bluuebunny/crossref_metadata_2025_split huggingface dataset:
ALPHA: A High Throughput System for Quantifying Growth In Aquatic Plants
Authors: Robinson Kassidy A. , Augoustides Victoria , Madenyika Tanaka , Sartor Ryan C. 
Published: July 2024

AbstractThe need for more sustainable agricultural systems is becoming increasingly apparent. The global demand for agricultural products — food, feed, fuel and fiber — will continue to increase as the global population continues to grow. This challenge is compounded by climate change. Not only does a changing climate make it difficult to maintain stable yields but current agricultural systems are a major source of greenhouse gas emissions and continue to drive the problem further. Therefore, future agricultural systems must not only increase production but also significantly decrease negative environmental impacts. One approach to addressing this is to begin breeding and cultivating new plant species that have fundamental sustainability advantages over our existing crops. The Lemnaceae, a.k.a duckweeds, are one such species that have potential to increase output and reduce the negative environmental impacts of agricultural production. Herein we describe the Automated Lab-scale PHenotyping Apparatus, ALPHA, for high-throughput phenotyping of Lemnaceae. ALPHA is being used for selective breeding of one species,Lemna gibba, toward the goal of creating a new crop for use in sustainable agricultural systems. ALPHA can be used on many small aquatic plant species to assess growth rates in different environmental conditions. A proof of principle use case is demonstrated where ALPHA is used to determine saltwater tolerance of 6 different varieties ofL. gibba.
A replicable and modular benchmark for long-read transcript quantification methods
Authors: Zare Jousheghani Zahra , Singh Noor Pratap , Patro Rob 
Published: July 2024

AbstractWe provide a replicable benchmark for long-read transcript quantification, and evaluate the performance of some recently-introduced tools on several synthetic long-read RNA-seq datasets. This benchmark is designed to allow the results to be easily replicated by other researchers, and the structure of the underlyingSnakemakeworkflow is modular to make the addition of new tools or new data sets relatively easy. In analyzing previously assessed simulations, we find discrepancies with recently-published results. We also demonstrate that the robustness of certain approaches hinge critically on the quality and “cleanness” of the simulated data.AvailabilityThe Snakemake scripts for the benchmark are available athttps://github.com/COMBINE-lab/lr_quant_benchmarks, the data used as input for the benchmarks (reference sequences, annotations, and simulated reads) are available athttps://doi.org/10.5281/zenodo.13130623.
Immunodominant extracellular loops ofTreponema pallidumFadL outer membrane proteins elicit antibodies with opsonic and growth-inhibitory activities
Authors: Delgado Kristina N. , Caimano Melissa J. , Orbe Isabel C. , Vicente Crystal F. , La Vake Carson J. , Grassmann André A. , Moody M. Anthony , Radolf Justin D. , Hawley Kelly L. 
Published: July 2024

AbstractThe global resurgence of syphilis has created a potent stimulus for vaccine development. To identify potentially protective antibodies (Abs) againstTreponema pallidum(TPA), we usedPyrococcus furiosusthioredoxin (PfTrx) to display extracellular loops (ECLs) from threeTPAouter membrane protein families (outer membrane factors for efflux pumps, eight-stranded β-barrels, and FadLs) to assess their reactivity with immune rabbit serum (IRS). Five ECLs from the FadL orthologs TP0856, TP0858 and TP0865 were immunodominant. Rabbits and mice immunized with these fivePfTrx constructs produced ECL-specific Abs that promoted opsonophagocytosis ofTPAby rabbit peritoneal and murine bone marrow-derived macrophages at levels comparable to IRS and mouse syphilitic serum. ECL-specific rabbit and mouse Abs also impaired viability, motility, and cellular attachment of spirochetes duringin vitrocultivation. The results support the use of ECL-based vaccines and suggest that ECL-specific Abs promote spirochete clearance via Fc receptor-independent as well as Fc receptor-dependent mechanisms.Author SummaryThe resurgence of syphilis emphasizes the critical need for vaccine development againstTreponema pallidum(TPA). Research utilizing immune rabbit serum (IRS) suggests that an effective syphilis vaccine should induce “functional” antibodies (Abs) capable of enhancing the opsonophagocytosis of treponemes by activated macrophages. Structural models ofTPAouter membrane proteins (OMPs), specifically the extracellular loops (ECLs), guided the identification of potential vaccine candidates. Antigenic analysis with IRS of individual ECLs from threeTPAOMP families scaffolded ontoPyrococcus furiosusthioredoxin (PfTrx) revealed five FadL antigenic ECLs. Immunization with immunodominant ECL antigens elicited robust ECL-specific Abs, demonstrating functional opsonic activity in the opsonophagocytosis assays. Furthermore, these Abs effectively inhibited the growth inhibition ofin vitro-cultivatedTPAin both rabbit and mouse models. Our findings underscore the value of antigenic analysis in identifying promisingTPAOMP ECL vaccine targets and highlight the multifaceted protective capacity of ECL Abs againstTPA. This approach also extends to identifying potential OMP vaccinogens in other bacterial pathogens, offering valuable insights for broader vaccine development strategies.
Spreading depolarizations exhaust neuronal ATP in a model of cerebral ischemia
Authors: Schoknecht Karl , Baeza-Lehnert Felipe , Hirrlinger Johannes , Dreier Jens P. , Eilers Jens 
Published: July 2024

AbstractSpreading depolarizations (SDs) have been identified in various brain pathologies. SDs increase the cerebral energy demand and, concomitantly, oxygen consumption, which indicates enhanced synthesis of adenosine triphosphate (ATP) by oxidative phosphorylation. Therefore, SDs are considered particularly detrimental during reduced supply of oxygen and glucose. However, measurements of intracellular neuronal ATP ([ATP]i), ultimately reporting the balance of ATP synthesis and consumption during SDs, have not yet been conducted.In this study, we investigated neuronal ATP homeostasis during SDs using 2-photon imaging in acute brain slices from adult mice, expressing the ATP sensor ATeam1.03YEMKin neurons. SDs were induced by application of potassium chloride or by oxygen and glucose deprivation (OGD) and were detected by recording the local field potential, extracellular potassium, as well as the intrinsic optical signal.We found that, in the presence of oxygen and glucose, SDs were accompanied by a substantial but transient drop in neuronal [ATP]i. OGD, which prior to SD was accompanied by a slight reduction in [ATP]ionly, led to an even larger, terminal drop in [ATP]iduring SDs. Subsequently, we investigated whether neurons could still regenerate ATP if oxygen and glucose were promptly resupplied following SD detection. The data show that ATP depletion was essentially reversible in most cells.Our findings indicate that SDs are accompanied by a substantial increase in ATP consumption beyond production. This, under conditions that mimic reduced blood supply, leads to a breakdown of [ATP]i. Therefore, our findings support therapeutic strategies targeting SDs after cerebral ischemia.Significance statementSpreading depolarizations occur in many brain pathologies, and are suggested to contribute to brain damage through a mismatch in energy supply and demand. However, measurements directly demonstrating an imbalance between ATP production and consumption, particularly in individual neurons, have not been reported. Here we show that spreading depolarizations lead to a transient decrease in intracellular neuronal ATP even in presence of ample glucose and oxygen. When the supply of oxygen and glucose was interrupted, ATP declined gradually until spreading depolarization led to the exhaustion of neuronal ATP. This process would be terminal without the renewed supply of oxygen and glucose. Therefore, therapies targeting spreading depolarizations could preserve neuronal ATP or delay its loss in brain pathologies.
HIV-1 Vif disrupts phosphatase feedback regulation at the kinetochore, leading to a pronounced pseudo-metaphase arrest
Authors: Ghone Dhaval , Evans Edward L. , Bandini Madison , Stephenson Kaelyn G. , Sherer Nathan M. , Suzuki Aussie 
Published: July 2024

AbstractVirion Infectivity Factor (Vif) of the Human Immunodeficiency Virus type 1 (HIV-1) targets and degrades cellular APOBEC3 proteins, key regulators of intrinsic and innate antiretroviral immune responses, thereby facilitating HIV-1 infection. While Vif’s role in degrading APOBEC3G is well-studied, Vif is also known to cause cell cycle arrest, but the detailed nature of Vif’s effects on the cell cycle has yet to be delineated. In this study, we employed high-temporal single-cell live imaging and super-resolution microscopy to monitor individual cells during Vif-induced cell cycle arrest. Our findings reveal that Vif does not affect the G2/M boundary as previously thought. Instead, Vif triggers a unique and robust pseudo-metaphase arrest, distinct from the mild prometaphase arrest induced by Vpr. During this arrest, chromosomes align properly and form the metaphase plate, but later lose alignment, resulting in polar chromosomes. Notably, Vif, unlike Vpr, significantly reduces the levels of both Protein Phosphatase 1 (PP1) and 2A (PP2A) at kinetochores, which regulate chromosome-microtubule interactions. These results unveil a novel role for Vif in kinetochore regulation that governs the spatial organization of chromosomes during mitosis.
Capillary connections between sensory circumventricular organs and adjacent parenchyma enable local volume transmission
Authors: Yao Yifan , Chen Yannan , Tomer Raju , Silver Rae 
Published: July 2024

AbstractAmong contributors to diffusible signaling are portal systems which join two capillary beds through connecting veins (Dorland 2020). Portal systems allow diffusible signals to be transported in high concentrations directly from one capillary bed to the other without dilution in the systemic circulation. Two portal systems have been identified in the brain. The first was discovered almost a century ago and connects the median eminence to the anterior pituitary gland (Popa & Fielding 1930). The second was discovered a few years ago, and links the suprachiasmatic nucleus to the organum vasculosum of the lamina terminalis, a sensory circumventricular organ (CVO) (Yao et al. 2021). Sensory CVOs bear neuronal receptors for sensing signals in the fluid milieu (McKinley et al. 2003). They line the surface of brain ventricles and bear fenestrated capillaries, thereby lacking blood brain barriers. It is not known whether the other sensory CVOs, namely the subfornical organ (SFO), and area postrema (AP) form portal neurovascular connections with nearby parenchymal tissue. This has been difficult to establish as the structures lie at the midline and protrude into the ventricular space. To preserve the integrity of the vasculature of CVOs and their adjacent neuropil, we combined iDISCO clearing and light-sheet microscopy to acquire volumetric images of blood vessels. The results indicate that there is a portal pathway linking the capillary vessels of the SFO and the posterior septal nuclei, namely the septofimbrial nucleus and the triangular nucleus of the septum. Unlike the latter arrangement, the AP and the nucleus of the solitary tract share their capillary beds. Taken together, the results reveal that all three sensory circumventricular organs bear specialized capillary connections to adjacent neuropil, providing a direct route for diffusible signals to travel from their source to their targets.
CIB2 function is distinct from Whirlin in the development of cochlear stereocilia staircase pattern
Authors: Giese Arnaud P. J. , Parker Andrew , Rehman Sakina , Brown Steve D. M. , Riazuddin Saima , Vander Kooi Craig W. , Bowl Michael R. , Ahmed Zubair M. 
Published: July 2024

SummaryVariations in genes coding for calcium and integrin binding protein 2 (CIB2) and whirlin cause deafness both in humans and mice. We previously reported that CIB2 binds to whirlin, and is essential for normal staircase architecture of auditory hair cells stereocilia. Here, we refine the interacting domains between these proteins and provide evidence that both proteins have distinct role in the development and organization of stereocilia bundles required for auditory transduction. Using a series of CIB2 and whirlin deletion constructs and nanoscale pulldown (NanoSPD) assays, we localized the regions of CIB2 that are critical for interaction with whirlin. AlphaFold 2 multimer, independently identified the same interacting regions between CIB2 and whirlin proteins, providing a detailed structural model of the interaction between the CIB2 EF2 domain and whirlin HHD2 domain. Next, we investigated genetic interaction between murineCib2andWhrnusing genetic approaches. Hearing in mice double heterozygous for functionally null alleles (Cib2KO/+;Whrnwi/+) was similar to age-matched wild type mice, indicating that partial deficiency for bothCib2andWhrndoes not impair hearing. Double homozygous mutant mice (Cib2KO/KO;Whrnwi/wi) had profound hearing loss and cochlear stereocilia exhibited a predominant phenotype seen in singleWhrnwi/wimutants. Furthermore, over-expression ofWhrninCib2KO/KOmice did not rescue the stereocilia morphology. These data suggest that, CIB2 is multifunctional, with key independent functions in development and/or maintenance of stereocilia staircase pattern in auditory hair cells.
Modular small RNA drives the emergence of virulence traits and environmental trade-offs inVibrio cholerae
Authors: Balasubramanian Deepak , Crist Cole , Almagro-Moreno Salvador 
Published: July 2024

ABSTRACTThe sole gain of laterally acquired virulence genes does not fully explain the transition of environmental strains into human pathogens. To date, the specific molecular drivers and fitness trade-offs that enable some strains within a population to undergo this process remain enigmatic. Here, we describe a small RNA (sRNA) with a unique modular structure that shapes the evolution of toxigenicVibrio cholerae, the agent of cholera. The sRNA comprises of a highly variable 5’ module located within theompUORF and a conserved 3’ one downstream from the gene. This atypical location confers a distinct bimodular structure to the OmpU-encoded sRNA (OueS), generating allelic variants that differentially contribute to the emergence of virulence potential in some strains and associated fitness trade-offs between human infection and environmental survival. Unlike environmental counterparts, the OueS allele from toxigenic strains controls phenotypes essential during host colonization: a) stringently inhibits biofilm formation via a novel sRNA-sRNA interaction by suppressing the iron-responsive sRNA RyhB, and b) confers resistance against intestinal bacteriophages by activating the recently discovered CBASS phage defense system. Toxigenic OueS is also required for successful intestinal colonization and, as the first known example of its kind, acts as a functional surrogate of the master virulence regulator ToxR, controlling over 84% of its regulome. On the other hand, isogenic strains encoding environmental alleles of OueS exhibit higher competitive fitness than those harboring toxigenic ones during colonization of natural reservoirs such as crustaceans and phytoplankton. Our findings provide critical insights into the evolution of toxigenicV. choleraeand reveal specific molecular mechanisms and fitness costs associated with the emergence of pathogenic traits in bacteria.
Enhancer AAVs for targeting spinal motor neurons and descending motor pathways in rodents and macaque
Authors: Kussick Emily , Johansen Nelson , Taskin Naz , Wynalda Brooke , Martinez Refugio , Groce Erin L. , Reding Melissa , Liang Elizabeth , Shulga Lyudmila , Huang Cindy , Casper Tamara , Clark Michael , Ho Windy , Gao Yuan , van Velthoven Cindy T.J. , Sobieski Cassandra , Ferrer Rebecca , Berg Melissa R. , Curtis Britni C. , English Chris , Day Jesse C. , Fortuna Michal , Donadio Nicholas , Newman Dakota , Yao Shenqin , Chakka Anish Bhaswanth , Goldy Jeff , Torkelson Amy , Guzman Junitta B. , Chakrabarty Rushil , Nguy Beagen , Guilford Nathan , Pham Trangthanh H. , Wright Vonn , Ronellenfitch Kara , Gudsnuk Kathryn , Thyagarajan Bargavi , Smith Kimberly A. , Dee Nick , Zeng Hongkui , Yao Zizhen , Tasic Bosiljka , Levi Boaz P. , Hodge Rebecca , Bakken Trygve E. , Lein Ed S. , Ting Jonathan T. , Daigle Tanya L. 
Published: July 2024

SummaryExperimental access to cell types within the mammalian spinal cord is severely limited by the availability of genetic tools. To enable access to lower motor neurons (LMNs) and LMN subtypes, which function to integrate information from the brain and control movement through direct innervation of effector muscles, we generated single cell multiome datasets from mouse and macaque spinal cords and discovered putative enhancers for each neuronal population. We cloned these enhancers into adeno-associated viral vectors (AAVs) driving a reporter fluorophore and functionally screened them in mouse. The most promising candidate enhancers were then extensively characterized using imaging and molecular techniques and further tested in rat and macaque to show conservation of LMN labeling. Additionally, we combined enhancer elements into a single vector to achieve simultaneous labeling of upper motor neurons (UMNs) and LMNs. This unprecedented LMN toolkit will enable future investigations of cell type function across species and potential therapeutic interventions for human neurodegenerative diseases.
Enzymatic synthesis of isotopically labeled hydrogen peroxide for mass spectrometry-based applications
Authors: Hoare Margaret , Tan Ruiyue , Militi Isabella , Welle Kevin A. , Swovick Kyle , Hryhorenko Jennifer R. , Ghaemmaghami Sina 
Published: July 2024

AbstractMethionine oxidation is involved in multiple biological processes including protein misfolding and enzyme regulation. However, it is often challenging to measure levels of methionine oxidation by mass spectrometry, in part due to the prevalence of artifactual oxidation that occurs during sample preparation and ionization steps of typical proteomic workflows. Isotopically labeled hydrogen peroxide (H218O2) can be used to block unoxidized methionines and enable accurate measurement ofin vivolevels of methionine oxidation. However, H218O2is an expensive reagent that can be difficult to obtain from commercial sources. Here, we report a method for synthesizing H218O2in house. Glucose oxidase catalyzes the oxidation of β-D-glucose and produces hydrogen peroxide in the process. We took advantage of this reaction to enzymatically synthesize H218O2from18O2and assessed its concentration, purity, and utility in measuring methionine oxidation levels by mass spectrometry.
Mechanism of neurodegeneration mediated by clonal inflammatory microglia
Authors: Vicario Rocio , Fragkogianni Stamatina , Pokrovskii Maria , Mayer Carina , Lopez-Rodrigo Estibaliz , Hu Yang , Ogishi Masato , Alberdi Araitz , Baako Ann , Ay Oyku , Plu Isabelle , Sazdovitch Véronique , Heritier Sebastien , Cohen-Aubart Fleur , Shor Natalia , Miyara Makoto , Nguyen-Khac Florence , Viale Agnes , Idbaih Ahmed , Amoura Zahir , Rosenblum Marc K. , Zhang Haochen , Karnoub Elias-Ramzey , Sashittal Palash , Jakatdar Akhil , Iacobuzio-Donahue Christine A. , Abdel-Wahab Omar , Tabar Viviane , Socci Nicholas D. , Elemento Olivier , Diamond Eli L , Boisson Bertrand , Casanova Jean-Laurent , Seilhean Danielle , Haroche Julien , Donadieu Jean , Geissmann Frederic 
Published: July 2024

SummaryLangerhans cell Histiocytosis (LCH) and Erdheim-Chester disease (ECD) are clonal myeloid disorders, associated with MAP-Kinase activating mutations and an increased risk of neurodegeneration. Surprisingly, we found pervasive PU.1+microglia mutant clones across the brain of LCH and ECD patients with and without neurological symptoms, associated with microgliosis, reactive astrocytosis, and neuronal loss. The disease predominated in the grey nuclei of the rhombencephalon, a topography attributable to a local proliferative advantage of mutant microglia. Presence of clinical symptoms was associated with a longer evolution of the disease and a larger size of PU.1+clones (p= 0.0003). Genetic lineage tracing of PU.1+clones suggest a resident macrophage lineage or a bone marrow precursor origin depending on patients. Finally, a CSF1R-inhibitor depleted mutant microglia and limited neuronal loss in mice suggesting an alternative to MAPK inhibitors. These studies characterize a progressive neurodegenerative disease, caused by clonal proliferation of inflammatory microglia (CPIM), with a decade(s)-long preclinical stage of incipient disease that represent a therapeutic window for prevention of neuronal death.
Aggregation Dynamics of a 150 kDa Aβ42 Oligomer: Insights from Cryo Electron Microscopy and Multimodal Analysis
Authors: Kamalaldinezabadi S. Shirin , Watzlawik Jens O. , Rosenberry Terrone L. , Paravastu Anant K. , Stagg Scott M. 
Published: July 2024

I.AbstractProtein misfolding is a widespread phenomenon that can result in the formation of protein aggregates, which are markers of various disease states, including Alzheimer’s disease (AD). In AD, amyloid beta (Aβ) peptides, particularly Aβ40 and Aβ42, are key players in the disease’s progression, as they aggregate to form amyloid plaques and contribute to neuronal toxicity. Recent research has shifted attention from solely Aβ fibrils to also include Aβ protofibrils and oligomers as potentially critical pathogenic agents. Particularly, oligomers demonstrate greater toxicity compared to other Aβ specie. Hence, there is an increased interest in studying the correlation between toxicity and their structure and aggregation pathway. The present study investigates the aggregation of a 150 kDa Aβ42 oligomer that does not lead to fibril formation over time. Using negative stain transmission electron microscopy (TEM), size exclusion chromatography (SEC), dynamic light scattering (DLS), and cryo-electron microscopy (cryo-EM), we demonstrate that 150 kDa Aβ42 oligomers form higher-order string-like assemblies over time. The strings are unique from the classical Aβ fibril structures. The significance of our work lies in elucidating molecular behavior of a novel non-fibrillar form of Aβ42 aggregate.
The structural basis for the selective antagonism of soluble TNF-alpha by variable new antigen receptors
Authors: Ubah Obinna C. , Lake Eric W. , Priyanka Stella , Shi Ke , Moeller Nicholas H. , Porter Andrew J. , Aihara Hideki , LeBeau Aaron M. , Barelle Caroline J. 
Published: July 2024

AbstractThe pro-inflammatory cytokine tumor necrosis factor-alpha (TNF)-α is synthesized as transmembrane TNF-α (tmTNF-α) where proteolytic processing releases soluble TNF-α (sTNF-α). tmTNF-α can act as either a ligand by activating TNF receptors, or a receptor that transmits outside-to-inside signals (reverse signalling) after binding to native receptors. All TNF-α therapies bind tmTNF-α and induce reverse signalling which can result in immunosuppression leading to infection. We present crystal structures of two anti-TNF-α Variable New Antigen Receptors (VNAR) in complex with sTNF-αviatwo distinct epitopes. The VNAR-D1 recognized an epitope that selectively engaged sTNF-α while VNAR-C4 bound an epitope that overlapped with other biologic therapies. In activated CD4+T cells, our VNARs did not bind tmTNF-α in contrast to commercially available therapies that demonstrated induction of reverse signalling. Our findings suggest that neutralisation through a unique mechanism may lead to anti-TNF-α agents with an improved safety profile that will benefit high-risk patients.