular matrix (ECM), and thickening of the adventitial layer. Mechanisms whereby progerin causes massive VSMC loss and vessel alterations remain poorly understood. Mature VSMC retain phenotypic plasticity and can switch to a synthetic/proliferative phenotype. Here we show that progerin expression in human and mouse VSMC causes a switch towards the synthetic/proliferative phenotype. This switch elicits some level of replication stress in normal cells, which is exacerbated in the presence of progerin, leading to telomere fragility, genomic instability, and ultimately VSMC death. Importantly, calcitriol prevents replication stress, telomere fragility, and genomic instability, reducing VSMC death. In addition, RNAseq analysis shows induction of a profibrotic and proinflammatory aging-associated secretory phenotype upon progerin expression in human primary VSMC. Our data suggest that phenotypic switch-induced replication stress might be an underlying cause of VSMC loss in progeria, which together with loss of contractile features and gain of profibrotic and proinflammatory signatures contribute to vascular stiffness in HGPS. Preventing the phenotypic switch-induced replication stress with compounds such as calcitriol might ameliorate CVD in HGPS patients.
DNA opening during transcription initiation by RNA polymerase II in atomic detail
Authors: Lapierre Jeremy , Hub Jochen S. 
Published: February 2022

AbstractRNA polymerase II (RNAP II) is a macro-molecular complex that synthesizes RNA by reading the DNA code, a process called transcription. During transcription initiation, RNAP II opens the double-stranded DNA to expose the DNA template to the active site. The molecular interactions driving and controlling the DNA opening are not well understood. We used all-atom molecular dynamics (MD) simulations to obtain a continuous atomistic pathway for the DNA opening process in human RNAP II. To achieve such large-scale and highly nonlinear transition, we steered the MD simulations along a combination of collective variables involving a guided DNA rotation and a set of path collective variables. The simulations reveal extensive interactions of the DNA with three protein loops near the active site, namely the rudder, fork loop 1, and fork loop 2. According to the simulations, these DNA–protein interactions support DNA opening by attacking Watson-Crick hydrogen bonds, and they stabilize the open DNA bubble by the formation of a wide set of DNA–protein salt bridges.
Janus Kinase 3 phosphorylation and the JAK/STAT pathway are positively modulated by follicle-stimulating hormone (FSH) in bovine granulosa cells
Authors: Zareifard Amir , Beaudry Francis , Ndiaye Kalidou 
Published: February 2022

AbstractJAK3 is a member of the JAK family of tyrosine kinase proteins involved in cytokine receptor-mediated intracellular signal transduction through the JAK/STAT signaling pathway. JAK3 was shown as differentially expressed in granulosa cells (GC) of bovine pre-ovulatory follicles suggesting that JAK3 could modulate GC function and activation/inhibition of downstream targets. We used JANEX-1, a JAK3 inhibitor, and FSH treatments and analyzed proliferation markers, steroidogenic enzymes and phosphorylation of target proteins including STAT3, CDKN1B/p27Kip1 and MAPK8IP3/JIP3. GC were treated with or without FSH in the presence or not of JANEX-1. Expression of steroidogenic enzyme CYP11A1, but not CYP19A1, was upregulated in GC treated with FSH and both were significantly decreased when JAK3 was inhibited. Proliferation markers CCND2 and PCNA were reduced in JANEX-1-treated GC and upregulated by FSH. Western blots analyses showed that JANEX-1 treatment reduced pSTAT3 amounts while JAK3 overexpression increased pSTAT3. Similarly, FSH treatment increased pSTAT3 even in JANEX-1-treated GC. UHPLC-MS/MS analyses revealed phosphorylation of specific amino acid residues within JAK3 as well as CDKN1B and MAPK8IP3 suggesting possible activation or inhibition post-FSH or JANEX-1 treatments. We show that FSH activates JAK3 in GC, which could phosphorylate target proteins and likely modulate other signaling pathways involving CDKN1B and MAPK8IP3.
Interference with lipoprotein maturation sensitizes methicillin-resistantStaphylococcus aureusto human group IIA secreted phospholipase A2and daptomycin
Authors: Kuijk Marieke M. , Wu Yongzheng , van Hensbergen Vincent P. , Shanlitourk Gizem , Payré Christine , Lambeau Gérard , Herrmann Jennifer , Müller Rolf , van Strijp Jos A.G. , Pannekoek Yvonne , Touqui Lhousseine , van Sorge Nina M. 
Published: February 2022

AbstractMethicillin-resistantStaphylococcus aureus(MRSA) has been classified as a high priority pathogen by the World Health Organization underlining the high demand for new therapeutics to treat infections. Human group IIA secreted phospholipase A2(hGIIA) is among the most potent bactericidal proteins against Gram-positive bacteria, includingS. aureus. To determine hGIIA-resistance mechanisms of MRSA we screened the Nebraska Transposon Mutant Library using a sublethal concentration of recombinant hGIIA. We identified and confirmed the role oflspA, encoding the lipoprotein signal peptidase LspA, as a new hGIIA resistance gene in bothin vitroassays and an infection model in hGIIA-transgenic mice. Increased susceptibility of thelspAmutant was associated with faster and increased cell wall penetration of hGIIA. Moreover,lspAdeletion also increased susceptibility to daptomycin, a last-resort antibiotic to treat MRSA infections. Exposure of MRSA wild-type to the LspA-specific inhibitors globomycin and myxovirescin A1 induced alspAmutant phenotype with regard to hGIIA and daptomycin killing. Analysis of >26,000S. aureusgenomes showed that LspA is highly sequence-conserved, suggesting that LspA inhibition could be applied universally. The role of LspA in hGIIA resistance was not restricted to MRSA sinceStreptococcus mutansandEnterococcus faecaliswere also more hGIIA-susceptible afterlspAdeletion or LspA inhibition, respectively. Overall, our data suggest that pharmacological blocking of LspA may disarm Gram-positive pathogens, including MRSA, to enhance clearance by innate host defense molecules and clinically-applied antibiotics.
Forecasting blockchain adoption in supply chains based on machine learning: evidence from Palestinian food SMEs
Authors: Hamdan Ihab K. A. , Aziguli Wulamu , Zhang Dezheng , Sumarliah Eli , Usmanova Kamila 
Published: February 2022

PurposeThis paper seeks to discover whether the technical, organisational and technology acceptance model (TAM) factors will significantly affect the adoption of blockchain technology (ABT) amongst SMEs.Design/methodology/approachThe research employs structural equation modelling (SEM) and a machine learning approach to identify factors influencing the ABT behaviour that leaders can use to predict the prospect of the ABT in their enterprises. Information was collected from 255 respondents representing 166 SMEs in the food industry, Palestine.FindingsThe analyses reveal that the ABT is positively and significantly shaped by TAM factors: (1) perceived benefits and (2) perceived ease of using blockchain. Simultaneously, the former is significantly influenced by compatibility and upper management support, while the latter is affected by complexity. Finally, education and training affect both factors.Originality/valueThis paper is amongst the first attempts to examine the ABT behaviour in the food industry using the integration of SEM and machine learning approach.