bluuebunny/crossref_metadata_2025_split huggingface dataset:
Superior target genes and pathways for RNAi mediated pest control revealed by genome wide analysis in the red flour beetleTribolium castaneum
Authors: Buer Benjamin , Dönitz Jürgen , Milner Martin , Mehlhorn Sonja , Hinners Claudia , Siemanowski-Hrach Janna , Ulrich Julia K. , Großmann Daniela , Cedden Doga , Nauen Ralf , Geibel Sven , Bucher Gregor 
Published: January 2024

AbstractAn increasing human population, the emergence of resistances against pesticides and their potential impact on the environment call for the development of new eco-friendly pest control strategies. RNA interference (RNAi) based pesticides have emerged as new option with the first products entering the market. Essentially, double stranded RNAs targeting essential genes of pests are either expressed in the plants or sprayed on their surface. Upon feeding, pests mount an RNAi response and die. However, it has remained unclear, whether RNAi based insecticides should target the same pathways as classic pesticides or whether the different mode of action would favor other processes. Moreover, there is no consensus on the best genes to be targeted. We performed a genome-wide screen in the red flour beetle to identify 905 RNAi target genes. Based on a validation screen and clustering, we identified the 192 most effective target genes in that species. The transfer to oral application in other beetle pests revealed a list of 34 superior target genes, which are an excellent starting point for application in other pests. GO and KEGG analyses of our genome wide dataset revealed that genes with high efficacy belonged mainly to basic cellular processes such as gene expression and protein homeostasis – processes not targeted by classic insecticides. In summary, our work revealed the best target genes and target processes for RNAi based pest control and we propose a procedure to transfer our short list of superior target genes to other pests.
SPOT-RASTR - a cryo-EM specimen preparation technique that overcomes problems with preferred orientation and the air/water interface
Authors: Esfahani Behrouz G. , Randolph Peter S. , Peng Ruizhi , Grant Timothy , Stroupe M. Elizabeth , Stagg Scott M. 
Published: January 2024

AbstractIn cryogenic electron microscopy (cryo-EM), specimen preparation remains a bottleneck despite recent advancements. Classical plunge freezing methods often result in issues like aggregation and preferred orientations at the air/water interface. Many alternative methods have been proposed, but there remains a lack a universal solution, and multiple techniques are often required for challenging samples. Here, we demonstrate the use of lipid nanotubes with nickel NTA headgroups as a platform for cryo-EM sample preparation. His-tagged specimens of interest are added to the tubules, and they can be frozen by conventional plunge freezing. We show that the nanotubes protect samples from the air/water interface and promote a wider range of orientations. The reconstruction of average subtracted tubular regions (RASTR) method allows for the removal of the nanotubule signal from the cryo-EM images resulting in isolated images of specimens of interest. Testing with β-galactosidase validates the method’s ability to capture particles at lower concentrations, overcome preferred orientations, and achieve near-atomic resolution reconstructions. Since the nanotubules can be identified and targeted automatically at low magnification, the method enables fully automated data collection. Furthermore, the particles on the tubes can be automatically identified and centered using 2D classification enabling particle picking without requiring prior information. Altogether, our approach that we call specimen preparation on a tube RASTR (SPOT-RASTR) holds promise for overcoming air-water interface and preferred orientation challenges and offers the potential for fully automated cryo-EM data collection and structure determination.
Conformational changes of the ABC Transporter BmrA Depend on Membrane Curvature
Authors: Damm Alicia , Paik Su-Jin , Sadhu Raj Kumar , Di-Cicco Aurélie , Manzi John , Castellana Michele , Margeat Emmanuel , Dahan Maxime , Sens Pierre , Lévy Daniel , Bassereau Patricia 
Published: January 2024

AbstractWhile mechanosensitive ion channels’ gating has been well documented, the effect of membrane mechanics, in particular membrane curvature, on the function of transporters remains elusive. Since conical shape transmembrane proteins locally deform membranes, conversely membrane bending could impact their conformations and their function. We tested this hypothesis using BmrA, a bacterial ABC exporter that exhibits large conformational changes upon ATP hydrolysis, switching between open and closed states with opposite V-shapes. After reconstitution in liposomes of different curvatures, we showed that BmrA ATPase activity decreases by 2.9-fold when their diameter decreases from 125 to 29 nm. Moreover, using single-molecule FRET, we observed that the fraction of closed conformations is significantly reduced in highly curved vesicles when adding ATP or non-hydrolysable AMP-PNP. Our results are well explained by a theoretical 2-states model including the effect of membrane mechanics on protein shape transition. Our work reveals that the functional cycle of conical transporters is curvature sensitive, to an extent depending on protein geometry.TeaserHigh membrane curvature strongly impacts the functional cycle of transporters.
Elucidation of chalkophomycin biosynthesis revealsN-hydroxypyrrole-forming enzymes
Authors: Crooke Anne Marie , Chand Anika K. , Cui Zheng , Balskus Emily P. 
Published: January 2024

ABSTRACTReactive functional groups, such asN-nitrosamines, impart unique bioactivities to the natural products in which they are found. Recent work has illuminated enzymaticN-nitrosation reactions in microbial natural product biosynthesis, motivating an interest in discovering additional metabolites constructed using such reactivity. Here, we use a genome mining approach to identify over 400 cryptic biosynthetic gene clusters (BGCs) encoding homologs of theN-nitrosating biosynthetic enzyme SznF, including the BGC for chalkophomycin, a CuII-binding metabolite that contains aC-type diazeniumdiolate andN-hydroxypyrrole. Characterizing chalkophomycin biosynthetic enzymes reveals previously unknown enzymes responsible forN-hydroxypyrrole biosynthesis, including the first prolyl-N-hydroxylase, and a key step in assembly of the diazeniumdiolate-containing amino acid graminine. Discovery of this pathway enriches our understanding of the biosynthetic logic employed in constructing unusual heteroatom-heteroatom bondcontaining functional groups, enabling future efforts in natural product discovery and biocatalysis.
The voltage-gated potassium channelShal(Kv4) contributes to active hearing inDrosophila
Authors: Gregory Eli S. , Xu YiFeng Y. J. , Lee Tai-Ting , Joiner Mei-ling A. , Kamikouchi Azusa , Su Matthew P. , Eberl Daniel F. 
Published: January 2024

AbstractThe full complement of ion channels which influence insect auditory mechanotransduction, and the mechanisms by which their influence is exerted, remain unclear.Shal(Kv4), aShakerfamily member encoding voltage-gated potassium channels inDrosophila melanogaster, has been shown to localize to dendrites in some neuron types, suggesting a potential role forShalinDrosophilahearing, including mechanotransduction. A GFP-protein trap was used to visualize the localization of theShalchannel in Johnston’s organ neurons responsible for hearing in the antenna.Shalprotein was localized to the cell body and the proximal dendrite region of sensory neurons, suggesting its involvement not only in general auditory function, but specifically in mechanotransduction. Electrophysiological recordings conducted to assess neural responses to auditory stimuli in mutantShalflies revealed significant decreases in auditory responses. Laser Doppler Vibrometer recordings indicated abnormal antennal free fluctuation frequencies in mutant lines, indicating an effect on active antennal tuning, and thus active transduction mechanisms. This suggests thatShalparticipates in coordinating energy-dependent antennal movements inDrosophilathat are essential for tuning the antenna to courtship song frequencies.Significance StatementThe study of fruit fly hearing has revealed mechanosensitive ion channels that participate in mechanotransduction, and as in mammalian hearing, energy-dependent mechanisms actively amplify and tune auditory processes. Identifying distinct roles played by different ion channels is essential to better understand this process. Here, we explore the influence of a specific voltage-gated potassium channel,Shal, on fly hearing, and find that it affects specific parts of the mechanotransduction process. Our research uncoversShal’slocalization in sensory dendrite regions of auditory neurons, where it contributes to shaping mechanotransduction and active antennal tuning. UnderstandingShal’s involvement in auditory function and mechanotransduction deepens our knowledge of fly hearing and unveils a key player in the coordination of energy-dependent active antennal movements.
Electrically silent KvS subunits associate with native Kv2 channels in brain and impact diverse properties of channel function
Authors: Ferns Michael , van der List Deborah , Vierra Nicholas C. , Lacey Taylor , Murray Karl , Kirmiz Michael , Stewart Robert G. , Sack Jon T. , Trimmer James S. 
Published: January 2024

AbstractVoltage-gated K+channels of the Kv2 family are highly expressed in brain and play dual roles in regulating neuronal excitability and in organizing endoplasmic reticulum - plasma membrane (ER- PM) junctions. Studies in heterologous cells suggest that the two pore-forming alpha subunits Kv2.1 and Kv2.2 assemble with “electrically silent” KvS subunits to form heterotetrameric channels with distinct biophysical properties. Here, using mass spectrometry-based proteomics, we identified five KvS subunits as components of native Kv2.1 channels immunopurified from mouse brain, the most abundant being Kv5.1. We found that Kv5.1 co-immunoprecipitates with Kv2.1 and to a lesser extent with Kv2.2 from brain lysates, and that Kv5.1 protein levels are decreased by 70% in Kv2.1 knockout mice and 95% in Kv2.1/2.2 double knockout mice. Multiplex immunofluorescent labelling of rodent brain sections revealed that in neocortex Kv5.1 immunolabeling is apparent in a large percentage of Kv2.1 and Kv2.2-positive layer 2/3 neurons, and in a smaller percentage of layer 5 and 6 neurons. At the subcellular level, Kv5.1 is co-clustered with Kv2.1 and Kv2.2 at ER-PM junctions in cortical neurons, although clustering of Kv5.1-containing channels is reduced relative to homomeric Kv2 channels. We also found that in heterologous cells coexpression with Kv5.1 reduces the clustering and alters the pharmacological properties of Kv2.1 channels. Together, these findings demonstrate that the Kv5.1 electrically silent subunit is a component of a substantial fraction of native brain Kv2 channels, and that its incorporation into heteromeric channels can impact diverse aspects of Kv2 channel function.
In silicoassessment of immune cross protection between BCoV and SARS-CoV-2
Authors: Querne Lana Bazan Peters , Bastos Fernanda Zettel , dos Anjos Adur Mikaela , Cavalheiro Vitória , Beirão Breno Castello Branco 
Published: January 2024

AbstractBackgroundHumans have long shared infectious agents with cattle, and the bovine-derived human common cold OC-43 CoV is a not-so-distant example of cross-species viral spill over of coronaviruses. Human exposure to the Bovine Coronavirus (BCoV) is certainly common, as the virus is endemic in most high-density cattle-raising regions. Since BCoVs are phylogenetically close to SARS-CoV-2, it is possible that cross-protection against COVID-19 occurs in people exposed to BCoV.MethodsThis article shows anin silicoinvestigation of human cross-protection to SARS-CoV-2 due to BCoV exposure. We determined HLA recognition and human B lymphocyte reactivity to BCoV epitopes using bioinformatics resources. A retrospective geoepidemiological analysis of COVID-19 was then performed to verify if BCoV/SARS-CoV-2 cross-protection could have occurred in the field. Brazil was used as a model for the epidemiological analysis of the impact of livestock density – as a proxy for human exposure to BCoV – on the prevalence of COVID-19 in people.ResultsAs could be expected from their classification in the sameBetacoronavirusgenus, we show that several human B and T epitopes are shared between BCoV and SARS-CoV-2. This raised the possibility of cross-protection of people from exposure to the bovine coronavirus. Analysis of field data added partial support to the hypothesis of viral cross-immunity from human exposure to BCoV. There was a negative correlation between livestock geographical density and COVID-19. Whole-Brazil data showed areas in the country in which COVID-19 prevalence was disproportionally low (controlled by normalization by transport infrastructure). Areas with high cattle density had lower COVID-19 prevalence in these low-risk areas.ConclusionsThese data are hypothesis-raising indications that cross-protection is possibly being induced by human exposure to the Bovine Coronavirus.
A C-terminal motif containing a PKC phosphorylation site regulates γ-Protocadherin-mediated dendrite arborization in the cerebral cortexin vivo
Authors: Hanes Camille M. , Mah Kar Men , Steffen David M. , Marcucci Charles G. , Fuller Leah C. , Burgess Robert W. , Garrett Andrew M. , Weiner Joshua A. 
Published: January 2024

ABSTRACTThePcdhggene cluster encodes 22 γ-Protocadherin (γ-Pcdh) cell adhesion molecules that critically regulate multiple aspects of neural development, including neuronal survival, dendritic and axonal arborization, and synapse formation and maturation. Each γ-Pcdh isoform has unique protein domains–a homophilically-interacting extracellular domain and a juxtamembrane cytoplasmic domain– as well as a C-terminal cytoplasmic domain shared by all isoforms. The extent to which isoform-specificvs.shared domains regulate distinct γ-Pcdh functions remains incompletely understood. Our previousin vitrostudies identified PKC phosphorylation of a serine residue within a shared C-terminal motif as a mechanism through which γ-Pcdh promotion of dendrite arborizationviaMARCKS is abrogated. Here, we used CRISPR/Cas9 genome editing to generate two new mouse lines expressing only non-phosphorylatable γ-Pcdhs, due either to a serine-to-alanine mutation (PcdhgS/A) or to a 15-amino acid C-terminal deletion resulting from insertion of an early stop codon (PcdhgCTD). Both lines are viable and fertile, and the density and maturation of dendritic spines remains unchanged in bothPcdhgS/AandPcdhgCTDcortex. Dendrite arborization of cortical pyramidal neurons, however, is significantly increased in both lines, as are levels of active MARCKS. Intriguingly, despite having significantly reduced levels of γ-Pcdh proteins, thePcdhgCTDmutation yields the strongest phenotype, with even heterozygous mutants exhibiting increased arborization. The present study confirms that phosphorylation of a shared C-terminal motif is a key γ-Pcdh negative regulation point, and contributes to a converging understanding of γ-Pcdh family function in which distinct roles are played by both individual isoforms and discrete protein domains.
A microglia clonal inflammatory disorder in Alzheimer’s Disease
Authors: Vicario Rocio , Fragkogianni Stamatina , Weber Leslie , Lazarov Tomi , Hu Yang , Hayashi Samantha Y. , Craddock Barbara P. , Socci Nicholas D. , Alberdi Araitz , Baako Ann , Ay Oyku , Ogishi Masato , Lopez-Rodrigo Estibaliz , Kappagantula Rajya , Viale Agnes , Iacobuzio-Donahue Christine A. , Zhou Ting , Ransohoff Richard M , Chesworth Richard ,   Netherlands Brain Bank, Abdel-Wahab Omar , Boisson Bertrand , Elemento Olivier , Casanova Jean-Laurent , Miller W. Todd , Geissmann Frederic 
Published: January 2024

SummarySomatic genetic heterogeneity resulting from post-zygotic DNA mutations is widespread in human tissues and can cause diseases, however few studies have investigated its role in neurodegenerative processes such as Alzheimer’s Disease (AD). Here we report the selective enrichment of microglia clones carrying pathogenic variants, that are not present in neuronal, glia/stromal cells, or blood, from patients with AD in comparison to age-matched controls. Notably, microglia-specific AD-associated variants preferentially target the MAPK pathway, including recurrent CBL ring-domain mutations. These variants activate ERK and drive a microglia transcriptional program characterized by a strong neuro-inflammatory response, bothin vitroand in patients. Although the natural history of AD-associated microglial clones is difficult to establish in human, microglial expression of a MAPK pathway activating variant was previously shown to cause neurodegeneration in mice, suggesting that AD-associated neuroinflammatory microglial clones may contribute to the neurodegenerative process in patients.One-Sentence SummaryA subset of Alzheimer Disease patients carry mutant microglia somatic clones which promote neuro-inflammation.
Metabolomic Profiles and Pathways in Osteoarthritic Human Cartilage: A Comparative Analysis with Healthy Cartilage
Authors: Welhaven Hope D. , Welfley Avery H. , Brahmachary Priyanka , Bergstrom Annika R. , Houske Eden , Glimm Matthew , Bothner Brian , Hahn Alyssa K. , June Ronald K. 
Published: January 2024

ABSTRACTObjectiveOsteoarthritis (OA) is a chronic joint disease with heterogenous metabolic pathology. To gain insight into OA-related metabolism, healthy and end-stage osteoarthritic cartilage were compared metabolically to uncover disease-associated profiles, classify OA-specific metabolic endotypes, and identify targets for intervention for the diverse populations of individuals affected by OA.DesignFemoral head cartilage (n=35) from osteoarthritis patients were collected post-total joint arthroplasty. Healthy cartilage (n=11) was obtained from a tissue bank. Metabolites from all cartilage samples were extracted and analyzed using liquid chromatography-mass spectrometry metabolomic profiling. Additionally, cartilage extracts were pooled and underwent fragmentation analysis for biochemical identification of metabolites.ResultsSpecific metabolites and metabolic pathways, including lipid- and amino acid pathways, were differentially regulated between osteoarthritis-derived and healthy cartilage. The detected alterations of amino acids and lipids highlight key differences in bioenergetic resources, matrix homeostasis, and mitochondrial alterations in osteoarthritis-derived cartilage compared to healthy. Moreover, metabolomic profiles of osteoarthritic cartilage separated into four distinct endotypes highlighting the heterogenous nature of OA metabolism and diverse landscape within the joint between patients.ConclusionsThe results of this study demonstrate that human cartilage has distinct metabolomic profiles between healthy and end-stage osteoarthritis patients. By taking a comprehensive approach to assess metabolic differences between healthy and osteoarthritic cartilage, and within osteoarthritic cartilage alone, several metabolic pathways with distinct regulation patterns were detected. Additional investigation may lead to the identification of metabolites that may serve as valuable indicators of disease status or potential therapeutic targets.
Spyglass: a framework for reproducible and shareable neuroscience research
Authors: Lee Kyu Hyun , Denovellis Eric L. , Ly Ryan , Magland Jeremy , Soules Jeff , Comrie Alison E. , Gramling Daniel P. , Guidera Jennifer A. , Nevers Rhino , Adenekan Philip , Brozdowski Chris , Bray Samuel R. , Monroe Emily , Bak Ji Hyun , Coulter Michael E. , Sun Xulu , Broyles Emrey , Shin Donghoon , Chiang Sharon , Holobetz Cristofer , Tritt Andrew , Rübel Oliver , Nguyen Thinh , Yatsenko Dimitri , Chu Joshua , Kemere Caleb , Garcia Samuel , Buccino Alessio , Frank Loren M. 
Published: January 2024

AbstractScientific progress depends on reliable and reproducible results. Progress can also be accelerated when data are shared and re-analyzed to address new questions. Current approaches to storing and analyzing neural data typically involve bespoke formats and software that make replication, as well as the subsequent reuse of data, difficult if not impossible. To address these challenges, we createdSpyglass, an open-source software framework that enables reproducible analyses and sharing of data and both intermediate and final results within and across labs. Spyglass uses the Neurodata Without Borders (NWB) standard and includes pipelines for several core analyses in neuroscience, including spectral filtering, spike sorting, pose tracking, and neural decoding. It can be easily extended to apply both existing and newly developed pipelines to datasets from multiple sources. We demonstrate these features in the context of a cross-laboratory replication by applying advanced state space decoding algorithms to publicly available data.New users can try out Spyglass on a Jupyter Hub hosted by HHMI and 2i2c:https://spyglass.hhmi.2i2c.cloud/.
Leptin Activated Hypothalamic BNC2 Neurons Acutely Suppress Food Intake
Authors: Tan Han L. , Yin Luping , Tan Yuqi , Ivanov Jessica , Plucinska Kaja , Ilanges Anoj , Herb Brian R. , Wang Putianqi , Kosse Christin , Cohen Paul , Lin Dayu , Friedman Jeffrey M. 
Published: January 2024

AbstractLeptin is an adipose tissue hormone that maintains homeostatic control of adipose tissue mass by regulating the activity of specific neural populations controlling appetite and metabolism1. Leptin regulates food intake by inhibiting orexigenic agouti-related protein (AGRP) neurons and activating anorexigenic pro-opiomelanocortin (POMC) neurons2. However, while AGRP neurons regulate food intake on a rapid time scale, acute activation of POMC neurons has only a minimal effect3–5. This has raised the possibility that there is a heretofore unidentified leptin-regulated neural population that suppresses appetite on a rapid time scale. Here, we report the discovery of a novel population of leptin-target neurons expressing basonuclin 2 (Bnc2) that acutely suppress appetite by directly inhibiting AGRP neurons. Opposite to the effect of AGRP activation, BNC2 neuronal activation elicited a place preference indicative of positive valence in hungry but not fed mice. The activity of BNC2 neurons is finely tuned by leptin, sensory food cues, and nutritional status. Finally, deleting leptin receptors in BNC2 neurons caused marked hyperphagia and obesity, similar to that observed in a leptin receptor knockout in AGRP neurons. These data indicate that BNC2-expressing neurons are a key component of the neural circuit that maintains energy balance, thus filling an important gap in our understanding of the regulation of food intake and leptin action.