bluuebunny/crossref_metadata_2025_split huggingface dataset:
A spatially-resolved transcriptional atlas of the murine dorsal pons at single-cell resolution
Authors: Nardone Stefano , Luca Roberto De , Zito Antonino , Klymko Nataliya , Nicoloutsopoulos Dimitris , Amsalem Oren , Brannigan Cory , Resch Jon M. , Jacobs Christopher L. , Pant Deepti , Veregge Molly , Srinivasan Harini , Grippo Ryan M. , Yang Zongfang , Zeidel Mark L. , Andermann Mark L. , Harris Kenneth D. , Tsai Linus T. , Arrigoni Elda , Verstegen Anne M. J. , Saper Clifford B. , Lowell Bradford B. 
Published: September 2023

ABSTRACTThe “dorsal pons”, or “dorsal pontine tegmentum” (dPnTg), is part of the brainstem. It is a complex, densely packed region whose nuclei are involved in regulating many vital functions. Notable among them are the parabrachial nucleus, the Kölliker Fuse, the Barrington nucleus, the locus coeruleus, and the dorsal, laterodorsal, and ventral tegmental nuclei. In this study, we applied single-nucleus RNA-seq (snRNA-seq) to resolve neuronal subtypes based on their unique transcriptional profiles and then used multiplexed error robust fluorescence in situ hybridization (MERFISH) to map them spatially. We sampled ∼1 million cells across the dPnTg and defined the spatial distribution of over 120 neuronal subtypes. Our analysis identified an unpredicted high transcriptional diversity in this region and pinpointed many neuronal subtypes’ unique marker genes. We also demonstrated that many neuronal subtypes are transcriptionally similar between humans and mice, enhancing this study’s translational value. Finally, we developed a freely accessible, GPU and CPU-powered dashboard (http://harvard.heavy.ai:6273/) that combines interactive visual analytics and hardware-accelerated SQL into a data science framework to allow the scientific community to query and gain insights into the data.
Frequent horizontal chromosome transfer between asexual fungal insect pathogens
Authors: Habig Michael , Grasse Anna V. , Müller Judith , Stukenbrock Eva H. , Leitner Hanna , Cremer Sylvia 
Published: September 2023

AbstractEntire chromosomes are typically only transmitted vertically from one generation to the next. The horizontal transfer of such chromosomes has long been considered improbable, yet gained recent support in several pathogenic fungi where it may affect the fitness or host specificity. To date, it is unknown how these transfers occur, how common they are and whether they can occur between different species. In this study, we show multiple independent instances of horizontal transfers of the same accessory chromosome between two distinct strains of the asexual entomopathogenic fungusMetarhizium robertsiiduring experimental co-infection of its insect host, the Argentine ant. Notably, only the one chromosome – but no other – was transferred from the donor to the recipient strain. The recipient strain, now harboring the accessory chromosome, exhibited a competitive advantage under certain host conditions. By phylogenetic analysis we further demonstrate that the same accessory chromosome was horizontally transferred in a natural environment betweenM. robertsiiand another congeneric insect pathogen,M. guizhouense. Hence horizontal chromosome transfer is not limited to the observed frequent events within species during experimental infections but also occurs naturally across species. The transferred accessory chromosome contains genes that might be involved in its preferential horizontal transfer, encoding putative histones and histone-modifying enzymes, but also putative virulence factors that may support its establishment. Our study reveals that both intra- and interspecies horizontal transfer of entire chromosomes is more frequent than previously assumed, likely representing a not uncommon mechanism for gene exchange.Significance StatementThe enormous success of bacterial pathogens has been attributed to their ability to exchange genetic material between one another. Similarly, in eukaryotes, horizontal transfer of genetic material allowed the spread of virulence factors across species. The horizontal transfer of whole chromosomes could be an important pathway for such exchange of genetic material, but little is known about the origin of transferable chromosomes and how frequently they are exchanged. Here, we show that the transfer of accessory chromosomes - chromosomes that are non-essential but may provide fitness benefits - is common during fungal co-infections and is even possible between distant pathogenic species, highlighting the importance of horizontal gene transfer via chromosome transfer also for the evolution and function of eukaryotic pathogens.
Proteome-scale characterisation of motif-based interactome rewiring by disease mutations
Authors: Kliche Johanna , Simonetti Leandro , Krystkowiak Izabella , Kuss Hanna , Diallo Marcel , Rask Emma , Nilsson Jakob , Davey Norman E. , Ivarsson Ylva 
Published: September 2023

AbstractWhole genome and exome sequencing are reporting on hundreds of thousands of missense mutations. Taking a pan-disease approach, we explored how mutations in the intrinsically disordered regions (IDRs) break or generate protein interactions mediated by short linear motifs. We created a peptide-phage display library tiling ∼57,000 peptides from the IDRs of the human proteome overlapping 12,301 single nucleotide variant associated with diverse phenotypes including cancer, metabolic diseases and neurological diseases. By screening 80 human proteins, we identified 366 mutation-modulated interactions, with half of the mutations diminishing binding, and half enhancing binding or creating novel interaction interfaces. The effects of the mutations were confirmed by affinity measurements. In cellular assays, the effects of motif-disruptive mutations were validated, including loss of a nuclear localisation signal in the cell division control protein CDC45 by a mutation associated with Meier-Gorlin syndrome. The study provides insights into how disease-associated mutations may perturb and rewire the motif-based interactome.
Subcortical volumes, frontal cortical thickness, and pro-inflammatory cytokines in schizophrenia versus methamphetamine-induced psychosis
Authors: Blake Lauren , Williams Kimberley Clare , Uhlmann Anne Alex , Temmingh Henk , Burger Antoinette , Stein Dan Joseph , Naudé Petrus J. W. 
Published: September 2023

AbstractBackground and HypothesisClinical features of schizophrenia and methamphetamine-induced psychosis (MAP) have significant overlap. Schizophrenia is associated with alterations in subcortical volumes and cortical thickness and pro-inflammatory cytokines, that may correlate with clinical features. However, analogous work on MAP is lacking. We hypothesise decreased frontal cortical thickness, amygdala and hippocampal volumes in schizophrenia and MAP compared to controls, with increased basal ganglia in schizophrenia compared to MAP.Study DesignParticipants included n=36 schizophrenia, n=27 MAP and 32 age- and sex-matched healthy controls. Diagnosis and symptom severity were determined with the Structured Clinical Interview for Axis I Disorders, and the Positive and Negative Syndrome Scale, respectively. Structural T1-weighted images were acquired using a 3-Tesla magnetic resonance imaging scanner. Serum peripheral cytokine concentrations were measured using a multiplex bead array.Study ResultsSchizophrenia and MAP participants showed decreased left amygdala volumes and frontal cortical thickness compared to controls. Schizophrenia participants had increased bilateral caudate, putamen, and nucleus accumbens (NAcc) volumes compared to controls, and greater right globus pallidus and NAcc volumes compared to MAP. Decreased left amygdala volumes and frontal cortical thickness were significantly associated with longer illness duration in schizophrenia and methamphetamine use in MAP. No significant differences were found in cytokine levels between groups or associations with neuroimaging measures.ConclusionsThis study highlights overlaps and differences in the psychobiology of schizophrenia and MAP.The novel discovery of increased globus pallidus and NAcc volumes in schizophrenia compared with MAP may show important distinctions in the neurobiology between these two conditions.
Convergent evolution of (βα)8-barrel fold methylene-tetrahydropterin reductases utilizing a common catalytic mechanism
Authors: Gehl Manuel , Demmer Ulrike , Ermler Ulrich , Shima Seigo 
Published: September 2023

ABSTRACTMethylene-tetrahydropterin reductases are folded in (βα)8barrel and catalyze the reduction of a methylene to a methyl group bound to a reduced pterin as C1carrier in various one-carbon (C1) metabolisms. F420-dependent methylene-tetrahydromethanopterin (methylene-H4MPT) reductase (Mer) and the flavin-independent methylene-tetrahydrofolate (methylene-H4F) reductase (Mfr) use a ternary complex mechanism for the direct transfer of a hydride from F420H2and NAD(P)H to the respective methylene group, whereas FAD-dependent methylene-H4F reductase (MTHFR) uses FAD as prosthetic group and a ping-pong mechanism to catalyze the reduction of methylene-H4F. A ternary complex structure of MTHFR is available and based on this structure, a catalytic mechanism was proposed, while no ternary complex structures of Mfr or Mer are reported. Here, Mer fromMethanocaldococcus jannaschii(jMer) was heterologously produced and the crystal structures of the enzyme with and without F420were determined. A ternary complex of jMer was modeled using a functional alignment approach based on the ternary complex structure of MTHFR and the modeled ternary complex of Mfr. Mutational analysis at the structurally conserved positions of the three reductases indicated that although these reductases share a limited sequence identity, the key catalytic glutamate residue is conserved and a common catalytic mechanism involving the formation of a 5-iminium cation of the methylene-tetrahydropterin intermediate is shared. A phylogenetic analysis indicated that the three reductases do not share one common ancestor and the conserved active site structures of the three reductases may be the result of convergent evolution.STATEMENTThis work provides evidence for a common catalytic mechanism of the functional class of methylene-tetrahydropterin reductases. Despite their very low sequence identity, they share a (βα)8-barrel structure with a similar active site geometry. Phylogenetic and mutational analyses suggested that these enzymes have developed from distinct ancestors as a result of convergent evolution. This work describes an example of a catalytic mechanism that emerged independently for several times during evolution in the three domains of life.
Detection of idiosyncratic gaze fingerprint signatures in humans
Authors: Crockford Sarah K. , Satta Eleonora , Severino Ines , Fiacchino Donatella , Vitale Andrea , Bertelsen Natasha , Busuoli Elena Maria , Mandelli Veronica , Lombardo Michael V. 
Published: September 2023

AbstractVariation in human gaze can be explained by a variety of factors. Within an individual, gaze patterns can be quite reliable and can be explained in part by heritable common genetic mechanisms. If individual gaze patterns are strongly idiosyncratic, could they enable highly accurate detection of individuals via a ‘gaze fingerprint’? And are gaze fingerprints linked to variation in phenotypes such as autistic traits, which are underpinned by heritable common genetic mechanisms and cause atypical and idiosyncratic gaze to manifest in early development? To answer these questions we utilized a stimulus-rich design where participants viewed 700 stimuli of complex natural scenes, repeated in two sessions separated by ∼1-2 weeks. Across independent discovery (n=105) and replication (n=46) datasets, we find that gaze fingerprinting occurs at high rates (52-63%) relative to chance (1-2%) when gaze similarity is averaged across stimuli. However, such averaging procedures hide a unique non-random individuating code represented as a multivariate ‘gaze fingerprint barcode’ pattern across all 700 stimuli. Within such barcodes, around 91-95% of all individuals had fingerprintable stimuli counts that were significantly higher than situations where identity is randomly permuted. Data-driven clustering of such barcodes results in each individual as its own unique cluster. Finally, increased ‘gaze fingerprintability’ is associated with decreased levels of autistic traits. Overall, this work showcases strong potential for gaze fingerprinting on large-scale data as well as potential translational relevance to conditions such as autism.
Decrypting the functional design of unmodified translation elongation factor P
Authors: Tomasiunaite Urte , Kielkowski Pavel , Krafczyk Ralph , Forné Ignasi , Imhof Axel , Jung Kirsten 
Published: September 2023

AbstractStalling of ribosomes during polypeptide synthesis due to consecutive proline motifs is a challenge faced by organisms across all kingdoms. To overcome this, bacteria employ translation elongation factor P (EF-P), while archaea and eukaryotes rely on a/eIF5A. Typically, these elongation factors become active only after undergoing post-translational modifications (PTMs) such as ß-lysinylation, (deoxy-)hypusinylation, rhamnosylation, or 5-aminopentanolyation. An exception to this rule is found in EF-P members of the PGKGP-subfamily, which remain unmodified. However, the mechanism behind the ability of certain bacteria to avoid metabolically and energetically costly PTMs, while retaining active EF-P, remains unclear. In this study, we investigated the design principles governing the full functionality of unmodified EF-Ps inEscherichia coli.We first screened for naturally unmodified EF-Ps that are active in anE. colireporter strain. We identified EF-P fromRhodomicrobium vannieliicapable of rescuing the growth deficiencies and changes in the proteome of anE. coliΔepmAmutant lacking the gene for the modifying EF-P-(R)-ß-lysine ligase. We then identified specific amino acids in domain I of the unmodified EF-P variant that affected its activity. Ultimately, we transferred these functional properties to other marginally active members of the PGKGP EF-P subfamily, resulting in fully functional unmodified variants inE. coli. These results have implications for the improved heterologous expression of polyproline-containing proteins inE. coliand offer applications in other bacterial hosts. Understanding the mechanisms that underlie the functionality of unmodified EF-P provides insights into cellular adaptations to optimize protein synthesis.
Depleting glioblastoma cells of very long-chain acyl-CoA synthetase 3 (ACSVL3) produces metabolic alterations in non-lipid pathways
Authors: Kolar Elizabeth A. , Shi Xiaohai , Clay Emily M. , Liu Yanqiu , Xia Shuli , Zhang Cissy , Le Anne , Watkins Paul A. 
Published: September 2023

ABSTRACTKnockout (KO) of the fatty acid-activation enzyme very long-chain acyl-CoA synthetase 3 (ACSVL3; SLC27A3) in U87MG glioblastoma cells reduced their malignant growth properties both in vitro and in xenografts. These U87-KO glioma cells grew at a slower rate, became adherence-dependent, and were less invasive than parental U87 cells. U87-KO cells produced fewer, slower-growing subcutaneous and intracranial tumors when implanted in NOD-SCID mice. Thus, depleting U87MG cells of ACSVL3 restored these cells to a phenotype more like that of normal astrocytes. To understand the mechanisms underlying these beneficial changes, we investigated several possibilities, including the effects of ACSVL3 depletion on carbohydrate metabolism. Proteomic and metabolomic profiling indicated that ACSVL3 KO produced changes in glucose and energy metabolism. Even though protein levels of glucose transporters GLUT1 and GLUT3 were reduced by KO, cellular uptake of labeled 2-deoxyglucose was unaffected. Glucose oxidation to CO2was reduced nearly 7-fold by ACSVL3 depletion, and the cellular glucose level was 25% higher in KO cells. Glycolytic enzymes were upregulated by KO, but metabolic intermediates were essentially unchanged. Surprisingly, lactate production and the levels of lactate dehydrogenase isozymes LDHA and LDHB were elevated by ACSVL3 KO. The activity of the pentose phosphate pathway was found to be lower in KO cells. Citric acid cycle enzymes, electron transport chain complexes, and ATP synthase protein levels were all reduced by ACSVL3 depletion. Mitochondria were elongated in KO cells, but had a more punctate morphology in U87 cells. The mitochondrial potential was unaffected by lack of ACSVL3. We conclude that the beneficial effects of ACSVL3 depletion in human glioblastoma cells may result in part from alterations in diverse metabolic processes that are not directly related to role(s) of this enzyme in fatty acid and/or lipid metabolism. (Supported by NIH 5R01NS062043 and KKI institutional funds.)
Histone acetylation in an Alzheimer’s disease cell model promotes homeostatic amyloid-reducing pathways
Authors: Xu Daniel C. , Sas-Nowosielska Hanna , Donahue Greg , Huang Hua , Pourshafie Naemeh , Good Charly R. , Berger Shelley L. 
Published: September 2023

AbstractAlzheimer’s Disease (AD) is a disorder characterized by cognitive decline, neurodegeneration, and accumulation of amyloid plaques and tau neurofibrillary tangles in the brain. Dysregulation of epigenetic histone modifications may lead to expression of transcriptional programs that play a role either in protecting against disease genesis or in worsening of disease pathology. One such histone modification, acetylation of histone H3 lysine residue 27 (H3K27ac), is primarily localized to genomic enhancer regions and promotes active gene transcription. We previously discovered H3K27ac to be more abundant in AD patient brain tissue compared to the brains of age-matched non-demented controls. In this study, we use iPSC-neurons derived from familial AD patients with an amyloid precursor protein (APP) duplication (APPDupneurons) as a model to study the functional effect of lowering CBP/P300 enzymes that catalyze H3K27ac primarily at gene enhancers. We found that homeostatic amyloid-reducing genes were upregulated in the APPDupneurons compared to non- demented controls. We lowered CBP/P300 to reduce H3K27ac, which led to decreased expression of numerous of these homeostatic amyloid-reducing genes, along with increased extracellular secretion of a toxic amyloid-β species, Aβ(1-42). Our findings suggest that epigenomic histone acetylation, including H3K27ac, drives expression of compensatory genetic programs in response to AD-associated insults, specifically those resulting from APP duplication, and thus may play a role in mitigating AD pathology in neurons.
Parallel pathways carrying direction and orientation selective retinal signals to layer 4 of mouse visual cortex
Authors: Wang Helen , Dey Oyshi , Lagos Willian N. , Behnam Noor , Callaway Edward M. , Stafford Benjamin K. 
Published: September 2023

SummaryParallel functional and anatomical visual pathways from the retina to primary visual cortex (V1) via the lateral geniculate nucleus (LGN) are common to many mammalian species, including mice, carnivores and primates. However, the much larger number of retinal ganglion cell (RGC) types that project to the LGN, as well as the more limited lamination of both the LGN and the thalamocortical-recipient layer 4 (L4) in mice, leaves considerable uncertainty about which visual features present in both retina and V1 might be inherited from parallel pathways versus extracted by V1 circuits in the mouse visual system. Here, we explored the relationships between functional properties of L4 V1 neurons and their RGC inputs by taking advantage of two Cre-expressing mouse lines — Nr5a1-Cre and Scnn1a-Tg3-Cre — that each label functionally and anatomically distinct populations of L4 neurons. Visual tuning properties of L4 V1 neurons were evaluated using Cre-dependent expression of GCaMP6s followed by 2-photon calcium imaging. RGCs providing input to these neurons (via LGN) were labeled and characterized using Cre-dependent trans-synaptic retrograde labeling with G-deleted rabies virus. We find significant differences in the tuning of Nr5a1-Cre versus Scnn1a-Tg3-Cre neurons for direction, orientation, spatial frequency, temporal frequency, and speed. Strikingly, a subset of the RGCs had tuning properties that matched the direction and orientation tuning properties of the L4 V1 neurons to which they provided input. Altogether, these results suggest that direction and orientation tuning of V1 neurons may be at least partly inherited from parallel pathways originating in the retina.
Connecting self-report and instrumental behavior during incubation of food craving in humans
Authors: Ruiz Nicholas A , Eckardt Devlin , Briand Lisa A , Wimmer Mathieu , Murty Vishnu P 
Published: September 2023

AbstractIncubation of craving is a phenomenon describing the intensification of craving for a reward over extended periods of abstinence from reinforcement. Animal models employ instrumental markers of craving to reward cues to examine incubation, while homologous human paradigms often rely on subjective self-reports. Here, we characterize a novel human paradigm that showed strong positive relationships between self-reports and instrumental markers of craving. Further, both measures expressed non-linear relationships with time since last consumption, which parallels homologous animal paradigms of incubation of craving.
Structural basis for peroxidase encapsulation in a protein nanocompartment
Authors: Jones Jesse A. , Andreas Michael P. , Giessen Tobias W. 
Published: September 2023

AbstractEncapsulins are self-assembling protein nanocompartments capable of selectively encapsulating dedicated cargo proteins, including enzymes involved in iron storage, sulfur metabolism, and stress resistance. They represent a unique compartmentalization strategy used by many pathogens to facilitate specialized metabolic capabilities. Encapsulation is mediated by specific cargo protein motifs known as targeting peptides (TPs), though the structural basis for encapsulation of the largest encapsulin cargo class, dye-decolorizing peroxidases (DyPs), is currently unknown. Here, we characterize a DyP-containing encapsulin from the enterobacterial pathogenKlebsiella pneumoniae. By combining cryo-electron microscopy with TP mutagenesis, we elucidate the molecular basis for cargo encapsulation. TP binding is mediated by cooperative hydrophobic and ionic interactions as well as shape complementarity. Our results expand the molecular understanding of enzyme encapsulation inside protein nanocompartments and lay the foundation for rationally modulating encapsulin cargo loading for biomedical and biotechnological applications.
Where the present gets remembered: Sensory regions communicate with the brain over the longest timescales
Authors: Cooper Greg , Blackburne George , Dekker Tessa , Das Ravi K , Skipper Jeremy I 
Published: September 2023

AbstractIn natural contexts, the brain simultaneously processes sensory information over diverse timescales. Here we reveal how this is reflected in the organisation of asynchronous connectivity in the brain. In 86 individuals watching feature-length movies during functional neuroimaging, we calculated the delay at peak connectivity between brain regions. We found the longest delays in received whole-brain functional connectivity within ‘sensory’ regions (:S 18 seconds). Two complementary dimensionality reduction approaches were used to probe the spatial organisation of connection delays and weights. First, clustering of received delays separated sensory, and transmodal/associative outputting regions, suggesting that putatively localised functions are associated with asynchronous local-to-whole-brain connectivity patterns. Next, we organised delayed connectivity maps by likeness, unveiling five orthogonal gradients of variation, each demonstrating associations between early-sensory and transmodal/associative regions. Together, these findings challenge contemporary conceptualisations of the brain’s temporal hierarchy by emphasising the role of sensory regions as sites of integration across timescales.