bluuebunny/crossref_metadata_2025_split huggingface dataset:
Advancing reproducibility can ease the ‘hard truths’ of synthetic biology
Authors: Lux Matthew W , Strychalski Elizabeth A , Vora Gary J 
Published: November 2023

AbstractReproducibility has been identified as an outstanding challenge in science, and the field of synthetic biology is no exception. Meeting this challenge is critical to allow the transformative technological capabilities emerging from this field to reach their full potential to benefit the society. We discuss the current state of reproducibility in synthetic biology and how improvements can address some of the central shortcomings in the field. We argue that the successful adoption of reproducibility as a routine aspect of research and development requires commitment spanning researchers and relevant institutions via education, incentivization and investment in related infrastructure. The urgency of this topic pervades synthetic biology as it strives to advance fundamental insights and unlock new capabilities for safe, secure and scalable applications of biotechnology.Graphical Abstract
Discovery and genome characterization of six new orthoparamyxoviruses in small Belgian mammals
Authors: Horemans Marie , Van Bets Jessica , Joly Maes Tibe , Maes Piet , Vanmechelen Bert 
Published: November 2023

Abstract
In the future, zoonotic spillover events are expected to occur more frequently. Consequences of such events have clearly been demonstrated by recent outbreaks of monkeypox, Ebola virus, and the well-known severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Virus discovery has proven to be an important tool in the preparation against viral outbreaks, generating data concerning the diversity, quantity, and ecology of the vertebrate virome. Orthoparamyxoviruses, a subfamily within the Paramyxoviridae, are important biosurveillance targets, since they include several known animal, human, and zoonotic pathogens such as Nipah virus, measles virus, and Hendra virus. During this study, 127 bat samples, thirty-four rodent samples, and seventeen shrew samples originating from Belgium were screened for orthoparamyxovirus presence using nested reverse transcription–polymerase chain reaction assays and nanopore sequencing. We present here the complete genomes of six putative new viral species, belonging to the genera Jeilongvirus and Henipavirus. Characterization of these genomes revealed significant differences in gene composition and organization, both within viruses of the same genus and between viruses of different genera. Remarkably, a previously undetected gene coding for a protein of unknown function was identified in the genome of a putative new Henipavirus. Additionally, phylogenetic analysis of jeilongviruses and henipaviruses reveals a division of both genera into two clades, one consisting of bat-borne viruses and the other consisting of rodent- and shrew-borne viruses, elucidating the need for proper reclassification.
Germline-targeting SOSIP trimer immunization elicits precursor CD4 binding-site targeting broadly neutralizing antibodies in infant macaques
Authors: Nelson Ashley N. , Shen Xiaoying , Vekatayogi Sravani , Zhang Shiyu , Ozorowski Gabriel , Dennis Maria , Sewall Leigh M. , Milligan Emma , Davis Dominique , Cross Kaitlyn A. , Chen Yue , van Schooten Jelle , Eudailey Joshua , Isaac John , Memon Saad , Weinbaum Carolyn , Stanfield-Oakley Sherry , Byrd Alliyah , Chutkan Suni , Berendam Stella , Cronin Kenneth , Yasmeen Anila , Alam S. Munir , LaBranche Celia C. , Rogers Kenneth , Shirreff Lisa , Cupo Albert , Derking Ronald , Villinger Francois , Klasse Per Johan , Ferrari Guido , Williams Wilton B. , Hudgens Michael G. , Ward Andrew B. , Montefiori David C. , Van Rompay Koen K.A. , Wiehe Kevin , Moore John P. , Sanders Rogier W. , De Paris Kristina , Permar Sallie R. 
Published: November 2023

AbstractA vaccine that can achieve protective immunity prior to sexual debut is critical to prevent the estimated 410,000 new HIV infections that occur yearly in adolescents. As children living with HIV can make broadly neutralizing antibody (bnAb) responses in plasma at a faster rate than adults, early childhood is an opportune window for implementation of a multi-dose HIV immunization strategy to elicit protective immunity prior to adolescence. Therefore, the goal of our study was to assess the ability of a B cell lineage-designed HIV envelope SOSIP to induce bnAbs in early life. Infant rhesus macaques (RMs) received either BG505 SOSIP or the germline-targeting BG505 GT1.1 SOSIP (n=5/group) with the 3M-052-SE adjuvant at 0, 6, and 12 weeks of age. All infant RMs were then boosted with the BG505 SOSIP at weeks 26, 52 and 78, mimicking a pediatric immunization schedule of multiple vaccine boosts within the first two years of life. Both immunization strategies induced durable, high magnitude binding antibodies and plasma autologous virus neutralization that primarily targeted the CD4-binding site (CD4bs) or C3/465 epitope. Notably, three BG505 GT1.1-immunized infants exhibited a plasma HIV neutralization signature reflective of VRC01-like CD4bs bnAb precursor development and heterologous virus neutralization. Finally, infant RMs developed precursor bnAb responses at a similar frequency to that of adult RMs receiving a similar immunization strategy. Thus, a multi-dose immunization regimen with bnAb lineage designed SOSIPs is a promising strategy for inducing protective HIV bnAb responses in childhood prior to adolescence when sexual HIV exposure risk begins.
Human cortical high-gamma power relates to movement speed and is disproportionately reduced after stroke
Authors: Haverland Benjamin , Timmsen Lena S. , Wolf Silke , Stagg Charlotte J. , Frontzkowski Lukas , Oostenveld Robert , Feldheim Jan , Higgen Focko L. , Gerloff Christian , Schulz Robert , Schneider Till R. , Schwab Bettina C. , Quandt Fanny 
Published: November 2023

AbstractMotor cortical high-gamma oscillations (60 to 90 Hz) occur at the onset of movement and are spatially focused over the contralateral primary motor cortex. Although high-gamma oscillations are widely recognized for their significance in human motor control, their precise function on a cortical level remains elusive. Importantly, their relevance in human stroke pathophysiology is unknown. Understanding the neurophysiological processes of motor coding could be an important step in improving motor recovery after stroke. We recorded magnetoencephalography data during a thumb movement speed task in 14 chronic stroke survivors, 15 age-matched control participants and 29 healthy young participants. Motor cortical high-gamma oscillations showed a strong relation withmovement speedas trials with highermovement speedwere associated with greater high-gamma power. Stroke survivors showed reduced cortical high-gamma power, surpassing the effect attributable to decreasedmovement speedin these participants. Even though motor skill acquisition was evident in all groups, it was not linked to high-gamma power. Our study is, to our knowledge, the first to quantify high-gamma oscillations after stroke, revealing a reduction in movement-related high-gamma power. Moreover, we provide strong evidence for a pivotal role of motor cortical high-gamma oscillations in encodingmovement speed.
Stress granule formation helps to mitigate neurodegeneration
Authors: Glineburg M. Rebecca , Yildirim Evrim , Gomez Nicolas , Li Xingli , Pak Jaclyn , Altheim Christopher , Waksmacki Jacob , McInerney Gerald , Barmada Sami J. , Todd Peter K. 
Published: November 2023

AbstractCellular stress pathways that inhibit translation initiation lead to transient formation of cytoplasmic RNA/protein complexes known as stress granules. Many of the proteins found within stress granules and the dynamics of stress granule formation and dissolution are implicated in neurodegenerative disease. Whether stress granule formation is protective or harmful in neurodegenerative conditions is not known. To address this, we took advantage of the alphavirus protein nsP3, which selectively binds dimers of the central stress granule nucleator protein G3BP (rininDrosophila) and markedly reduces stress granule formation without directly impacting the protein translational inhibitory pathways that trigger stress granule formation. InDrosophilaand rodent neurons, reducing stress granule formation with nsP3 had modest impacts on lifespan even in the setting of serial stress pathway induction. In contrast, reducing stress granule formation in models of ataxia, amyotrophic lateral sclerosis and frontotemporal dementia largely exacerbated disease phenotypes. These data support a model whereby stress granules mitigate, rather than promote, neurodegenerative cascades.
2D and 3D multiplexed subcellular profiling of nuclear instability in human cancer
Authors: Coy Shannon , Cheng Brian , Lee Jong Suk , Rashid Rumana , Browning Lindsay , Xu Yilin , Chakrabarty Sankha S. , Yapp Clarence , Chan Sabrina , Tefft Juliann B. , Scott Emily , Spektor Alexander , Ligon Keith L. , Baker Gregory J. , Pellman David , Sorger Peter K. , Santagata Sandro 
Published: November 2023

AbstractNuclear atypia, including altered nuclear size, contour, and chromatin organization, is ubiquitous in cancer cells. Atypical primary nuclei and micronuclei can rupture during interphase; however, the frequency, causes, and consequences of nuclear rupture are unknown in most cancers. We demonstrate that nuclear envelope rupture is surprisingly common in many human cancers, particularly glioblastoma. Using highly-multiplexed 2D and super-resolution 3D-imaging of glioblastoma tissues and patient-derived xenografts and cells, we link primary nuclear rupture with reduced lamin A/C and micronuclear rupture with reduced lamin B1. Moreover, ruptured glioblastoma cells activate cGAS-STING-signaling involved in innate immunity. We observe that local patterning of cell states influences tumor spatial organization and is linked to both lamin expression and rupture frequency, with neural-progenitor-cell-like states exhibiting the lowest lamin A/C levels and greatest susceptibility to primary nuclear rupture. Our study reveals that nuclear instability is a core feature of cancer, and links nuclear integrity, cell state, and immune signaling.
Predator Odor Stressor, 2,3,5-trimethyl-3-thiazoline (TMT): Assessment of stress reactive behaviors during an animal model of traumatic stress in rats
Authors: Ornelas Laura C. , Besheer Joyce 
Published: November 2023

ABSTRACTAnimal models utilizing predator odor stress are important in understanding implications for post-traumatic stress disorder. 2,5-dihydro-2,4,5-trimethylthiazoline (TMT) has been used to measure stress reactive behaviors during TMT exposure, indicative of stress coping behaviors. In addition, long-term consequences of stress including contextual-induced stress memory, anxiety-like and hyperarousal behaviors, and subsequent increases in alcohol self- administration can also be examined after TMT exposure.In this article, we describe the TMT exposure protocol used in our lab and how we measure different stress-reactive behaviors that rats engage in during the TMT exposure. Rats are placed in Plexiglas chambers that contains white bedding on the bottom of the chamber and a metal basket in the top right corner that contains a filter paper on which 10 µL of TMT is pipetted onto. During the 10 min exposure, rats can move around the chamber freely. Exposures are recorded by a video camera for later analysis.During TMT exposure, rats engage in a variety of stress-reactive behaviors, including digging and immobility behavior. These are two distinctly different types of stress-induced behavioral coping strategies to measure individual differences in stress responsivity. To examine individual differences, we group rats into TMT-subgroups based on time spent engaging in digging or immobility behavior. We calculate a digging/immobility ratio score in which we divide the total time spent digging by the total time spent immobile. A cut-off strategy is used such that rats with a criterion ratio score below 1.0 are classified as TMT-1 (i.e., low digging/high immobility; greater passive coping) and rats with a ratio score above 1.0 are classified as TMT-2 (i.e., high digging/low immobility; greater active coping).In the present paper, we provide a detailed description of the TMT exposure protocol and step- by-step process in evaluation of stress-reactive behaviors.Basic Protocol 1:Predator Odor Stressor Exposure using TMTBasic Protocol 2:Description of Stress-Reactive Behaviors during TMT Exposure and Formation of TMT-subgroups
Progressive degeneration in a newDrosophilamodel of Spinocerebellar Ataxia type 7
Authors: Sujkowski Alyson L. , Ranxhi Bedri , Prifti Matthew V. , Alam Nadir , Todi Sokol V. , Tsou Wei-Ling 
Published: November 2023

AbstractSpinocerebellar ataxia type 7 (SCA7) is a progressive neurodegenerative disorder resulting from abnormal expansion of polyglutamine (polyQ) in its disease protein, ataxin-7 (ATXN7). ATXN7 is part of Spt-Ada-Gcn5 acetyltransferase (SAGA), an evolutionarily conserved transcriptional coactivation complex with critical roles in chromatin remodeling, cell signaling, neurodifferentiation, mitochondrial health and autophagy. SCA7 is dominantly inherited and characterized by genetic anticipation and high repeat-length instability. Patients with SCA7 experience progressive ataxia, atrophy, spasticity, and blindness. There is currently no cure for SCA7, and therapies are aimed at alleviating symptoms to increase quality of life. Here, we report novelDrosophilalines of SCA7 with polyQ repeats in wild-type and human disease patient range. We find that ATXN7 expression has age- and polyQ repeat length-dependent reduction in survival and retinal instability, concomitant with increased ATXN7 protein aggregation. These new lines will provide important insight on disease progression that can be used in the future to identify therapeutic targets for SCA7 patients.
Fire traps in the wet subtropics: new perspectives from Hong Kong
Authors: Chan Aland H. Y. , Coomes David A. 
Published: November 2023

AbstractFires undermine efforts to restore degraded forests in the wet tropics and subtropics. Grasslands and shrublands established after fires are more fire-susceptible than forests and tend to be set alight more often, creating a positive feedback loop that curbs succession (i.e. create a fire trap). Understanding the factors that underpin the strength of these fire traps could transform restoration programmes by identifying the steps needed to escape them.Fire traps are notoriously challenging to quantify because multiple factors influence fire occurrence and vegetation recovery. Here we used multi-decadal satellite imagery from Landsat to create a 34-year time series of burn areas and vegetation dynamics in wet subtropical Hong Kong. These dynamic maps were then used to characterise (1) the influence of successional stage on fire occurrence, having accounted for topographical and ignition source imbalances using neighbourhood analyses and entropy balancing (EBAL) weights, and (2) recovery time to the next successional stage by survival analysis with EBAL weights.Our analyses revealed that fire regimes in the wet subtropics are defined by strong fire-vegetation feedbacks. Grasslands and shrublands were 20 and 9 times more susceptible to fires than forests in similar topographic positions. Human activities compounded these differences by disproportionally introducing more ignition sources to grasslands (2.3 times) and shrublands (2.0 times) than to forests.Burnt shrublands recovered to forests faster (19 years) than grasslands (40 years). Proximity to forest patches had strong positive effects on recovery rates, highlighting the importance of seed sources. Post-fire recovery was faster on wetter northwest-facing sites and valleys. Overall, topography strongly influenced recovery processes but hardly affected fires occurrence.Synthesis and applications. Our study provides the first quantification of fire-trap processes in the wet subtropics, which provides new opportunities for evidence-based fire suppression and post-fire restoration. Our results suggest that (1) fire traps could be mitigated by fire-suppression programmes as the traps are currently exacerbated by ignition source imbalance; (2) establishing green fire breaks represent an effective fire suppression measure in the wet subtropics; and (3) active restoration could target areas where models predict sluggish post-fire natural regeneration.
Aberrant hippocampal Ca2+micro-waves following synapsin-dependent adeno-associated viral expression of Ca2+indicators
Authors: Masala Nicola , Mittag Manuel , Ambrad Giovannetti Eleonora , O’Neil Darik A. , Distler Fabian , Rupprecht Peter , Helmchen Fritjof , Yuste Rafael , Fuhrmann Martin , Beck Heinz , Wenzel Michael , Kelly Tony 
Published: November 2023

AbstractGenetically encoded calcium indicators (GECIs) such as GCaMP are invaluable tools in neuroscience to monitor neuronal activity using optical imaging. The viral transduction of GECIs is commonly used to target expression to specific brain regions, can be conveniently used with any mouse strain of interest without the need for prior crossing with a GECI mouse line and avoids potential hazards due to the chronic expression of GECIs during development. A key requirement for monitoring neuronal activity with an indicator is that the indicator itself minimally affects activity. Here, using common adeno-associated viral (AAV) transduction procedures, we describe spatially confined aberrant Ca2+micro-waves slowly travelling through the hippocampus following expression of GCaMP6, GCaMP7 or R-CaMP1.07 driven by the synapsin promoter with AAV-dependent gene transfer, in a titre-dependent fashion. Ca2+micro-waves developed in hippocampal CA1 and CA3, but not dentate gyrus (DG) nor neocortex, were typically first observed at 4 weeks after viral transduction, and persisted up to at least 8 weeks. The phenomenon was robust, observed across laboratories with various experimenters and setups. Our results indicate that aberrant hippocampal Ca2+micro-waves depend on the promoter and viral titre of the GECI, density of expression as well as the targeted brain region. We used an alternative viral transduction method of GCaMP which avoids this artifact. The results show that commonly used Ca2+-indicator AAV transduction procedures can produce artefactual Ca2+responses. Our aim is to raise awareness in the field of these artefactual transduction-induced Ca2+micro-waves and we provide a potential solution.Impact statement: Common AAV transduction procedures induce artefactual spatially confined Ca2+waves in the hippocampus.
FLASHQuant: a fast algorithm for proteoform quantification in top-down proteomics
Authors: Kim Jihyung , Jeong Kyowon , Kaulich Philipp T. , Winkels Konrad , Tholey Andreas , Kohlbacher Oliver 
Published: November 2023

ABSTRACTLiquid chromatography-mass spectrometry (LC-MS) based top-down proteomics (TDP) is an essential method for the analysis of intact proteoforms. The accurate quantification of individual proteoforms is a crucial step in identifying proteome-wide alterations in different biological conditions. Label-free quantification (LFQ) is the most common method for proteoform quantification as it requires no additional costly labeling. In TDP, due to frequent co-elution and complex signal structures, overlapping signals deriving from multiple proteoforms complicate accurate quantification. Here, we introduce FLASHQuant for MS1-level LFQ analysis in TDP, which is capable of automatically resolving and quantifying co-eluting proteoforms. FLASHQuant performs highly accurate and reproducible quantification in short runtimes of just a few minutes per LC-MS run. To validate the proteoforms reported by FLASHQuant, we evaluated them with identified proteoforms confirmed by tandem mass spectrometry, which showed high match rates. FLASHQuant is publicly available as platform-independent open-source software athttps://openms.org/flashquant/.
Protocol for 3D Virtual Histology of Unstained Human Brain Tissue using Synchrotron Radiation Phase-Contrast Microtomography
Authors: Lee Ju Young , Donato Sandro , Mack Andreas F. , Mattheus Ulrich , Tromba Giuliana , Longo Elena , D’Amico Lorenzo , Mueller Sebastian , Shiozawa Thomas , Bause Jonas , Scheffler Klaus , Longo Renata , Hagberg Gisela E. 
Published: November 2023

AbstractX-ray phase-contrast micro computed tomography using synchrotron radiation (SR PhC-µCT) offers unique 3D imaging capabilities for visualizing microstructure of the human brain. Its applicability for unstained soft tissue is an area of active research. Acquiring images from a tissue block without needing to section it into thin slices, as required in routine histology, allows for investigating the microstructure in its natural 3D space. This paper presents a detailed step-by-step guideline for imaging unstained human brain tissue at resolutions of a few micrometers with SR PhC-µCT implemented at SYRMEP, the hard X-ray imaging beamline of Elettra, the Italian synchrotron facility. We present examples of how blood vessels and neurons appear in the images acquired with isotropic 5 µm and 1 µm voxel sizes. Furthermore, the proposed protocol can be used to investigate important biological substrates such as neuromelanin or corpora amylacea. Their spatial distribution can be studied using specifically tailored segmentation tools that are validated by classical histology methods. In conclusion, SR PhC-µCT using the proposed protocols, including data acquisition and image processing, offers viable means of obtaining information about the anatomy of the human brain at the cellular level in 3D.
Metabolic Regulation of Single Synaptic Vesicle Exo- and Endocytosis in Hippocampal Synapses
Authors: Myeong Jongyun , Stunault Marion I , Klyachko Vitaly A , Ashrafi Ghazaleh 
Published: November 2023

SUMMARYGlucose has long been considered a primary source of energy for synaptic function. However, it remains unclear under what conditions alternative fuels, such as lactate/pyruvate, contribute to powering synaptic transmission. By detecting individual release events in cultured hippocampal synapses, we found that mitochondrial ATP production from oxidation of lactate/pyruvate regulates basal vesicle release probability and release location within the active zone (AZ) evoked by single action potentials (APs). Mitochondrial inhibition shifted vesicle release closer to the AZ center, suggesting that the energetic barrier for vesicle release is lower in the AZ center that the periphery. Mitochondrial inhibition also altered the efficiency of single AP evoked vesicle retrieval by increasing occurrence of ultrafast endocytosis, while inhibition of glycolysis had no effect. Mitochondria are sparsely distributed along hippocampal axons and we found that nerve terminals containing mitochondria displayed enhanced vesicle release and reuptake during high-frequency trains, irrespective of whether neurons were supplied with glucose or lactate. Thus, synaptic terminals can entirely bypass glycolysis to robustly maintain the vesicle cycle using oxidative fuels in the absence of glucose. These observations further suggest that mitochondrial metabolic function not only regulates several fundamental features of synaptic transmission but may also contribute to modulation of short-term synaptic plasticity.HighlightsSynapses can sustain neurotransmission across various activity levels by bypassing glycolysis and utilizing oxidative fuels.Mitochondria, but not glycolysis, regulate release probability and nanoscale organization of vesicle release within the active zone.Mitochondrial inhibition increases the occurrence of vesicle retrieval via ultra-fast endocytosis.Mitochondrial localization in nerve terminals enhances vesicle release and retrieval in the absence of glucose, representing a form of synaptic plasticity.