bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hindlimb Muscle Representations in Mouse Motor Cortex Defined by Viral Tracing
Authors: Maurer Lauren , Brown Maia , Saggi Tamandeep , Kolarcik Christi L. 
Published: May 2022

AbstractDescending pathways from the cortex to the spinal cord are involved in the control of natural movement. Although mice are widely used in the study of the neurobiology of movement and as models of neurodegenerative disease, an understanding of motor cortical organization is lacking, particularly for hindlimb muscles. In this study, we used the retrograde transneuronal transport of rabies virus to compare the organization of descending cortical projections to fast- and slow-twitch hindlimb muscles surrounding the ankle joint in mice. Although the initial stage of virus transport from the soleus muscle (predominantly slow-twitch) appeared to be more rapid than that associated with the tibialis anterior muscle (predominantly fast-twitch), the rate of further transport of the virus to cortical projection neurons in layer V was equivalent for the two injected muscles. After appropriate survival times, dense concentrations of layer V projection neurons were identified in three cortical areas: the primary motor cortex (M1), secondary motor cortex (M2), and primary somatosensory cortex (S1). The origin of the cortical projections to each of the two injected muscles overlapped almost entirely within these cortical areas. This organization suggests that cortical projection neurons maintain a high degree of specificity, even when they are involved in controlling muscles with different functional roles (fast-versus slow-twitch, extensor versus flexor). Our results represent an important addition to the understanding of the mouse motor system and lay the foundation for future studies investigating the mechanisms underlying motor system dysfunction and degeneration in diseases such as amyotrophic lateral sclerosis and spinal muscular atrophy.
Coordination of Pickpocket ion channel delivery and dendrite growth in Drosophila sensory neurons
Authors: Mitchell Josephine W. , Midillioglu Ipek , Schauer Ethan , Wang Bei , Han Chun , Wildonger Jill 
Published: May 2022

AbstractSensory neurons enable an organism to perceive external stimuli, which is essential for survival. The sensory capacity of a neuron depends on the elaboration of its dendritic arbor and the delivery of sensory ion channels to the dendritic membrane. However, it is not well understood how ion channels are trafficked to sensory dendrites and whether their delivery is coordinated with dendrite growth. We investigated the trafficking of the DEG/ENaC/ASIC ion channel Pickpocket (Ppk) in peripheral sensory neurons in fruit fly larvae. We used CRISPR-Cas9 genome engineering to tag endogenous Ppk1 and visualize it live, including monitoring Ppk1 membrane localization via a novel secreted split-GFP approach. Strikingly, Ppk1 is present throughout the membrane of actively growing dendrites, and Ppk1 density scales in proportion to the dendritic membrane, even when dynein-mediated transport to dendrites is disrupted. Our data suggest that Ppk1 is integral to the membrane of growing dendrites and implicate the recycling endosome GTPase Rab11 in the forward trafficking of Ppk1 to dendrites. Together, our results suggest that Ppk channel transport is coordinated with dendrite morphogenesis, thus ensuring proper ion channel levels and distribution in sensory dendrites.Author SummaryPeripheral sensory neurons are essential for an organism to interact with its environment. Neurons are composed of signal-receiving dendrites and a signal-sending axon. Ion channels distributed throughout sensory dendrites transduce external stimuli into chemical signals, however the mechanisms that localize ion channels to sensory dendrites are not well understood. Both the composition of ion channels in the dendrites and the structure of a sensory neuron’s dendritic arbor are important for how it functions to sense external stimuli. Using live imaging and genomic engineering, we have discovered that the localization of a sensory ion channel, Pickpocket, in fruit fly sensory neurons is coordinated with growth of the dendritic arbor and that Pickpocket levels scale in proportion to dendrite length, even when transport to dendrites is disrupted. We also developed a novel genetically encoded approach to visualize the membrane expression of proteins in a living organism utilizing the split-GFP system. We found that both the secretory and endosomal networks mediate the forward trafficking of Pickpocket during neuronal morphogenesis, thus coordinating membrane growth with ion channel delivery. Our findings reveal that actively growing sensory dendrites are equipped with the ion channels needed for sensing external stimuli.
Gpr88deletion impacts motivational control independently of striatal dopamine function
Authors: Spark Daisy L. , Vermeulen Michela H. , Rueda Patricia , de la Fuente Gonzalez Rocío , Sepehrizadeh Tara , De Veer Michael , la Cour Clotilde Mannoury , Fornito Alex , Langiu Monica , Stewart Gregory D. , Nithianantharajah Jess , Langmead Christopher J. 
Published: May 2022

AbstractBackgroundDisrupted motivational control is a common—but poorly treated—feature of psychiatric disorders. Aberrant mesolimbic dopamine signalling is implicated in motivational symptoms, however direct manipulations to these pathways have yielded suboptimal therapeutic effects. GPR88 is an orphan G protein-coupled receptor highly expressed in the striatum on medium spiny neurons, and therefore well-placed to modulate striatal signalling. While the phenotype ofGpr88knockout mice supports a disruption of motivational pathways, it is unclear whether GPR88 is involved in reward valuation and/or effort-based decision making in a sex-dependent manner, and if this involves altered dopamine function.MethodsIn male and femaleGpr88knockout mice, we used touchscreen-based progressive ratio, with and without reward devaluation, and effort-related choice tasks to assess motivation and cost/benefit decision making, respectively. To explore whether these motivational behaviours were related to altered striatal dopamine, we quantified expression of dopamine-related genes and/or proteins, and used [18F]DOPA PET and GTPγ[35S] binding to assess pre- and postsynaptic dopamine function, respectively.ResultsWe show that male and femaleGpr88knockout mice display greater motivational drive than wild-type mice, which was maintained following reward devaluation. Further, we show that cost/benefit decision making is impaired in male, but not female,Gpr88knockout mice. Surprisingly, we found thatGpr88deletion had no effect on striatal dopamine by any of the measures assessed.ConclusionOur results highlight that GPR88 regulates motivational control of behaviour through a dopaminergic-independent mechanism, providing further support for GPR88 as target for mood symptoms in psychiatric disorders.
Whole-transcriptomic profiling of human cerebral cortex tissues reveals microglia-associated molecular subtypes
Authors: Zhuang Jiali 
Published: May 2022

AbstractMicroglia is one of the major immune cell types in the human brain and plays pivotal roles in regulating inflammatory and immune response in healthy as well as disease states. By analyzing whole transcriptomic data derived from a large cohort of postmortem cortex tissues, we identified two distinct microglial subtypes within the population. The main difference between the two subtypes lies in the differential expression levels of the C1q complex components, Fc γ receptor (CD16) components and CD14. We validated our discovery in independent cohorts of brain autopsy tissues as well as in RNA-seq data generated from isolated microglia. Future investigations into the causes and physiological implications of these subtypes may shed more light on the homeostasis and regulation of the immune related processes in the brain.
Strength of selection potentiates distinct adaptive responses in an evolution experiment with outcrossing yeast
Authors: Phillips Mark A. , Briar Rupinderjit K. , Scaffo Marcus , Zhou Shenghao , Sandoval-Powers Megan , Burke Molly K. 
Published: May 2022

AbstractExperimental evolution studies with sexually-reproducing populations consistently find that adaptation is highly polygenic and fueled by standing genetic variation. However, studies vary substantially with respect to other evolutionary dynamics. Resolving these discrepancies is a crucial next step as we move toward extrapolating findings from laboratory systems to natural populations. Differences in experimental parameters between studies can perhaps answer these questions, and here we assess how one such parameter - selection intensity - influences outcomes. We subject populations of outcrossingSaccharomyces cerevisiaeto zero, moderate, and high ethanol stress for ∼200 generations and ask: 1) does stronger selection lead to greater changes in allele frequencies at adaptive sites; and 2) do targets of selection vary with intensity? With respects to sites with large effects, we find some evidence for positive correlations between selection intensity and allele frequency change. While we observe shared genomic responses across treatments, we also identify treatment-specific responses. Combined with evidence of phenotypic trade-offs between treatments, our findings support the hypothesis that selection intensity influences evolutionary outcomes due to pleiotropic and epistatic interactions. We conclude that it should be a major consideration when attempting to generalize inferences across studies; in other words, we argue that different intensities of selection effectively create distinct environments and genotype-by-environment interactions. Lastly, our results demonstrate the importance of clearly-defined controls in experimental evolution. Despite working with a presumably lab-adapted model system, without this element we would not have been able to distinguish genomic responses to ethanol stress from those associated with laboratory conditions.
Creating a thermostable beta-glucuronidase switch for homogeneous immunoassay by disruption of conserved salt bridges at diagonal interfaces
Authors: Zhu Bo , Qian Cheng , Tang Haoxuan , Kitaguchi Tetsuya , Ueda Hiroshi 
Published: May 2022

ABSTRACTThe Escherichia coli beta-glucuronidase (GUS) has been used as a reporter enzyme in molecular biology and has been engineered to enzyme switches for the development of homogeneous biosensors. Here, we developed a thermostable GUS enzyme switch from a thermostable GUS mutant TR3337 by disrupting a conserved salt bridge (H514-E523) between the diagonal subunits of its homotetramer. A combinatorial library (240 variants) was screened by a novel high-throughput strategy, and a mutant DLW (H514D/M516L/Y517W) was found to be a functional enzyme switch in a caffeine-recognizing immunosensor. The molecular dynamics simulations were performed to predict the topology change around position 514, and the sidechain flip of D514 (repulsion with E523) was observed in the DLW mutant. Up to 1.8-fold of the signal-to-background ratio was confirmed when measured at 45 °C, which makes the DLW mutant a versatile tool for developing the thermostable immunosensors for in vitro and in cellulo applications.Table of contents graphic
The synergistic effects of the VH families and CH regions of multimeric IgM on its interaction with FcμR, and antigen
Authors: Ling Wei-Li , Gan Samuel Ken-En 
Published: May 2022

AbstractAs the primary response antibody with increasing interest as a therapeutic antibody format, IgM is also the largest antibody structure among the five major human isotypes. Spontaneously forming pentamer and hexamers, IgM has avidity effects that could compensate for weaker interactions, although steric hindrances can occur for certain epitopes. With recent evidence of the heavy chain constant region affecting antigen binding and the VH families of the V-regions affecting FcR engagement found on other isotypes, we investigated CDR-grafted Trastuzumab and Pertuzumab VH1-7 IgMs for biolayer interferometry. From our panel of the 14 IgM variants, the V-regions holistically affected FcμR binding, and the IgM C-region modulated Her2 engagements with contributions from the V-regions and influences from protein L binding at the Vκ. These findings revealed the oligomerization effect of IgMs to play a significant role in both FcμR and antigen binding that is distinct from the other isotypes that can guide the development and protein en-gineering of IgM therapeutics.
DEGRONOPEDIA - a web server for proteome-wide inspection of degrons
Authors: Szulc Natalia A. , Stefaniak Filip , Piechota Małgorzata , Cappannini Andrea , Bujnicki Janusz M. , Pokrzywa Wojciech 
Published: May 2022

ABSTRACTThe ubiquitin-proteasome system is a proteolytic pathway that removes damaged and unwanted proteins. Their selective turnover is initiated by ubiquitin (Ub) attachment, mainly by Ub ligases that recognize substrates through their short linear motifs termed degrons. A degradation-targeting degron comprises a nearby Ub-modified residue and an intrinsically disordered region (IDR) involved in interaction with the proteasome. Degron-signaling has been studied over the last decades, yet there are no resources for systematic screening of degron sites to facilitate studies on their biological significance, such as targeted protein degradation approaches. To bridge this gap, we developed DEGRONOPEDIA, a web server that allows exploration of degron motifs in the proteomes of seven model organisms and maps these data to Lys, Cys, Thr, and Ser residues that can undergo ubiquitination and to IDRs proximal to them, both in sequence and structure. The server also reports the post-translational modifications and pathogenic mutations within the degron and its flanking regions, as these can modulate the degron’s accessibility. Degrons often occur at the amino or carboxyl end of a protein substrate, acting as initiators of the N-/C-degron pathway, respectively. Therefore, since they may appear following the protease cleavage, DEGRONOPEDIA simulate sequence nicking based on experimental data and theoretical predictions and screen for emerging degron motifs. Moreover, we implemented machine learning to predict the stability of the N-/C-termini, facilitating the identification of substrates of the N-/C-degron pathways. We are confident that our tool will stimulate research on degron-signaling providing output information in a ready-to-validate context. DEGRONOPEDIA can be freely accessed atdegronopedia.com.
A social media-based framework for quantifying temporal changes to wildlife viewing intensity: Case study of sea turtles before and during COVID-19
Authors: Papafitsoros Kostas , Adam Lukáš , Schofield Gail 
Published: May 2022

AbstractDocumenting how human pressure on wildlife changes over time is important to minimise potential adverse effects through implementing appropriate management and policy actions; however, obtaining objective measures of these changes and their potential impacts is often logistically challenging, particularly in the natural environment. Here, we developed a modular stochastic model that infers the ratio of actual viewing pressure on wildlife in consecutive time periods (years) using social media, as this medium is widespread and easily accessible. Pressure was calculated from the number of times individual animals appeared in social media in pre-defined time windows, accounting for time-dependent variables that influence them (e.g. number of people with access to social media). Formulas for the confidence intervals of viewing pressure ratios were rigorously developed and validated, and corresponding uncertainty was quantified. We applied the developed framework to calculate changes to wildlife viewing pressure on loggerhead sea turtles (Caretta caretta) at Zakynthos island (Greece) before and during the COVID-19 pandemic (2019-2021) based on 2646 social media entries. Our model ensured temporal comparability across years of social media data grouped in time window sizes, by correcting for the interannual increase of social media use. Optimal sizes for these windows were delineated, reducing uncertainty while maintaining high time-scale resolution. The optimal time window was around 7-days during the peak tourist season when more data were available in all three years, and >15 days during the low season. In contrast, raw social media data exhibited clear bias when quantifying changes to viewing pressure, with unknown uncertainty. The framework developed here allows widely-available social media data to be used objectively when quantifying temporal changes to wildlife viewing pressure. Its modularity allowed viewing pressure to be quantified for all data combined, or subsets of data (different groups, situations or locations), and could be applied to any site supporting wildlife exposed to tourism.
Competition-cooperation in the chemoautotrophic ecosystem of Movile Cave – first metagenomic approach on sediments
Authors: Chiciudean Iulia , Russo Giancarlo , Bogdan Diana Felicia , Levei Erika Andrea , Faur Luchiana , Hillebrand-Voiculescu Alexandra , Moldovan Oana Teodora , Banciu Horia Leonard 
Published: May 2022

AbstractBackgroundMovile Cave (Dobrogea, SE Romania) hosts a subterranean chemoautotrophically-based ecosystem supported by a sulfidic thermal aquifer analogous to the deep-sea hydrothermal ecosystems. Our current understanding of Movile Cave microbiology has been confined to the thermal water proximity (no more than 2 m distant), with most studies focusing on the water-floating mat, which likely acts as the primary production powerhouse in this sulfidic ecosystem. To gain more insightful information on the functioning of the sulfidic Movile Cave ecosystem, we employed a metagenomics-resolved approach to reveal the microbiome diversity, metabolic potential, and interactions and infer its roles within the food webs in the sediments beyond the sulfidic thermal waters.ResultsA customized bioinformatics pipeline led to the recovery of 106 high-quality metagenome-assembled genomes from 7 cave sediment metagenomes. Assemblies’ taxonomy spanned 19 bacterial and three archaeal phyla withAcidobacteriota, Chloroflexota, Proteobacteria, Planctomycetota, Ca. Patescibacteria,Thermoproteota, Methylomirabilota, andCa. Zixibacteria as prevalent phyla. Functional gene analyses allowed prediction of CO2fixation, methanotrophy, sulfur and ammonia oxidation as possibly occurring in the explored sediments. Species Metabolic Coupling Analysis of metagenome-scale metabolic models revealed the highest competition-cooperation interactions in the sediments collected at the farthest distance from the sulfidic water. As a result of simulated metabolic interactions, autotrophs and methanotrophs were hypothesized as major donors of exchanged metabolites in the sediment communities. Cross-feeding dependencies were assumed only towards ‘currency’ molecules and inorganic compounds (O2, PO43-, H+, Fe2+, Cu2+) in the sediment nearby sulfidic water, whereas hydrogen sulfide and methanol are predictably traded exclusively among communities dwelling in the distant gallery.ConclusionsThese findings suggest that the primary production potential of the Movile Cave expands way beyond its hydrothermal waters, enhancing our understanding of ecological interactions inside chemolithoautotrophically based subterranean ecosystems and their functioning.
Systematic evaluation of high level visual deficits and lesions in posterior cerebral artery stroke
Authors: Robotham Ro Julia , Rice Grace E , Leff Alex P , Lambon Ralph Matthew A , Starrfelt Randi 
Published: May 2022

AbstractKnowledge about the consequences of stroke on high level vision comes primarily from single case studies of patients selected based on their behavioural profiles with deficits in the recognition of a specific visual category such as faces or words. There are, however, no systematic, detailed, large-scale evaluations of the more typical clinical behavioural and lesion profiles of impairments in high level vision that may follow posterior cerebral artery (PCA) stroke. These goals were met by the current study through the data collected in the Back of the Brain (BoB) project: to date, the largest (N=64) and most detailed examination of patients with cortical PCA strokes selected based on lesion location rather than behavioural symptoms.We present here two complementary analyses of the structural neuroimaging data and key indices of behavioural performance with the visual processing words, objects and faces: (1) a multivariate multiple regression analysis to establish the relationships between lesion volume, lesion laterality or the presence of a bilateral lesion with performance on words, objects and faces; and, (2) a voxel-based correlational method (VBCM) analysis to establish whether there are distinct or separate regions within the PCA territory that underpin the visual processing of these categories.In contrast to the characterization of specific stroke syndromes like pure alexia or prosopagnosia in the literature, most patients in our cohort showed more general deficits in high level vision (n=22) or no deficits at all (n=21). Category-selective deficits were rare (n=6), and were only found for words, which, interestingly could follow left or right hemisphere lesions. The lesion analyses mainly confirmed the pattern reported in more selective cases: word recognition impairments are associated with a left-sided pattern of damage and face recognition deficits with a bilateral albeit right-dominant lesion pattern. Importantly, however, both general and more selective impairment may follow from left or right unilateral as well as bilateral lesions.While the findings provide partial support for the relative laterality of posterior brain regions supporting reading in the left and, to a lesser extent, face processing in the right hemisphere, the results suggest that both hemispheres are involved in the visual processing of faces, words and objects. This has ramifications for researchers studying the healthy brain and for clinicians working with patients with PCA stroke. Clinicians are recommended to carry out formal assessment of face, word and object recognition as most patients are expected to present with a mixed picture of deficits.