bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dlg5 and Cadherins are key to peripheral glia integrity
Authors: Mriga Das , Duo Cheng , Till Matzat , Vanessa J. Auld 
Published: November 2022

ABSTRACTGlial cells in the peripheral nerve wrap axons to insulate them and ensure efficient conduction of neuronal signals. In the myelin sheath, it is proposed that the autotypic tight junctions and adherens junctions form glia-glia complexes that stabilize the glia sheath in myelinating glia. Yet the role of adhesion junctions in non-myelinating glia of vertebrates or invertebrates has not been clearly established. Many components of adhering junctions contain PDZ (PSD-95, Dlg, ZO1) domains or are recruited to these junctions by PDZ binding motifs. To test for the role of PDZ domain proteins in glial sheath formation, we carried out an RNAi screen usingDrosophila melanogasterto knockdown each of the 66 predicted PDZ domain proteins in the peripheral glia. We identified six PDZ genes with potential roles in glial morphology, and further investigated Discs-large 5 (Dlg5), a scaffolding protein with no previously known function in glia. Knockdown of Dlg5 disrupts subperineurial glia (SPG) morphology, including gaps in the membrane that coincide with disruption of septate junction proteins. To further our investigation of Dlg5, we focused on cadherins and found both N-Cadherin and E-Cadherin are expressed throughout peripheral glia. Knockdown of E-Cadherin phenocopied the loss of Dlg5 leading to gaps in the SPG and septate junctions while only simultaneous loss of both N-Cadherins (NCad, and CadN2) had the same effect. The loss of all three Cadherins enhanced these phenotypes as did loss of Dlg5 when paired with cadherin knockdown. This leads to a model where Dlg5 plays a role in conjunction with cadherins in glial membrane stabilization and septate junction formation in the subperineurial glia.
Impaired HIV-specific T-cell responses in HIV andS. mansonicoinfected Ugandans
Authors: Obuku Andrew Ekii , Sharma Ashish , Rukundo Anjellina , Odong Matthew , Auma Betty , Serwanga Jennifer , Nkangi Ronald , Okello Joseph , Nakitto Zahara , Joloba Moses , Pantaleo Giuseppe , Kaleebu Pontiano , Sekaly Rafik 
Published: November 2022

AbstractFishing communities surrounding Lake Victoria in Uganda show an HIV-1 prevalence of 28% and incidence rates of 5%. More than 50% of the fishermen on the shores of Lake Victoria are infected withS. mansoni. Fishermen are more likely to die of AIDS related illness than farmers in the Lake Victoria region.Using polychromatic flow cytometry and mesoscale discovery platform, HIV specific and non-specific responses were measured and compared within individuals when HIV andS. mansonicoinfected and after theS. mansoniwas cleared.Sixty-two unique clusters of cells in the UMAP space were identified after stimulations with GAG PTE POOL-1 and GAG PTE POOL-2 independently. However, the frequency of only three clusters is significantly higher after S.mansoniclearance. In addition,S. mansoniinfection is associated with higher IL-9 and IL-10 and lower IL-15 in HIV andS. mansonicoinfected individuals. IL-9 concentration at enrolment visit predicts CD4 decline.S. mansoniinfection negatively affects HIV specific and non-specific immune responses in HIV andS. mansonicoinfected individuals.
Synchro-PASEF allows precursor-specific fragment ion extraction and interference removal in data-independent acquisition
Authors: Skowronek Patricia , Krohs Florian , Lubeck Markus , Wallmann Georg , Itang Ericka , Koval Polina , Wahle Maria , Thielert Marvin , Meier Florian , Willems Sander , Raether Oliver , Mann Matthias 
Published: November 2022

ABSTRACTData-independent acquisition (DIA) methods have become increasingly popular in mass spectrometry (MS)-based proteomics because they enable continuous acquisition of fragment spectra for all precursors simultaneously. However, these advantages come with the challenge of correctly reconstructing the precursor-fragment relationships in these highly convoluted spectra for reliable identification and quantification. Here we introduce a scan mode for the combination of trapped ion mobility spectrometry (TIMS) with parallel accumulation – serial fragmentation (PASEF) that seamlessly and continuously follows the natural shape of the ion cloud in ion mobility and peptide precursor mass dimensions. Termed synchro-PASEF, it increases the detected fragment ion current several-fold at sub-second cycle times. Consecutive quadrupole selection windows move synchronously through the mass and ion mobility range, defining precursor-quadrupole relationships. In this process, the quadrupole slices through the peptide precursors, which separates fragment ion signals of each precursor into adjacent synchro-PASEF scans. This precisely defines precursor – fragment relationships in ion mobility and mass dimensions and effectively deconvolutes the DIA fragment space. Importantly, the partitioned parts of the fragment ion transitions provide a further dimension of specificity via a lock and key mechanism. This is also advantageous for quantification, where signals from interfering precursors in the DIA selection window do not affect all partitions of the fragment ion, allowing to retain only the specific parts for quantification. Overall, we establish the defining features of synchro-PASEF and explore its potential for proteomic analyses.
History information emerges in the cortex during learning
Authors: Marmor Odeya , Helmchen Fritjof , Gilad Ariel 
Published: November 2022

AbstractWe learn from our experience but the underlying neuronal mechanisms incorporating past information to facilitate learning is relatively unknown. Specifically, which cortical areas encode history-related information and how is this information modulated across learning? To study the relationship between history and learning, we continuously imaged cortex-wide calcium dynamics as mice learn to use their whiskers to discriminate between two different textures. We mainly focused on comparing the same trial type with different history information, i.e., a different preceding trial. We found history information in barrel cortex (BC) during stimulus presentation. Importantly, history information in BC emerged only as the mouse learned the task. Next, we also found learning-dependent history information in rostrolateral (RL) association cortex that emerges before stimulus presentation, preceding activity in BC. History information was also found in other cortical areas and was not related to differences in body movements. Interestingly, a binary classifier could discriminate history information at the single trial level just as well as current information both in BC and RL. These findings suggest that past experience emerges in the cortex around the time of learning, starting from higher-order association area RL and propagating down (i.e., top-down projection) to lower-order BC where it can be integrated with incoming sensory information. This integration between the past and present may facilitate learning.
Predestined neutrophil heterogeneity in homeostasis varies in transcriptional and phenotypic response toCandida
Authors: Scherer Allison K. , Hopke Alex , Xu Shuying , Viens Adam , Alexander Natalie J. , Timmer Kyle D. , Archambault Dakota , Floyd Daniel , Atallah Natalie J. , Rhee Catherine , Cetinbas Murat , Scadden David T. , Irimia Daniel , Sykes David B. , Sadreyev Ruslan I. , Mansour Michael K. 
Published: November 2022

ABSTRACTOnce perceived to be homogenous effector cells, neutrophils have since been shown to exhibit population heterogeneity. Here, we established an experimental model of clonal neutrophil heterogeneity using conditionally immortalized clonal granulocyte monocyte progenitors (GMPs) and their mature neutrophil progeny. Transcriptional and epigenetic profiling showed conserved genome-wide signatures of transcription and chromatin accessibility that were specific to individual GMP clones and their paired neutrophil progeny, suggesting that clone specificity is established as early as the GMP stage. Clone-specific genes in vital regulatory pathways were pre-programmed and exhibited delayed expression in the mature neutrophil stage. The clone-specific gene expression in the mature neutrophils paired to enhancer activation in their parental GMPs. To determine whether transcriptional heterogeneity predicted the response to fungal pathogens, neutrophil clones were functionally profiled. Clones demonstrated heterogeneous responses to fungal pathogensin vitroand revealed neutrophil subsets with evidence for tailored functional responses toCandida spp. as well as specific transcriptional and epigenetic patterns that may explain these differences. Together, this work establishes that heterogenous GMP and neutrophil compartments exist under homeostatic conditions and that these represent predefined clusters that are uniquely adapted to control invasive fungal pathogens.Short SummaryClonal neutrophil progenitors demonstrate heterogeneity in transcription and chromatin accessibility which may inform response to later fungal challenges.
Divergent outcomes of direct conspecific pathogen strain interaction and plant co-infection suggest consequences for disease dynamics
Authors: Bellah Hadjer , Seiler Nicolas F. , Croll Daniel 
Published: November 2022

AbstractPlant diseases are often caused by co-infections of multiple pathogens with the potential to aggravate disease severity. In genetically diverse pathogen species, co-infections can also be caused by multiple strains of the same species. However, the outcome of such mixed infections by different conspecific genotypes is poorly understood. The interaction among pathogen strains with complex lifestyles outside and inside of the host are likely shaped by diverse traits including metabolic capacity and the ability to overcome host immune responses. To disentangle competitive outcomes among pathogen strains, we investigated the fungal wheat pathogenZymoseptoria tritici. The pathogen infects wheat leaves in complex strain assemblies and highly diverse populations persist between growing seasons. We investigated a set of 14 genetically different strains collected from the same field to assess both competitive outcomes under culture conditions and on the host. Growth kinetics of co-cultured strains significantly deviated from single strain expectations indicating competitive exclusion depending on the strain genotype. We found similarly complex outcomes of lesion development on plant leaves following co-infections by the same pairs of strains. While some pairings suppressed overall damage to the host, other combinations exceeded expectations of lesion development based on single strain outcomes. Strain competition outcomes in absence of the host were poor predictors of outcomes on the host suggesting that the interaction with the plant immune system adds significant complexity. Intraspecific co-infection dynamics likely make important contributions to disease severity and need to be integrated for a more complete understanding of host-pathogen dynamics in the environment.ImportancePlants are often attacked by a multitude of pathogens simultaneously. Different pathogen species can either facilitate or constrain the colonization by other pathogen species. Hence, natural infections are often the outcome of complex interactions between pathogens. To what extent the simultaneous colonization of genetically different strains of the same pathogen species matters for disease outcomes remains largely unclear though. We assessed the outcome of interactions between strains of the fungal wheat pathogen Zymoseptoria tritici. In absence of the host, strains cultured in pairs were growing differently compared to strains cultured alone. When infecting wheat leaves either with single or pairs of strains, we found also highly variable outcomes. Importantly, interactions between strains outside of the host were only poorly explaining how strains would interact when on the host. This suggests that pathogen strains engage in complex interactions shaped by their environment. Understanding the nature of such interactions within pathogen species will improve our ability to manage crop plant infections in the wild.
Neofunctionalized carbonic anhydrases in the biosynthesis of neuroactive plant alkaloids
Authors: Nett Ryan S. , Dho Yaereen , Tsai Chun , Wonderlick Daria , Low Yun-Yee , Sattely Elizabeth S. 
Published: November 2022

ABSTRACTPlants synthesize numerous alkaloids that mimic animal neurotransmitters. The diversity of alkaloid structures is achieved through the generation and tailoring of unique carbon scaffolds. However, many neuroactive alkaloids belong to a scaffold class for which no biosynthetic route or enzyme catalyst is known. By studying highly coordinated, tissue-specific gene expression in plants that produce neuroactive Lycopodium alkaloids, we identified a new enzyme class for alkaloid biosynthesis: neofunctionalized α-carbonic anhydrases (CAHs). We show that three CAH-like (CAL) enzymes are involved in a cryptic biosynthetic route to a key bicyclic precursor of the Lycopodium alkaloids, and additionally, we describe a series of oxidative tailoring steps that generate the optimized acetylcholinesterase inhibition activity of huperzine A. Our findings suggest a broader involvement of CAL enzymes in specialized metabolism and provide an example for how successive scaffold tailoring steps can drive potency against a natural protein target of interest.
Cholinergic modulation supports dynamic switching of resting state networks through selective DMN suppression
Authors: Sanda Pavel , Hlinka Jaroslav , van den Berg Monica , Skoch Antonin , Bazhenov Maxim , Keliris Georgios A. , Krishnan Giri P. 
Published: November 2022

AbstractBrain activity during the resting state is widely used to examine brain organization, cognition and alterations in disease states. While it is known that neuromodulation and the state of alertness impact resting-state activity, neural mechanisms behind such modulation of resting-state activity are unknown. In this work, we used a computational model to demonstrate that change in excitability and recurrent connections, due to cholinergic modulation, impacts resting-state activity. The results of such modulation in the model match closely with experimental work on direct cholinergic modulation of Default Mode Network (DMN) in rodents. We further extended our study to the human connectome derived from diffusion-weighted MRI. In human resting-state simulations, an increase in cholinergic input resulted in a brain-wide reduction of functional connectivity. Furthermore, selective cholinergic modulation of DMN closely captured experimentally observed transitions between the baseline resting state and states with suppressed DMN fluctuations associated with attention to external tasks. Our study thus provides insight into potential neural mechanisms for the effects of cholinergic neuromodulation on resting-state activity and its dynamics.
RNA-mediated double-strand break repair in human cells
Authors: Jeon Youngkyu , Ferrari Margherita Maria , Channagiri Tejasvi , Xu Penghao , Balachander Sathya , Park Vivian S. , Marsili Stefania , Pursell Zachary F. , Jonoska Nataša , Storici Francesca 
Published: November 2022

SummaryDouble-strand breaks (DSBs) in DNA are challenging lesions to repair. Human cells employ at least three DSB repair mechanisms, with a preference for non-homologous end joining (NHEJ) over homologous recombination (HR) and microhomology-mediated end joining (MMEJ)1,2. In contrast to HR, NHEJ and MMEJ do not utilize a DNA template molecule to recover damaged and/or lost nucleotides2. NHEJ directly ligates broken DNA ends, while MMEJ exploits the alignment of short microhomologies on the DSB sides and is associated with deletions of the sequence between the microhomologies3,4. It is unknown whether and to what extent a transcript RNA has a direct role in DSB-repair mechanisms in mammalian cells. Here, we show that both coding and non-coding transcript RNA facilitates DSB repair in a sequence-specific manner in human cells. Depending on its sequence complementarity with the broken DNA ends, the transcript RNA could promote the repair of a DSB or gap in its DNA gene via NHEJ or MMEJ, or mediate RNA-templated repair. The transcript RNA influences DSB repair by NHEJ and MMEJ even when the transcription level is low. The results demonstrate an unexpected role of transcript RNA in directing the way DSBs are repaired in human cells and maintaining genome stability.
Cryo-EM structures of mitochondrial respiratory complex I fromDrosophila melanogaster
Authors: Agip Ahmed-Noor A. , Chung Injae , Sanchez-Martinez Alvaro , Whitworth Alexander J. , Hirst Judy 
Published: November 2022

AbstractRespiratory complex I powers ATP synthesis by oxidative phosphorylation, exploiting the energy from NADH oxidation by ubiquinone to drive protons across an energy-transducing membrane.Drosophila melanogasteris a candidate model organism for complex I due to its high evolutionary conservation with the mammalian enzyme, well-developed genetic toolkit, and complex physiology for studies in specific cell types and tissues. Here, we isolate complex I fromDrosophilaand determine its structure, revealing a 43-subunit assembly with high structural homology to its 45-subunit mammalian counterpart, including a hitherto unknown homologue to subunit NDUFA3. The major conformational state of theDrosophilaenzyme is the mammalian-type ‘ready-to-go’ active resting state, with a fully ordered and enclosed ubiquinone-binding site, but a subtly altered global conformation related to changes in subunit ND6. The mammalian-type ‘deactive’ pronounced resting state is not observed: in two minor states the ubiquinone-binding site is unchanged, but a deactive-typeπ-bulge is present in ND6-TMH3. Our detailed structural knowledge ofDrosophilacomplex I provides a foundation for new approaches to disentangle mechanisms of complex I catalysis and regulation in bioenergetics and physiology.
Resting mitochondrial complex I fromDrosophila melanogasteradopts a helix-locked state
Authors: Padavannil Abhilash , Murari Anjaneyulu , Rhooms Shauna-Kay , Owusu-Ansah Edward , Letts James A. 
Published: November 2022

AbstractRespiratory complex I is a proton-pumping oxidoreductase key to bioenergetic metabolism. Biochemical studies have found a divide in the behavior of complex I in metazoans that aligns with the evolutionary split between Protostomia and Deuterostomia. Complex I from Deuterostomia including mammals can adopt an off-pathway “deactive” state, whereas complex I from Protostomia cannot. The presence of off-pathway states complicates the interpretation of structural results and has led to considerable mechanistic debate. Here we report the structure of mitochondrial complex I from the thoracic muscles of the model protostomianDrosophila melanogaster. We show that, althoughD. melanogastercomplex I (Dm-CI) does not deactivate the resting state ofDm-CI adopts multiple conformations. We identify a new helix-locked open state in which an N-terminal α-helix on the NDUFS4 subunit wedges between the peripheral and membrane arms. Comparison of theDm-CI structure and conformational states to those observed in bacteria, yeast and mammals provides insight into the roles of subunits across organisms, explains whyDm-CI does not deactivate and reveals incompatibilities with current mechanistic models of complex I turnover. Additionally, theDm-CI structure and novel regulatory mechanism will allow for the development of more selective pesticides for agriculture and human disease.
Evaluation of the taxonomic accuracy and pathogenicity prediction power of 16 primer sets amplifying single copy marker genes in thePseudomonas syringaespecies complex
Authors: Fautt Chad , Hockett Kevin L. , Couradeau Estelle 
Published: November 2022

ABSTRACTThe Pseudomonas syringae species complex is comprised of several closely related species of bacterial plant pathogens. Here, we use in-silico methods to assess 16 PCR primer sets designed for broad identification of isolates throughout the species complex. We evaluate their in-silico amplification rate in 2,161 publicly available genomes, the correlation between pairwise amplicon sequence distance and whole genome average nucleotide identity (ANI), and we train naïve Bayes classification models to quantify classification resolution. Further, we show the potential for using single amplicon sequence data to predict an important determinant of host specificity and range, type III effector protein repertoires.
FUS regulates RAN translation through modulating the G-quadruplex structure of GGGGCC repeat RNA inC9orf72-linked ALS/FTD
Authors: Fujino Yuzo , Ueyama Morio , Ishiguro Taro , Ozawa Daisaku , Ito Hayato , Sugiki Toshihiko , Murata Asako , Ishiguro Akira , Gendron Tania F. , Mori Kohji , Tokuda Eiichi , Taminato Tomoya , Konno Takuya , Koyama Akihide , Kawabe Yuya , Takeuchi Toshihide , Furukawa Yoshiaki , Fujiwara Toshimichi , Ikeda Manabu , Mizuno Toshiki , Mochizuki Hideki , Mizusawa Hidehiro , Wada Keiji , Ishikawa Kinya , Onodera Osamu , Nakatani Kazuhiko , Petrucelli Leonard , Taguchi Hideki , Nagai Yoshitaka 
Published: November 2022

AbstractAbnormal expansions of GGGGCC repeat sequence in the noncoding region of theC9orf72gene is the most common cause of familial amyotrophic lateral sclerosis and frontotemporal dementia (C9-ALS/FTD). The expanded repeat sequence is translated into dipeptide repeat proteins (DPRs) by noncanonical repeat-associated non-AUG (RAN) translation. Since DPRs play central roles in the pathogenesis of C9-ALS/FTD, we here investigate the regulatory mechanisms of RAN translation, focusing on the effects of RNA-binding proteins (RBPs) targeting GGGGCC repeat RNAs. Using C9-ALS/FTD model flies, we demonstrated that the ALS/FTD-linked RBP FUS suppresses RAN translation and neurodegeneration in an RNA-binding activity-dependent manner. Moreover, we found that FUS directly binds to and modulates the G-quadruplex structure of GGGGCC repeat RNA as an RNA chaperone, resulting in the suppression of RAN translationin vitro. These results reveal a previously unrecognized regulatory mechanism of RAN translation by G-quadruplex-targeting RBPs, providing therapeutic insights for C9-ALS/FTD and other repeat expansion diseases.
Substantial Neutralization Escape by the SARS-CoV-2 Omicron Variant BQ.1.1
Authors: Miller Jessica , Hachmann Nicole P. , Collier Ai-ris Y. , Lasrado Ninaad , Mazurek Camille R. , Patio Robert C. , Powers Olivia , Surve Nehalee , Theiler James , Korber Bette , Barouch Dan H. 
Published: November 2022

ABSTRACTOmicron BA.5 has been the globally dominant SARS-CoV-2 variant and has demonstrated substantial neutralization escape compared with prior variants. Additional Omicron variants have recently emerged, including BA.4.6, BF.7, BA.2.75.2, and BQ.1.1, all of which have the Spike R346T mutation. In particular, BQ.1.1 has rapidly increased in frequency, and BA.5 has recently declined to less than half of viruses in the United States. Our data demonstrate that BA.2.75.2 and BQ.1.1 escape NAbs induced by infection and vaccination more effectively than BA.5. BQ.1.1 NAb titers were lower than BA.5 NAb titers by a factor of 7 in two cohorts of individuals who received the monovalent or bivalent mRNA vaccine boosters. These findings provide the immunologic context for the rapid increase in BQ.1.1 prevalence in regions where BA.5 is dominant and have implications for both vaccine immunity and natural immunity.