bluuebunny/crossref_metadata_2025_split huggingface dataset:
14-3-3 binding maintains the Parkinson’s associated kinase LRRK2 in an inactive state
Authors: Martinez Fiesco Juliana A. , Li Ning , Alvarez de la Cruz Astrid , Metcalfe Riley D. , Beilina Alexandra , Cookson Mark R. , Zhang Ping 
Published: November 2024

AbstractLeucine-rich repeat kinase 2 (LRRK2) is a central player in cellular signaling and a significant contributor to Parkinson’s disease (PD) pathogenesis. 14-3-3 proteins are essential regulators of LRRK2, modulating its activity. Here, we present the cryo- electron microscopy structure of the LRRK2:14-3-32autoinhibitory complex, showing that a 14-3-3 dimer stabilizes an autoinhibited LRRK2 monomer by binding to key phosphorylation sites and the COR-A and COR-B subdomains within the Roc-COR GTPase domain of LRRK2. This interaction locks LRRK2 in an inactive conformation, restricting LRR domain mobility and preventing dimerization and oligomer formation. Our mutagenesis studies reveal that PD-associated mutations at the COR:14-3-3 interface and within the GTPase domain reduce 14-3-3 binding, diminishing its inhibitory effect on LRRK2. These findings provide a structural basis for understanding how LRRK2 likely remains dormant within cells, illuminate aspects of critical PD biomarkers, and suggest therapeutic strategies to enhance LRRK2-14-3-3 interactions to treat PD and related disorders.
Single CAR-Dual target: Intracranial Delivery of Anti-PD-L1 CAR T Cells Effectively Eradicates Glioma and Immunosuppressive Cells in the Tumor Microenvironment
Authors: Ulloa-Navas Maria J. , Luo Yan , Sanchez-Garavito Jesus E , Qie Yaqing , Jones Vanessa K , Brooks Mieu M , Aramburu-Berckemeyer Manuela , Hundal Tanya , Gadd Martha E. , Gomez-Palmero Cristina , Brim Andrew D. , Rivera-Valentin Rocio , Basil Aleeshba N. , Tutor-New Frederick Q. , Hirdler Jacob B. , Irani Sarosh R , Dronca Roxana , Kharfan-Dabaja Mohamed A , Ren Yingxue , Dong Haidong , Qin Hong , Quinones-Hinojosa Alfredo 
Published: November 2024

SUMMARYWith the goal to overcome the limited treatment options and poor prognosis of glioblastoma (GBM), we have developed a PD-L1-targeting CAR T cell therapy, MC9999. In vitro experiments with MC9999 CAR T cells derived from GBM patients exhibited potent, antigen-specific cytotoxicity against autologous tumor cells and immunosuppressive cells within the tumor microenvironment (TME). In an orthotopic GBM model using patient-derived brain tumor-initiating cells, the intracranial delivery of MC9999 CAR T cells eradicated established tumors and improved survival. Single-cell RNA sequencing indicated that MC9999 CAR T cells activate interferon pathways, leading to GBM cell apoptosis. Multi-immunohistochemistry confirmed localized PD-L1 expression on tumor cells and TME-residing macrophages, but not in neurons or glia in patient tissue. The local delivery of MC9999 CAR T cells may be a safe, effective approach for simultaneously targeting PD-L1-positive GBM and its immunosuppressive TME and a strategy to overcome immune evasion and enhance the therapeutic potency of CAR T cell therapy against GBM.
Neuronal heterogeneity of normalization strength in a circuit model
Authors: Song Deying , Ruff Douglas , Cohen Marlene , Huang Chengcheng 
Published: November 2024

AbstractThe size of a neuron’s receptive field increases along the visual hierarchy. Neurons in higher-order visual areas integrate information through a canonical computation called normalization, where neurons respond sublinearly to multiple stimuli in the receptive field. Neurons in the visual cortex exhibit highly heterogeneous degrees of normalization. Recent population recordings from visual cortex find that the interactions between neurons, measured by spike count correlations, depend on their normalization strengths. However, the circuit mechanism underlying the heterogeneity of normalization is unclear. In this work, we study normalization in a spiking neuron network model of visual cortex. The model produces a range of neuronal heterogeneity of normalization strength and the heterogeneity is highly correlated with the inhibitory current each neuron receives. Our model reproduces the dependence of spike count correlations on normalization as observed in experimental data, which is explained by the covariance with the inhibitory current. We find that neurons with stronger normalization are more sensitive to contrast differences in images and encode information more efficiently. In addition, networks with more heterogeneity in normalization encode more information about visual stimuli. Together, our model provides a mechanistic explanation of heterogeneous normalization strengths in the visual cortex, and sheds new light on the computational benefits of neuronal heterogeneity.
The pentameric chloride channel BEST1 is activated by extracellular GABA
Authors: Pant Swati , Tam Stephanie W. , Long Stephen B. 
Published: November 2024

AbstractBestrophin 1 (BEST1) is chloride channel expressed in the eye, central nervous system (CNS), and other tissues in the body. A link between BEST1 and the principal inhibitory neurotransmitter γ-aminobutyric acid (GABA) has been proposed. The most appreciated receptors for extracellular GABA are the GABABG-protein coupled receptors and the pentameric GABAAchloride channels, both of which have fundamental roles in the CNS. Here, we demonstrate that BEST1 is directly activated by GABA. Through functional studies and atomic-resolution structures of human and chicken BEST1, we identify a GABA binding site on the channel’s extracellular side and determine the mechanism by which GABA binding induces opening of the channel’s central gate. This same gate is activated by intracellular [Ca2+], indicating that BEST1 is controlled by ligands from both sides of the membrane. The studies demonstrate that BEST1, which shares no structural homology with GABAA, is a GABA-activated chloride channel. The physiological implications of this finding remain to be studied.Significance Statementγ-aminobutyric acid (GABA) is the principal inhibitory neurotransmitter in the central nervous system. Extracellular GABA is primarily sensed by GABABG-protein coupled receptors, and GABAApentameric chloride channels. We show that the chloride channel bestrophin-1 (BEST1) is also activated by extracellular GABA. The application of GABA, but not glycine or other endogenous molecules we tested, markedly potentiates chloride currents through the channel. Structural studies combined with electrophysiology and other functional studies reveal the mechanism of GABA activation. GABA binding within the outer entryway of the channel allosterically controls its gate, ‘the neck’. Molecular interactions with GABA resemble those in GABAAreceptors, despite a lack of homology between the channels. The physiological significance of GABA-activation in BEST1 remains to be studied.
A modular gate system for autonomous control of rodent behavior
Authors: Lester Adam W. , Kaur Gurnoor , Djafri Nadira , Madhav Manu S. 
Published: November 2024

AbstractRodent mazes have been used for decades to study the neural basis of behavior. Advancements in rapid prototyping techniques and access to affordable electronics allows laboratories with sufficient expertise in engineering and programming to customize and construct maze apparatuses and behavioral tasks, thereby increasing the ability of their studies to answer specific scientific questions. We designed and built a rodent gate system that lowers this bar of expertise even further. The NC4gate system is a robust mechanical design that can be built using low-cost hardware and execute thousands of cycles before maintenance. Up to 512 gates can be controlled using a single computer. Users can control the gates interactively using a Python-based graphical interface and programmatically using an extensible API. We hope that the open-source hardware / software and extensive documentation enables laboratories to build these affordable and robust gates and seamlessly incorporate automatic behavior control into their existing or new rodent tasks.Significance StatementRodent mazes are used by thousands of laboratories and research institutions across the world to study learning and memory, as well as the effects of pharmacological, genetic and environmental manipulations. Ideally, maze and task designs should be customized to the scientific questions at hand. It is challenging, however, for many laboratories to build, program, and operate custom mazes, requiring them instead to rely on expensive and proprietary commercial solutions. The most complex components of most mazes are moving gates that restrict and direct rodent behavior. Here we provide the open-source hardware and software for a gate system that is extensible, affordable and robust, removing this critical barrier to customized mazes.
A Multi-Strain, Biofilm-Forming Cocktail ofBacillusspp. andPediococcusspp. Alters the Microbial Composition on Polyethylene Calf Housing Surfaces
Authors: Reynolds C.A. , Scuderi R.A. , Skidmore A.L. , Duniere L. , Morrison S.Y. 
Published: November 2024

ABSTRACTApplication of a beneficial microbial cocktail ofBacillusspp. andPediococcusspp. was evaluated first for adherence to polyethylene calf hutch material, and second, to determine if application in situ to individual calf hutches post-cleaning influenced surface recolonization by enteric pathogens. Three treatments were utilized: 1) no application (NC), 2) chlorine-free, distilled water (DW), or 3) an application of a microbial inoculant containingBacillusspp. andPediococcusspp. at a concentration of 0.4 g/m2of hutch space (LF). Thirty-six 15 × 15 cm pieces of naïve, sterile polyethylene calf hutch material received either NC or LF, were incubated at 28°C, and bacterial growth was evaluated by total aerobic plate counts at 24, 48, and 72 h post-application. Thirty polyethylene calf hutches (n = 10/treatment) were randomized to either NC, DW, or LF 24 h after cleaning. Calves were placed in the hutches 24 h after treatment application and monitored daily for 28 d. In situ surface samples were randomized by time from five unique locations within the calf hutch interior: 24 h post-cleaning, then 24 h, 7 d, 14 d, and 21 d post-application. Total aerobic plate counts and culture-independent approaches RT-qPCR and 16S amplicon sequencing were used to detect and identify the composition of the bacterial community in situ. The bacteria in the inoculant were able to successfully colonize on polyethylene, and application to individual polyethylene calf housing in situ influenced microbial diversity and reduced the presence of some undesirable bacteria on high-contact interior surfaces.IMPORTANCEDue to its multifactorial nature, neonatal calf diarrhea can be difficult to manage on farms. Clean housing environments are a critical disease control point, especially for calves less than one month of age. Application of a beneficial biofilm-forming bacterial product after cleaning of neonatal calf housing may influence the microbial communities present on the surface, particularly those that may present disease risk to calves in early life.
Divergent Visuomotor Strategies in Teleosts: Neural Circuit Mechanisms in Zebrafish andDanionella cerebrum
Authors: Fouke Kaitlyn E. , He Zichen , Loring Matthew D. , Naumann Eva A. 
Published: November 2024

AbstractMany animals respond to sensory cues with species-specific coordinated movements to successfully navigate their environment. However, the neural mechanisms that support diverse sensorimotor transformations across species with distinct navigational strategies remain largely unexplored. By comparing related teleost species, zebrafish (Danio rerio, ZF) andDanionella cerebrum(DC), we investigated behavioral patterns and neural architectures during the visually guided optomotor response (OMR). Closed-loop behavioral tracking during visual stimulation revealed that larvalZFemploy burst-and-glide locomotion, while larvalDCdisplay continuous, smooth swimming punctuated with sharp directional turns. AlthoughDCachieve higher average speeds, they lack the direction-dependent velocity modulation observed inZF. Whole-brain two-photon calcium imaging and tail tracking in head-fixed fish reveals that both species exhibit direction-selective motion encoding in homologous regions, including the retinorecipient pretectum, withDCexhibiting fewer binocular, direction-selective neurons overall. Kinematic analysis of head-fixed behavior reveals thatDCsustain significantly longer directed swim events across all stimuli thanZF, highlighting the divergent visuomotor strategies, withZFreducing tail movement duration in response to oblique, turn-inducing stimuli. Lateralized motor-associated neural activity in the medial and anterior hindbrain of both species suggests a shared circuit motif, with distinct neural circuits that independently control movement vigor and direction. These findings highlight the diversity in visuomotor strategies among teleost species, underscored by shared sensorimotor neural circuit motifs, and establish a robust framework for unraveling the neural mechanisms driving continuous and discrete visually guided locomotion, paving the way for deeper insights into vertebrate sensorimotor functions.Research HighlightsLarval DCexhibit faster swimming thanZF, matching the direction of visual motion.DCexecute OMR in smooth, curved swimming patterns, interspersed with sharp directional turns.ZFandDCshare similar visuomotor neural architecture, recruiting pretectal and hindbrain regions.ZFandDCdemonstrate lateralized encoding of turns, particularly in medial hindbrain neurons.In BriefLarvalDanionella cerebrumrespond to global visual motion cues in smooth, low-angle swimming patterns, interspersed with sharp directional turns, swimming consistently faster than zebrafish. Fouke et al. use behavioral tracking of freely moving and head fixed fish to reveal an evolutionarily conserved visuomotor neural architecture transforming visual motion cues into species-specific locomotor behaviors.Graphical Abstract
Advancing protein display on bacterial spores through an extensive survey of coat components
Authors: Chappell Todd C. , Nicks Trevor B. , Cheng Jan-Fang , Tarver Angela , Lee Jessica A. , Kalia Arushi , Nair Nikhil U. 
Published: November 2024

ABSTRACTThe profound stability of bacterial spores makes them a promising platform for biotechnological applications like biocatalysis, bioremediation, drug delivery, etc. However, though theBacillus subtilisspore is composed of >40 proteins, only ∼12 have been explored as fusion carriers for protein display. Here, we assessed the suitability of 33 spore proteins (SPs) as enzyme display carriers by direct allele tagging at native genomic loci. Of the 33 SP investigated, 26 formed functional fusions with β-glucuronidase (GUS) – a ∼272 kDa homotetramer. This almost triples the number of SPs assessed for enzyme display and doubles the number of functional fusions documented in the literature. We quantitatively assessed the 1) SP promoter activation dynamics during growth, 2) supported GUS activity on spores, 3) surface availability, 4) protection from thermal and proteolytic degradation, and 5) compatibility of co-expression of many of these fusions. Multi-copy expression and pairwise co-expression of the most promising SP-GUS fusions highlighted the complexity of spore structure/assembly and difficulty in predicting compatibility between different SPs fusions. We also assessed the suitability of engineered spores to degrade PET (polyethylene terephthalate) films and found that surface exposed SPs were most effective. Beyond the broad survey, a key outcome of our work was the identification of SscA (smallsporecoat assembly proteinA) as an effective spore display carrier. SscA supported enzyme activity at least fourfold higher than any other SP, including the well-established and popular anchor, CotY. We attribute this to the biochemical and genetic features of SscA; its promoter demonstrated early and sustained activation relative to other SPs and its small size (∼3 KDa) likely minimally interferes with enzyme folding, oligomerization, and activity. Although the specific localization of SscA within the spore coat has not been established, its hydrophobic nature and low surface availability suggests that it assembles internally within the spore coat, which makes it highly stabilizing and suitable for many biocatalytic applications. Overall, this work serves as a knowledgebase to advance the biotechnological utility ofB. subtilisspores.
Unbiased data-driven analysis of five amyloid-beta peptides for biomarker investigations in familial Alzheimer’s disease
Authors: Llorente-Saguer Isaac , Gabriele Rebecca , Bradshaw Teisha , Leckey Claire A. , Belder Christopher R.S. , Chávez-Gutiérrez Lucía , de Silva Rohan , Fox Nick C. , Wray Selina , Oxtoby Neil P. , Arber Charles 
Published: November 2024

Structured AbstractINTRODUCTIONChanges to the relative abundance of amyloid-beta (Aβ) peptides are hallmarks of Alzheimer’s disease (AD). iPSC-derived neurons offer a physiological model of Aβ production. We employed unbiased, data-driven analyses to investigate combinations of Aβ peptides as AD biomarkers and the relative contribution of peptides to AD pathogenesis.METHODSWe measured Aβ37, Aβ38, Aβ40, Aβ42 and Aβ43 in ten iPSC-neuronal cultures fromPSEN1mutation carriers. We combined these data with published cell model data and used linear weighted combinations to 1) distinguish AD from controls, and 2) predict age-at-onset forPSEN1mutations.RESULTSData-driven approaches distinguished Aβ42 and Aβ43 from shorter peptides, providing unbiased evidence for their contribution to disease. Weighted linear combinations of Aβ peptides outperform Aβ42/40 and provide insights into relative peptide contribution as biomarkers; the optimal ratio for all data is represented as (21 · Aβ37 + 10 · Aβ38 + 69 · Aβ40)/(94 · Aβ42 + 6 · Aβ43).DISCUSSIONThe algorithm discovered herein can be further refined to improve biomarkers for AD.
Visual speech enhances auditory onset timing and envelope tracking through distinct mechanisms
Authors: Cao Cody Zhewei , Stacey William C , Wasade Vibhangini S , Towle Vernon L , Tao James X , Wu Shasha , Issa Naoum P , Brang David 
Published: November 2024

AbstractSeeing a speaker’s face facilitates speech recognition in challenging listening environments. Prior work has shown that visual speech contains timing information to aid auditory speech processing, yet how these signals are integrated within the auditory system during audiovisual speech perception remains poorly understood. Observation of preparatory mouth movements may initiate phase reset of intrinsic oscillations, potentially sensitizing the auditory system for receptive speech processing, while observation of mouth movements post speech onset may facilitate entrainment to the speech envelope. Yet, little work has been done to test whether visual speech enhances encoding of auditory speech onset, speech envelope tracking, or both, and through independent or overlapping mechanisms. To investigate this, we examined the ways in which visual speech timing information alters theta band power and phase using human intracranial electroencephalography (iEEG) recordings in a large group of patients with epilepsy (n= 21). Prior to speech onset, preparatory mouth movements elicited theta phase reset (increased inter-trial phase coherence; ITPC) throughout the superior temporal gyrus (STG), which is thought to enhance speech onset encoding. Following speech onset, visual speech modulated theta ITPC only at anterior STG electrodes while theta power was modulated at posterior STG electrodes. Pre- and post-speech onset were spatially and temporally dissociated, consistent with the hypothesis that audiovisual speech onset encoding and envelope tracking mechanisms are partially distinct. Crucially, congruent and incongruent visual speech, designed here to have identical visual timing information about speech onset time, but different visual mouth evolution, produced only a small difference in the phase of theta band oscillations in the anterior STG, highlighting a more restricted role of visual speech in ongoing auditory entrainment. These results support the hypothesis that visual speech improves the precision of auditory speech encoding through two separate mechanisms, with auditory speech onset encoded throughout the entire STG and ongoing speech envelope tracking within anterior STG.
Dengue Protease-Mediated Activation and Polarization of Macrophages
Authors: Misra Rajdip , Mukherjee Kaustuv , Karmakar Joyshree , Pal Uttam , Maiti Nakul C 
Published: November 2024

AbstractControlled activation of macrophages to achieve desired phenotypes in vivo and in vitro could lead to possible treatments for several inflammatory and proliferative diseases. This investigation uniquely established that dengue protease enhances the polarization and activation of human and murine macrophages following extracellular exposure. It was observed that macrophages have a robust response to extracellularly administered purified dengue NS2B/NS3 protease; it stimulated the macrophages in classical M1 directions and enhanced both the mitogen-activated protein kinases (MAPK) and c-Jun N-terminal kinases (JNK). The cells exhibited an increase in the intracellular levels of proinflammatory cytokines such as IL-2, IL-6, IL-12, and IFN-γ and an elevation of phosphorylated versions of Akt, P38 MARK, SAPK, and ERK. In tandem, this investigation also established that the heightened responses of stimulated cells were associated with an increase in the cellular reactive oxygen species (ROS) level and the nuclear translocation of the NF-κB (P65) protein. The cell viability assay showed that NS2B/NS3 protease exerts no major toxic effect on macrophages after 24 hours of treatment, even at a dosage (20 μg/ml) which was four times higher than the effective dose (5 μg/ml). Remarkably, we also observed that the native form of the viral protease, which drives its enzyme activities, had no bearing on the antigenic qualities of the enzyme. Thus, our study highlighted the efficacy of dengue viral NS2B/NS3 protease as a non-toxic ex vivo macrophage activating/polarizing agent and may serve a vital role in macrophage-based cell therapy in the near future.
Multi-level transcriptional regulation of embryonic sex determination and dosage compensation by the X-signal elementsex-1
Authors: Jash Eshna , Tan Zoey M. , Rakozy Audry I. , Azhar Anati Alyaa , Mendoza Hector , Csankovszki Györgyi 
Published: November 2024

AbstractTheC. elegansnuclear hormone receptorsex-1is known to be an embryonic X-signal element that repressesxol-1, the sex-switch gene that is the master regulator of sex determination and dosage compensation. Several prior studies onsex-1function have suggested thatsex-1may have additional downstream roles beyond the regulation ofxol-1expression. In this study we characterize some of these additional roles ofsex-1in regulating the dual processes of sex determination and dosage compensation during embryogenesis. Our study reveals thatsex-1acts on many of the downstream targets ofxol-1in axol-1-independent manner. Further analysis of these shared but independently regulated downstream targets uncovered thatsex-1mediates the expression of hermaphrodite- and male-biased genes during embryogenesis. We validatedsex-1binding on one of these downstream targets, the male-developmental geneher-1.Our data suggests a model wheresex-1exhibits multi-level direct transcriptional regulation on several targets, includingxol-1and genes downstream ofxol-1,to reinforce the appropriate expression of sex-biased transcripts in XX embryos. Furthermore, we found thatxol-1 sex-1double mutants show defects in dosage compensation. Our study provides evidence that misregulation ofdpy-21, one of the components of the dosage compensation complex, and the subsequent misregulation of H4K20me1 enrichment on the X chromosomes, may contribute to this defect.