bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic tools that target mechanoreceptors produce reliable labeling of bladder afferents
Authors: Tran Emily L. , Stuedemann Sara A. , Link Olivia D. , Crawford LaTasha K. 
Published: September 2022

AbstractMechanosensitive bladder sensory neurons are critical for sensing bladder distention, but their role in bladder pain and bladder pathology is poorly understood, due in part, to the challenges of identifying mechanoreceptors in tissue sections. A lot of what is known about how disease alters sensory innervation of the bladder comes from studies that traditionally focus on nociceptive nerve terminals. In seeking tools to characterize the role of non-nociceptive afferents in the bladder, we first examined neurofilament heavy (NFH), a marker for medium to large-diameter myelinated A fibers, in combination with the common marker for peptidergic nociceptors, calcitonin gene-related peptide (CGRP). While there was partial overlap between NFH and CGRP, 87% of NFH fibers were CGRP-negative, underscoring the abundance of non-nociceptive A fibers nerve terminals in the bladder. Two mouse lines that have been used for genetic labeling of mechanoreceptors of the skin were tested for their ability to label bladder afferents. Once crossed to Cre-dependent reporter lines, tyrosine kinase B (TrkB) TrkBCreER2 mice can be used to label A-delta mechanoreceptors while receptor tyrosine kinase ret protooncogene (Ret) RetCreER2 mice can label a combination of A-beta mechanoreceptors and non-peptidergic nociceptors in adult mice (late Ret). Both mouse lines produced successful labeling of bladder nerve terminals demonstrating partial overlap with NFH and minimal overlap with CGRP. Thus, we have identified new genetic strategies to investigate CGRP-negative subpopulations of bladder afferents that remain largely uncharacterized in studies that target peptidergic nociceptors. These tools can help elucidate the role of mechanosensitive afferents in bladder pathophysiology and urologic chronic pain.
NPAS4 supports drug-cue associations and relapse-like behavior through regulation of the cell type-specific activation balance in the nucleus accumbens
Authors: Hughes Brandon W. , Tsvetkov Evgeny , Siemsen Benjamin M. , Snyder Kirsten. K. , Akiki Rose Marie , Wood Daniel J. , Penrod Rachel D. , Scofield Michael D. , Berto Stefano , Taniguchi Makoto , Cowan Christopher W. 
Published: September 2022

AbstractUse of addictive substances creates powerful drug-cue associations that often trigger relapse. Drug seeking is gated in the nucleus accumbens (NAc) by competing activation of D1 dopamine receptor-expressing medium spiny neurons (D1-MSNs) that promote, and D2 dopamine receptor-expressing neurons (D2-MSNs) that oppose, drug seeking. We show here that the ensemble of neurons in the NAc that induce the neuronal activity-regulated transcription factor, Neuronal PAS Domain Protein 4 (NPAS4), is required for cocaine-context associations. In addition, NPAS4 functions within NAc D2-MSNs to govern the activation balance of NAc D1-MSNs and D2-MSNs necessary for drug-context memories and cue-induced cocaine, but not sucrose, seeking. NPAS4 regulates drug-cue associations and preponderant D1-MSN activation by influencing a program of gene expression that blocks cocaine-induced potentiation of prefrontal cortical excitatory drive onto D2-MSNs. Together our findings reveal that NPAS4 is a key player governing NAc MSN cell-type activation balance and promoting drug-cue associations and relapse vulnerability.
How inhibitory and excitatory inputs gate output of the inferior olive
Authors: Loyola Sebastián , Hoogland Tycho M. , Negrello Mario , Hoedemaker Hugo , Romano Vincenzo , De Zeeuw Chris I. 
Published: September 2022

AbstractThe inferior olive provides the climbing fibers to Purkinje cells in the cerebellar cortex, where they elicit all-or-none complex spikes and control major forms of plasticity. Given their important role in both short-term and long-term coordination of cerebellum-dependent behaviors, it is paramount to understand the factors that determine the output of olivary neurons. Here, we investigate how the inhibitory and excitatory inputs to the olivary neurons interact with each other, generating spiking patterns of olivary neurons that ride on their intrinsic oscillations. Using dual color optogenetic stimulation and whole cell recordings we demonstrate how intervals between the inhibitory input from the cerebellar nuclei and excitatory input from the mesodiencephalic junction affect phase and gain of the olivary output at both the sub- and suprathreshold level. When the excitatory input is activated approximately 50 ms after the inhibitory input, the phase of the intrinsic oscillations becomes remarkably unstable and the excitatory input can hardly generate any olivary spike. Instead, when the excitatory input is activated approximately 150 ms after the inhibitory input, the excitatory input can optimally drive olivary spiking, riding on top of the first cycle of the subthreshold oscillations that have been powerfully reset by the preceding inhibitory input. Simulations of a large-scale network model of the inferior olive highlight to what extent the synaptic interactions penetrate in the neuropil, generating quasi-oscillatory spiking patterns in large parts of the olivary subnuclei, the size of which also depends on the relative timing of the inhibitory and excitatory inputs.
Pseudokinase HPO-11 inhibits nonsense-mediated decay to ensure genome stability in C. elegans
Authors: Zhao Qian , Gromoff Erika D , Yang Wei , Schwarz Jennifer , Tittel Lena , Schulze Ekkehard , Warscheid Bettina , Baumeister Ralf , Qi Wenjing 
Published: September 2022

AbstractDNA double-strand breaks (DSBs) are highly toxic DNA lesions that can induce mutations and chromosome rearrangement therefore causing genome instability (GIN). In response to DSBs, cells activate the DNA damage response by hierarchical assembly of signaling and repair mechanisms. This involves recruitment of the repair factors at DSB sites, local chromatin remodeling, cell cycle arrest and, eventually, DNA repair or apoptosis. Studies investigating mechanisms ensuring genome stability have so far mostly focused on DNA-protein interactions and signal transduction in response to DNA damage. Emerging evidence in the last decade suggests that post-transcriptional control of gene expression by RNA-binding proteins also participates in maintaining genome integrity. However, how specific control of RNA fate mechanistically affects genome stability is still poorly understood. Here, we report that the pseudokinase HPO-11 ensures genome integrity in C. elegans. Loss of hpo-11 leads to accumulation of R-loops, increased DSBs and germline apoptosis, as well as an elevated mutation rate in the somatic cells. In addition, inhibition of nonsense mediated decay (NMD) reduces DSBs and germline apoptosis in the absence of hpo-11. We find that HPO-11 physically interacts with SMG-2, the core factor of NMD, and prevents degradation of specific transcripts by NMD, thus contributing to maintenance of genome stability. Furthermore, knock-down of hpo-11 human homologs NRBP1/2 also results in increased DNA DSBs, and NRBP1/2 physically interact with the human SMG-2 orthologue UPF1. In summary, our work identifies an evolutionarily conserved role of HPO-11 to protect genome stability via suppressing abnormal mRNA decay by NMD.
Early detection of late blight in potato by whole-plant redox imaging
Authors: Hipsch Matanel , Michael Yaron , Lampl Nardy , Sapir Omer , Cohen Yigal , David Helman , Rosenwasser Shilo 
Published: September 2022

AbstractLate blight caused by the oomycete Phytophthora infestans is a most devastating disease of potatoes (Solanum tuberosum). Its early detection is crucial for suppressing disease spread. Necrotic lesions are normally seen in leaves at 4 dpi (days post inoculation) when colonized cells are dead, but early detection of the initial biotrophic growth stage, when the pathogen feeds on living cells, is challenging. Here, the biotrophic growth phase of P. infestans was detected by whole-plant redox imaging of potato plants expressing chloroplast-targeted reduction-oxidation sensitive green fluorescent protein (chl-roGFP2). Clear spots on potato leaves with a lower chl-roGFP2 oxidation state were detected as early as 2 dpi, before any visual symptoms were recorded. These spots were particularly evident during light-to-dark transitions and reflected mislocalization of chl-roGFP2 outside the chloroplasts, demonstrating perturbation of the chloroplast import system by the pathogen. Image analysis based on machine learning enabled systematic identification and quantification of spots and unbiased classification of infected and uninfected leaves in inoculated plants. Comparing redox to chlorophyll fluorescence imaging showed that infected leaf areas which exhibit mislocalized chl-roGFP2 also showed reduced non-photochemical quenching (NPQ) and enhanced quantum PSII yield (ΦPSII) compared to the surrounding leaf areas. The data suggest that mislocalization of chloroplast-targeted proteins is an efficient marker of late blight infection and demonstrate how it can be utilized for nondestructive monitoring of the disease biotrophic stage using whole-plant redox imaging.
PKCβ facilitates leukemogenesis in chronic lymphocytic leukaemia by promoting constitutive BCR-mediated signaling
Authors: Hay Jodie , Tarafdar Anuradha , Holroyd Ailsa , Moka Hothri A. , Dunn Karen M. , Alshayeb Alzahra , Lloyd Bryony H. , Cassels Jennifer , Malik Natasha , Khan Ashfia F. , Sou IengFong , Lees Jamie , Almuhanna Hassan N. B. , Kalakonda Nagesh , Slupsky Joseph R. , Michie Alison M. 
Published: September 2022

AbstractB cell antigen receptor (BCR) signaling competence is critical for pathogenesis of chronic lymphocytic leukemia (CLL). Defining key proteins that facilitate these networks aid in the identification of targets for therapeutic exploitation. We previously demonstrated that reduced PKCα function in mouse hematopoietic stem/progenitor cells (HPSCs) resulted in PKCβII upregulation and generation of a poor-prognostic CLL-like disease. Here, prkcb knockdown in HSPCs leads to reduced survival of PKCα-KR-expressing CLL-like cells, concurrent with reduced expression of the leukemic markers CD5 and CD23. SP1 promotes elevated expression of prkcb in PKCα-KR expressing cells enabling leukemogenesis. Global gene analysis revealed an upregulation of genes associated with B cell activation in PKCα-KR expressing cells, coincident with upregulation of PKCβII: supported by activation of key signaling hubs proximal to the BCR and elevated proliferation. Ibrutinib (BTK inhibitor) or enzastaurin (PKCβII inhibitor) treatment of PKCα-KR expressing cells and primary CLL cells showed similar patterns of Akt/mTOR pathway inhibition, supporting the role for PKCβII in maintaining proliferative signals in our CLL mouse model. Ibrutinib or enzastaurin treatment also reduced PKCα-KR-CLL cell migration towards CXCL12. Overall, we demonstrate that PKCβ expression facilitates leukemogenesis and identify that BCR-mediated signaling is a key driver of CLL development in the PKCα-KR model.Statement of SignificancePKCβ facilitates leukemogenesis of CLL, driven through an SP1-regulated transcriptional program and promotes BCR signaling. Thus far, PKCβ is the only kinase within the BCR signaling pathway, a key pathway in driving CLL pathogenesis, implicated in the generation of neoplastic B lineage cells.
Distinct patterns of PV and SST GABAergic neuronal activity in the basal forebrain during olfactory-guided behavior in mice
Authors: Moss Elizabeth H. , Tantry Evelyne K. , Le Elaine , Chin Pey-Shyuan , Ambrosi Priscilla , Brandel-Ankrapp Katie L. , Arenkiel Benjamin R. 
Published: September 2022

ABSTRACTSensory perception relies on the flexible detection and interpretation of stimuli across variable contexts, conditions, and behavioral states. The basal forebrain is a hub for behavioral state regulation, supplying dense cholinergic and GABAergic projections to various brain regions involved in sensory processing. Of GABAergic neurons in the basal forebrain, parvalbumin (PV) and somatostatin (SST) subtypes serve opposing roles towards regulating behavioral states. To elucidate the role of basal forebrain circuits in sensory-guided behavior, we investigated GABAergic signaling dynamics during odor-guided decision-making. We used fiber photometry to record cell type-specific basal forebrain activity during an odor discrimination task and correlated temporal patterns of PV and SST neuronal activity with olfactory task performance. We found that while both PV-expressing and SST-expressing GABAergic neurons were excited during trial initiation, PV neurons were selectively suppressed by reward whereas SST neurons were excited. Notably, chemogenetic inhibition of BF SST neurons modestly altered decision bias to favor reward-seeking while optogenetic inhibition of BF PV neurons during odor presentations improved discrimination accuracy. Together, these results suggest that the bidirectional activity of GABAergic basal forebrain neuron subtypes distinctly influence perception and decision-making during olfactory guided behavior.SIGNIFICANCE STATEMENTThis study reveals distinct roles for basal forebrain GABAergic neurons in odor perception and odor-guided decision-making. Fiber photometry shows that basal forebrain parvalbumin-expressing neurons are selectively suppressed by rewards, while somatostatin-expressing neurons are activated, establishing the unique recruitment of these GABAergic neurons during behavioral reinforcement. Chemogenetic and optogenetic interventions demonstrate divergent roles for these neuronal subtypes in reward-seeking behavior and odor perception. This research provides new insights into how GABAergic neurons in the basal forebrain shape sensory perception and decision-making.
Nearest neighbor search on embeddings rapidly identifies distant protein relations
Authors: Schütze Konstantin , Heinzinger Michael , Steinegger Martin , Rost Burkhard 
Published: September 2022

AbstractSince 1992, all state-of-the-art (SOTA) methods for fast and sensitive identification of evolutionary, structural, and functional relations between proteins (also referred to as “homology detection”) use sequences and sequence-profiles (PSSMs). Protein Language Models (pLMs) generalize sequences, possibly capturing the same constraints as PSSMs, e.g., through embeddings. Here, we explored how to use such embeddings for nearest neighbor searches to identify relations between protein pairs with diverged sequences (remote homology detection for levels of <20% pairwise sequence identity, PIDE). While this approach excelled for proteins with single domains, we demonstrated the current challenges applying this to multi-domain proteins and presented some ideas how to overcome existing limitations, in principle. We observed that sufficiently challenging data set separations were crucial to provide deeply relevant insights into the behavior of nearest neighbor search when applied to the protein embedding space, and made all our methods readily available for others.
Linking mesozooplankton and SAR11 bacteria in Oxygen Deficient Zones and the open ocean
Authors: Fuchsman Clara A. , Hays Matthew D. , Huanca-Valenzuela Paulina , Gregory Benjamin P. , Plough Louis V. , Duffy Megan E. , Keil Richard G. , Peng Xuefeng 
Published: September 2022

AbstractThe gravitational biological pump is not large enough to account for microbial heterotrophic activity in the mesopelagic ocean. Migrating zooplankton may be a key source of organic matter transport to depth. Here we show signatures of zooplankton in the suspended organic matter at the zooplankton vertical migration depth in the Eastern Tropical North Pacific Oxygen Deficient Zone (ETNP ODZ). We examine the mesozooplankton community in metagenomic depth profiles using the mitochondrial cytochrome c oxidase (COI) gene as a marker in the ETNP and Eastern Tropical South Pacific (ETSP) ODZs and at the oxic Hawaii Ocean Timeseries (HOT). Additionally, eukaryotic transcripts (polyA-selected) were examined for zooplankton in the ETNP. While zooplankton eDNA increased in the ODZ, zooplankton eRNA decreased in the ODZ, similar to previous net-based data, implying that eDNA is better preserved under anoxia. At all stations, Cnidaria, often missed in net-based data, contributed greatly to the zooplankton eDNA/eRNA. SAR11 abundance, determined from the single-copy core gene (rpoB), significantly correlated with zooplankton eDNA, with R2values >0.8 at all stations. Strong correlations between SAR11 and zooplankton have not been previously reported, but are logical as SAR11 bacteria consume and zooplankton excrete simple dissolved organic compounds. SAR11 bacteria possessed genes to utilize urea and taurine in the ODZ, both compounds known to be excreted by zooplankton. In ODZs, SAR11 bacteria preferentially used the taurine degradation pathway leading to C and N assimilation, not the pathway for organic S assimilation, probably due to additional sources of organic S in ODZs.
RTEL-1 and DNA polymerase theta promote subtelomeric DNA synthesis and telomere fusion in C. elegans
Authors: Lister-Shimauchi Evan H. , Brady Morgan , Frenk Stephen , Harris Braxton , Ortiz Ana-Maria Leon , Memili Aylin , Nguyen Minh , Boulton Simon , Ahmed Shawn 
Published: September 2022

AbstractInterstitial telomere sequences (ITS) are degenerate telomere tracts scattered along chromosome arms whose functions are not well understood. We found that critically shortened telomeres of C. elegans telomerase mutants initiate DNA synthesis within ITS tracts that were close to or far from a telomere. Some ITS tracts were targeted recurrently. RTEL-1 dismantles T-loops and recombination intermediates, and DNA polymerase theta (POLQ-1) promotes end-joining using short segments of microhomology. In telomerase mutants, RTEL-1 and POLQ-1 promoted telomere fusion and DNA synthesis at subtelomeric ITS tracts. RTEL-1 is known to suppress homologous recombination, and we found that RTEL-1 similarly suppressed POLQ-1-mediated double-strand break repair. Mutation signatures characteristic of repair by POLQ-1 occurred during initiation of subtelomeric DNA synthesis and at subsequent template shifting events. We propose that RTEL-1 and POLQ-1 play distinct essential roles in subtelomeric DNA synthesis, a process that may contribute significantly to telomere fusion and tumor genome evolution.
Simple, low-cost production of DNA MS2 virus-like particles as molecular diagnostic controls
Authors: Crone Michael A. , Freemont Paul S. 
Published: September 2022

AbstractSuitable controls are integral for the validation and continued quality assurance of diagnostic workflows. Plasmids, DNA or in vitro transcribed RNA are often used to validate novel diagnostic workflows, however, they are poorly representative of clinical samples. RNA phage virus-like particles packaged with exogenous RNA have been used in clinical diagnostics as workflow controls, serving as surrogates for infectious viral particles. Comparable controls for DNA viruses are more challenging to produce, with analogous DNA phages being infectious and packaging of DNA within RNA phages requiring complex purification procedures and expensive chemical linkers. We present a simple and inexpensive method to produce MS2 virus-like particles, packaged with DNA, that makes use of affinity chromatography for purification and enzymatic production of exogenous DNA suitable for packaging. The produced virus-like particles were packaged with Hepatitis B Virus DNA and were then quantified using droplet digital PCR and calibrated against the WHO international standard using a commercial assay in an accredited clinical laboratory.
Effects of stimulus rate and periodicity on auditory cortical entrainment to continuous sounds
Authors: Momtaz Sara , Bidelman Gavin M. 
Published: September 2022

AbstractThe neural mechanisms underlying the exogenous coding and neural entrainment to rapid auditory stimuli have seen a recent surge of interest. However, few studies have characterized how parametric changes in stimulus presentation alter entrained responses. Applying inter-trial phase-locking (ITPL) and phase-locking value (PLV) analyses applied to high-density human electroencephalogram (EEG) data, we investigated the degree to which the brain entrains to speech vs. non-speech (i.e., click) sounds within and across tokens. Passive cortico-acoustic tracking was investigated in N=24 normal young adults utilizing EEG time-frequency and source analyses that isolated neural activity stemming from both auditory temporal cortices. We parametrically manipulated the rate and periodicity of repetitive, continuous speech and click stimuli to investigate how speed and jitter in ongoing sounds stream affect oscillatory entrainment. Both stimulus domains showed rightward hemisphere asymmetry in phase-locking strength with stronger and earlier responses to speech vs. clicks. Neuronal synchronization to speech was enhanced at 4.5 Hz (the putative universal rate of speech) and showed a differential pattern to that of clicks, particularly at higher rates. Phase-locking to speech decreased with increasing jitter but entrainment to speech remained superior to clicks. Surprisingly, click were invariant to periodicity manipulations. Our findings provide evidence that the brain’s neural entrainment to complex sounds is enhanced and more sensitized when processing speech relative to non-speech sounds. That this specialization is apparent even under passive listening suggests a priority of the auditory system for synchronizing to behaviorally-relevant signals.
LARP1 regulates metabolism and mTORC1 activity in cancer
Authors: Chettle James , Dedeic Zinaida , Fischer Roman , Vendrell Iolanda , Campo Leticia , Easton Alistair , Browne Molly , Morris Josephine , Schwenzer Hagen , Lascaux Pauline , Gijsbers Rik , Pires Elisabete , Royston Daniel J. , Ferguson David J. P. , Coosemans An , Kessler Benedikt , McCullagh James , Ahmed Ahmed A. , Ramadan Kristijan , Bushell Martin , Harris Adrian L. , Goding Colin R. , Blagden Sarah P. 
Published: September 2022

AbstractThe protein mammalian target of rapamycin (mTOR) is a master regulator of cell homeostasis. Although mTOR is aberrantly overactivated in 70% ovarian cancers, mTOR cascade inhibitors (such as those blocking the kinase activity of mTOR itself or upstream kinases PI3K/AKT) have demonstrated disappointing activity in ovarian cancer clinical trials. These findings indicate that, despite its pivotal role in normal cells, hyperactivated mTOR does not act as a master regulator of metabolism in this cancer context. Surprisingly, we have identified that the RNA binding protein LARP1, a known phospho-target of mTORC1 and activator of ribosomal biogenesis, is responsible for metabolic reprogramming in mTOR-dysregulated cancers. LARP1 post-transcriptionally regulates the expression of several hundred rate-limiting enzymes involved in multiple aspects of metabolism, including glycolysis and oxidative phosphorylation. Through this mechanism LARP1 sustains ATP production and mTORC1 localisation on the lysosome, thereby activating cell proliferation despite the scarcity of extracellular nutrients. Our findings show that, by sustaining global cellular metabolism in response to growth factor signalling, LARP1 has a central post-transcriptional role in controlling mTORC1 localisation and driving cancer progression, a key cancer hallmark.