bluuebunny/crossref_metadata_2025_split huggingface dataset:
Free ferrous ions sustain activity of mammalian stearoyl-CoA desaturase-1
Authors: Shen Jiemin , Wu Gang , Pierce Brad S. , Tsai Ah-Lim , Zhou Ming 
Published: March 2023

AbstractMammalian stearoyl-CoA desaturase-1 (SCD1) introduces a double-bond to a saturated long-chain fatty acid and the reaction is catalyzed by a diiron center, which is well-coordinated by conserved histidine residues and is thought to remain with enzyme. However, we find that SCD1 progressively loses its activity during catalysis and becomes fully inactive after nine turnovers. Further studies show that the inactivation of SCD1 is due to the loss of an iron (Fe) ion in the diiron center, and that the addition of free ferrous ions (Fe2+) sustains the enzymatic activity. Using SCD1 labeled with Fe isotope, we further show that free Fe2+is incorporated into the diiron center only during catalysis. We also discover that the diiron center in SCD1 has prominent electron paramagnetic resonance signals in its diferric state, indicative of distinct coupling between the two ferric ions. These results reveal that the diiron center in SCD1 is structurally dynamic during catalysis and that labile Fe2+in cells could regulate SCD1 activity, and hence lipid metabolism.
The energy landscape for R-loop formation by the CRISPR-Cas Cascade complex
Authors: Kauert Dominik J. , Madariaga-Marcos Julene , Rutkauskas Marius , Wulfken Alexander , Songailiene Inga , Sinkunas Tomas , Siksnys Virginijus , Seidel Ralf 
Published: March 2023

The discovery1,2and the pioneering applications3of CRISPR-Cas effector complexes have provided powerful gene-editing tools. The effector complexes are guided to the targeted genomic locus by the complementarity of their CRISPR RNA (crRNA)4,5. Recognition of double-stranded DNA targets proceeds via DNA unwinding and base-pairing between crRNA and the DNA target strand resulting in the formation of an R-loop structure5,6. Full R-loop formation is the prerequisite for the subsequent DNA cleavage. While the CRISPR-Cas technology is easy to use, efficient and highly versatile, therapeutic applications are hampered by the off-target effects due to the recognition of unintended sequences with multiple mismatches7. This process is still poorly understood on a mechanistic level8,9. Particularly, the lack of insight into the energetics and dynamics of the R-loop formation hinders a direct modelling of the R-loop formation for off-target prediction.Here we set up ultrafast DNA unwinding experiments based on plasmonic DNA nanorotors to follow the R-loop formation by the Cascade effector complex in real time, close to base pair resolution. We directly resolve a weak global downhill bias of the energy landscape of the forming R-loop followed by a steep uphill bias for the final base pairs. We furthermore show a modulation of the landscape by base flips and mismatches. These data provide that Cascade-mediated R-loop formation occurs on short time scales in single base pair steps of sub-millisecond duration, but on longer time scales in six–base pair intermediate steps in agreement with the structural periodicity of the crRNA-DNA hybrid. We expect that the knowledge about the energy landscapes of R-loop formation of CRISPR-Cas effector complexes will pave the way for a detailed understanding and prediction of off-target recognition10.
Genetic mapping identifies Homer1 as a developmental modifier of attention
Authors: Gershon Zachary , Bonito-Oliva Alessandra , Kanke Matt , Terceros Andrea , Rankin Genelle , Fak John , Harada Yujin , Iannone Andrew F. , Gebremedhin Millennium , Fabella Brian , De Marco García Natalia V. , Sethupathy Praveen , Rajasethupathy Priya 
Published: March 2023

SUMMARYAttention is required for most higher-order cognitive functions. Prior studies have revealed functional roles for the prefrontal cortex and its extended circuits to enabling attention, but the underlying molecular processes and their impacts on cellular and circuit function remain poorly understood. To develop insights, we here took an unbiased forward genetics approach to identify single genes of large effect on attention. We studied 200 genetically diverse mice on measures of pre-attentive processing and through genetic mapping identified a small locus on chromosome 13 (95%CI: 92.22-94.09 Mb) driving substantial variation (19%) in this trait. Further characterization of the locus revealed a causative gene, Homer1, encoding a synaptic protein, where down-regulation of its short isoforms in prefrontal cortex (PFC) during early postnatal development led to improvements in multiple measures of attention in the adult. Subsequent mechanistic studies revealed that prefrontalHomer1down-regulation is associated with GABAergic receptor up-regulation in those same cells. This enhanced inhibitory influence, together with dynamic neuromodulatory coupling, led to strikingly low PFC activity at baseline periods of the task but targeted elevations at cue onset, predicting short-latency correct choices. Notably high-Homer1, low-attentional performers, exhibited uniformly elevated PFC activity throughout the task. We thus identify a single gene of large effect on attention - Homer1 – and find that it improves prefrontal inhibitory tone and signal-to-noise (SNR) to enhance attentional performance. A therapeutic strategy focused on reducing prefrontal activity and increasing SNR, rather than uniformly elevating PFC activity, may complement the use of stimulants to improve attention.
Motor nerves direct the development of the sympathetic nervous system
Authors: Erickson Alek , Motta Alessia , Kastriti Maria Eleni , Edwards Steven , Lallemend Francois , Hadjab Saida , Ruhrberg Christiana , Schwarz Quenten , Fried Kaj , Bonanomi Dario , Adameyko Igor 
Published: March 2023

ABSTRACTThe sympathetic nervous system controls a wide spectrum of bodily functions including operation of vessels, cardiac rhythm, and the “flight or fight response”. Sympathetic neurons, which are neural crest-derived, develop in coordination with presynaptic motor nerves extending from the central nervous system (CNS). By using nerve-selective genetic ablations, we revealed that sympathetic ganglia development depends on CNS-derived motor innervation. In the absence of preganglionic motor nerves, trunk sympathetic chain ganglia were fragmented and smaller in size, while cervical ganglia were severely misshapen. Sympathetic neurons were misplaced along sensory fibers and projected towards abnormal paths, in some cases invading the sensory dorsal root ganglia. The misplaced progenitors of sympathoblasts corresponded to the nerve-associated, neural crest-derived Schwann cell precursors (SCPs). Notably, we found that SCPs activate the autonomic marker PHOX2B while migrating along motor nerves towards the region of the dorsal aorta in wildtype embryos, suggesting that SCP differentiate into sympathetic neurons while still nerve-associated in motor-ablated embryos. Ligand-receptor prediction from single cell transcriptomic data coupled with functional studies identified Semaphorin 3A/3F as candidate motor nerve-derived signals influencing neural crest migration along axons. Thus, motor nerves control the placement of sympathoblasts and their subsequent axonal navigation during critical periods of sympathetic chain development.
Hidden from plain sight: NovelChlamydiotadiversity emerging from screening genomic and metagenomic data
Authors: Davison Helen R. , Hurst Gregory D.D. 
Published: March 2023

AbstractChlamydiotaare an ancient and hyperdiverse Phylum of obligate intracellular bacteria. The best characterized representatives are pathogens or parasites of mammals, but it is thought that their most common hosts are microeukaryotes like Amoebozoa. The diversity in taxonomy, evolution, and function of non-pathogenicChlamydiotaare slowly being described. Here we use data mining techniques and genomic analysis to extend our current knowledge ofChlamydiotadiversity and its hosts, in particular the OrderParachlamydiales. We extract oneRhabdochlamydiaceaeand threeSimkaniaceaegenomes from NCBI Short Read Archive deposits of ciliate and algal genome sequencing projects. We then use these to identify a further 14 and 8 genomes respectively amongst existing, unidentified environmental assemblies. From these data we identify two novel clades with host associated data, for which we propose the names ‘CandidatusSacchlamydia’ (FamilyRhabdochlamydiaceae)and ‘CandidatusAmphrikania’ (FamilySimkaniaceae), as well as a third new clade of environmental MAGs ‘CandidatusAcheromydia’ (FamilyRhabdochlamydiaceae). The extent of uncharacterized diversity within theRhabdochlamydiaceaeandSimkaniaceaeis indicated by 16 of the 22 MAGs being evolutionarily distant from currently characterised genera. Within our limited data, we observe great predicted diversity inParachlamydialesmetabolism and evolution, including the potential for metabolic and defensive symbioses as well as pathogenicity. These data provide an imperative to link genomic diversity in metagenomics data to their associated eukaryotic host, and to develop onward understanding of the functional significance of symbiosis with this hyperdiverse clade.Graphical Abstract
Structured connectivity in the output of the cerebellar cortex
Authors: Gruver Kim M. , Jiao Jenny W. Y. , Fields Eviatar , Song Sen , Sjöström Per Jesper , Watt Alanna J. 
Published: March 2023

AbstractCircuits in the brain are built from connections between neurons, where the spatial organization and functional properties of these connections determines circuit function. In the cerebellum, Purkinje cells transmit information to neurons in the cerebellar nuclei, but how Purkinje cell – nuclear neuron connections are organized remains unclear. Here, we explored the connections between Purkinje cells and cerebellar nuclear neurons using whole-cell electrophysiology and optogenetics to produce spatial connectivity maps of cerebellar cortical output. We observed non-random connectivity between Purkinje cells and their target neurons, with inputs to cerebellar nuclear neurons clustering along cerebellar transverse zones. While many nuclear neurons received inputs from a single zone, a number of different connectivity motifs were observed. Neurons receiving inputs from all four zones were more common than predicted by a random model and showed topographic organization in the nucleus. Finally, we observed that small Purkinje cell inputs were sufficient to pause the output of nuclear neurons, suggesting that widespread Purkinje cell synchrony may not be necessary to influence cerebellar output. These findings reveal cerebellar nuclear neurons as an important locus of multimodal cerebellar integration.
Noradrenergic Tone is Not Required for Neuronal Activity-Induced Rebound Sleep in Zebrafish
Authors: Benoit Eleanor , Lyons Declan G , Rihel Jason 
Published: March 2023

AbstractSleep pressure builds during wakefulness, but the mechanisms underlying this homeostatic process are poorly understood. One zebrafish model suggests that sleep pressure increases as a function of global neuronal activity, such as during sleep deprivation or acute exposure to drugs that induce widespread brain activation. Given that the arousal-promoting noradrenergic system is important for maintaining heightened neuronal activity during wakefulness, we hypothesised that genetic and pharmacological reduction of noradrenergic tone during drug-induced neuronal activation would dampen subsequent rebound sleep in zebrafish larvae. Unexpectedly, dampening noradrenergic tone with the α2-adrenoceptor agonist clonidine during acute caffeine or pentylenetetrazol treatment enhanced subsequent rebound sleep, while stimulating noradrenergic signalling during caffeine exposure with a cocktail of α1- and β-adrenoceptor agonists did not enhance sleep. Similarly, CRISPR/Cas9-mediated elimination of thedopamine β-hydroxylase(dbh) gene, which encodes an enzyme required for noradrenalin synthesis, enhanced baseline sleep in larvae but did not prevent additional rebound sleep following acute induction of neuronal activity. Across all drug conditions,c-fosexpression immediately after drug exposure varied inversely with noradrenergic tone and correlated strongly with the amount of induced rebound sleep. These results are consistent with a model in which increases in neuronal activity, as reflected by brain-wide levels ofc-fosinduction, drive a sleep pressure signal that promotes rebound sleep independently of noradrenergic tone.
Neural Selectivity for Real-World Object Size In Natural Images
Authors: Luo Andrew F. , Wehbe Leila , Tarr Michael J. , Henderson Margaret M. 
Published: March 2023

1AbstractReal-world size is a functionally important high-level visual property of objects that supports interactions with our physical environment. Critically, real-world-size is robust over changes in visual appearance as projected onto our retinae such that large and small objects are correctly perceived to have different real-world sizes. To better understand the neural basis of this phenomenon, we examined whether the neural coding of real-world size holds for objects embedded in complex natural scene images, as well as whether real-world size effects are present for both inanimate and animate objects, whether low- and mid-level visual features can account for size selectivity, and whether neural size tuning is best described by a linear, logarithmic, or exponential neural coding function. To address these questions, we used a large-scale dataset of fMRI responses to natural images combined with per-voxel regression and contrasts. Importantly, the resultant pattern of size selectivity for objects embedded in natural scenes was aligned with prior results using isolated objects. Extending this finding, we also found that size coding exists for both animate and inanimate objects, that low-level visual features cannot account for neural size preferences, and size tuning functions have different shapes for large versus small preferring voxels. Together, these results indicate that real-world size is an ecologically significant dimension in the larger space of behaviorally-relevant cortical representations that support interactions with the world around us.
Cryo-EM structure of the human Sirtuin 6-nucleosome complex
Authors: Chio Un Seng , Rechiche Othman , Bryll Alysia R. , Zhu Jiang , Feldman Jessica L. , Peterson Craig L. , Tan Song , Armache Jean-Paul 
Published: March 2023

AbstractSirtuin 6 (SIRT6) is a multifaceted protein deacetylase/deacylase and a major target for small-molecule modulators of longevity and cancer. In the context of chromatin, SIRT6 removes acetyl groups from histone H3 in nucleosomes, but the molecular basis for its nucleosomal substrate preference is unknown. Our cryo-electron microscopy structure of human SIRT6 in complex with the nucleosome shows that the catalytic domain of SIRT6 pries DNA from the nucleosomal entry-exit site and exposes the histone H3 N-terminal helix, while the SIRT6 zinc-binding domain binds to the histone acidic patch using an arginine anchor. In addition, SIRT6 forms an inhibitory interaction with the C-terminal tail of histone H2A. The structure provides insights into how SIRT6 can deacetylate both H3 K9 and H3 K56.TeaserThe structure of the SIRT6 deacetylase/nucleosome complex suggests how the enzyme acts on both histone H3 K9 and K56 residues.
Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1
Authors: Abini-Agbomson Stephen , Gretarsson Kristjan , Shih Rochelle M. , Hsieh Laura , Lou Tracy , Ioannes Pablo De , Vasilyev Nikita , Lee Rachel , Wang Miao , Simon Matthew , Armache Jean-Paul , Nudler Evgeny , Narlikar Geeta , Liu Shixin , Lu Chao , Armache Karim-Jean 
Published: March 2023

AbstractThe intricate regulation of chromatin plays a key role in controlling genome architecture and accessibility. Histone lysine methyltransferases regulate chromatin by catalyzing the methylation of specific histone residues but are also hypothesized to have equally important non-catalytic roles. SUV420H1 di- and tri-methylates histone H4 lysine 20 (H4K20me2/me3) and plays crucial roles in DNA replication, repair, and heterochromatin formation, and is dysregulated in several cancers. Many of these processes were linked to its catalytic activity. However, deletion and inhibition of SUV420H1 have shown distinct phenotypes suggesting the enzyme likely has uncharacterized non-catalytic activities. To characterize the catalytic and non-catalytic mechanisms SUV420H1 uses to modify chromatin, we determined cryo- EM structures of SUV420H1 complexes with nucleosomes containing histone H2A or its variant H2A.Z. Our structural, biochemical, biophysical, and cellular analyses reveal how both SUV420H1 recognizes its substrate and H2A.Z stimulates its activity, and show that SUV420H1 binding to nucleosomes causes a dramatic detachment of nucleosomal DNA from histone octamer. We hypothesize that this detachment increases DNA accessibility to large macromolecular complexes, a prerequisite for DNA replication and repair. We also show that SUV420H1 can promote chromatin condensates, another non-catalytic role that we speculate is needed for its heterochromatin functions. Together, our studies uncover and characterize the catalytic and non-catalytic mechanisms of SUV420H1, a key histone methyltransferase that plays an essential role in genomic stability.
TREM2 and APOE do not modulate phagocytic clearance of dying cells in the live mammalian brain
Authors: Damisah Eyiyemisi C. , Rai Anupama , Hill Robert A. , Tong Lei , Grutzendler Jaime 
Published: March 2023

AbstractTREM2 and APOE are two major risk factors for Alzheimer’s disease (AD) that have been proposed to play crucial roles in microglia pathophysiology by affecting their ability to phagocytose cellular debris or aggregated proteins. In this study, we investigated for the first time the impact of TREM2 and APOE on the removal of dying neurons in the live brain by implementing a targeted photochemical method for programmed cell death induction combined with high-resolution two-photon imaging. Our findings showed that the deletion of either TREM2 or APOE did not affect the dynamics of microglia engagement with dying neurons or their efficiency in phagocytosing corpses. Interestingly, while microglia that encapsulate amyloid deposits were capable of phagocytosing dying cells without disengaging from plaques or moving their cell bodies; in the absence of TREM2, microglia cell bodies were observed to readily migrate towards dying cells, further disengaging from plaques. Our data suggest that TREM2 and APOE variants are unlikely to increase risk of AD through impaired corpse phagocytosis.SummaryHigh-resolution two-photon imaging of programmed cell death in the live mouse brain reveals that neither TREM2 nor APOE modulate microglia phagocytosis of neuronal corpses. However, TREM2 regulates microglia migratory behavior towards dying cells in the vicinity of amyloid plaques.
Trinucleotide building blocks enable exponential ribozyme-catalysed RNA replication and open-ended growth of diverse RNA sequence pools
Authors: Attwater James , Augustin Teresa , Curran Joseph F. , Kwok Samantha , Gianni Edoardo , Holliger Philipp 
Published: March 2023

AbstractRNA replication is considered a crucial stage in the origins of life. However, both enzymatic and non-enzymatic RNA replication cycles are impeded by the “strand separation problem” (SSP), a form of product inhibition arising from the extraordinary stability of RNA duplexes and their rapid kinetics of reannealing. Here we show that RNA trinucleotide triphosphates (triplets) can overcome the SSP by binding to and kinetically trapping dissociated RNA strands in a single-stranded form, while simultaneously serving as substrates for RNA replication by a triplet polymerase ribozyme (TPR). This enabled exponential replication of both (+) and (−) strands of double-stranded RNAs by the TPR when driven by coupled pH and freeze-thaw cycles. We demonstrate replication of a fragment of the ribozyme itself, and open-ended amplification of random RNA sequence pools over >70 cycles, with emergence of partial, distributive TPR self-replication and triplet codon drift towards a primordial genetic code.One-sentence summaryRNA trinucleotide substrates together with simple physicochemical cycles enable RNA-catalysed replication of double-stranded RNA and partial, distributive self-replication of an RNA polymerase ribozyme.
Metabolic interplay betweenProteus mirabilisandEnterococcus faecalisfacilitates polymicrobial biofilm formation and invasive disease
Authors: Hunt Benjamin C. , Brix Vitus , Vath Joseph , Guterman Beryl L. , Taddei Steven M. , Learman Brian S. , Brauer Aimee L. , Shen Shichen , Qu Jun , Armbruster Chelsie E. 
Published: March 2023

SummaryPolymicrobial biofilms play an important role in the development and pathogenesis of CAUTI.Proteus mirabilisandEnterococcus faecalisare common CAUTI pathogens that persistently co-colonize the catheterized urinary tract and form biofilms with increased biomass and antibiotic resistance. In this study, we uncover the metabolic interplay that drives biofilm enhancement and examine the contribution to CAUTI severity. Through compositional and proteomic biofilm analyses, we determined that the increase in biofilm biomass stems from an increase in the protein fraction of the polymicrobial biofilm matrix. We further observed an enrichment in proteins associated with ornithine and arginine metabolism in polymicrobial biofilms compared to single-species biofilms. We show that L-ornithine secretion byE. faecalispromotes arginine biosynthesis inP. mirabilis,and that disruption of this metabolic interplay abrogates the biofilm enhancement we seein vitroand leads to significant decreases in infection severity and dissemination in a murine CAUTI model.
Psychophysical pain encoding in the cingulate cortex predicts responsiveness of electrical stimulation
Authors: Caston Rose M. , Smith Elliot H. , Davis Tyler S. , Singh Hargunbir , Rahimpour Shervin , Rolston John D. 
Published: March 2023

AbstractBackgroundThe anterior cingulate cortex (ACC) plays an important role in the cognitive and emotional processing of pain. Prior studies have used deep brain stimulation (DBS) to treat chronic pain, but results have been inconsistent. This may be due to network adaptation over time and variable causes of chronic pain. Identifying patient-specific pain network features may be necessary to determine patient candidacy for DBS.HypothesisCingulate stimulation would increase patients’ hot pain thresholds if non-stimulation 70-150 Hz activity encoded psychophysical pain responses.MethodsIn this study, four patients who underwent intracranial monitoring for epilepsy monitoring participated in a pain task. They placed their hand on a device capable of eliciting thermal pain for five seconds and rated their pain. We used these results to determine the individual’s thermal pain threshold with and without electrical stimulation. Two different types of generalized linear mixed-effects models (GLME) were employed to assess the neural representations underlying binary and graded pain psychophysics.ResultsThe pain threshold for each patient was determined from the psychometric probability density function. Two patients had a higher pain threshold with stimulation than without, while the other two patients had no difference. We also evaluated the relationship between neural activity and pain responses. We found that patients who responded to stimulation had specific time windows where high-frequency activity was associated with increased pain ratings.ConclusionStimulation of cingulate regions with increased pain-related neural activity was more effective at modulating pain perception than stimulating non-responsive areas. Personalized evaluation of neural activity biomarkers could help identify the best target for stimulation and predict its effectiveness in future studies evaluating DBS.