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4261 Publications

Showing 1-10 of 4261 results
04/15/26 | Transformation-tolerant object recognition in tree shrews despite lacking a fovea
Meyer EE, Ong WS, Song C, Cottaris NP, Zhang L, Collina J, Brainard DH, Arcaro MJ
bioRxiv. 2026 Apr 14:. doi: 10.64898/2026.04.10.717715

Object recognition depends on the ability to extract stable representations across changes in how they are viewed, yet it remains unclear how this capacity depends on visual acuity and cortical hierarchy. We combined behavioral testing and computational modeling to determine whether tree shrews, close relatives of primates with lower spatial acuity, can perform transformation-tolerant object recognition. Front-end modeling incorporating species-specific optics and photoreceptor sampling showed that, when scaled for acuity, tree shrew retinal filtering preserves the similarity structure of natural image categories relevant for object recognition. Behaviorally, tree shrews reliably discriminated complex objects across variations in position, scale, and viewpoint, including when embedded within natural scenes, and generalized to novel exemplars. Their recognition behavior was best explained by visual features emphasizing differences in global shape and size between objects and by representations from intermediate and deep layers of hierarchical neural network models. These results demonstrate that visual processing supporting object-level generalization can arise within visual systems lacking high-acuity front-end optics and establish the tree shrew as a key model for understanding the computational and evolutionary origins of high-level vision.

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04/10/26 | Imaging around the globe: Tailoring microscopy outreach to local research demands.
Schmidt A, Balasubramanian H, Komoto S, Malacrida L, Prats C, Reiche M, Aaron J, Chew T
J Microsc. 2026 Apr 10:. doi: 10.1111/jmi.70087

The global microscopy community has made wide efforts in imaging technology dissemination, especially to lower- and middle-income countries. Yet, many efforts have not fully realised their aim of increased, sustained microscopy utilisation. To guide future outreach initiatives towards more positive results, we analysed over 2300 unique applications across seven recent international microscopy workshops. We found significant differences in research priorities, as well as in microscopy experience and applications between lower- and higher-income regions. We discuss the importance of tailoring technology dissemination, training curricula, and capacity-building to these regional variations.

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04/10/26 | Sex-specific plasticity mechanisms mediating fear extinction
Graham K, Pomeroy-Tuck J, O’Brien GK, Kent-Webber L, Drillen AL, Coddington L, Zhao X, Bloss EB
bioRxiv. 2026 Apr 10:. doi: 10.64898/2026.04.10.717763

There is strong evidence that synaptic plasticity is a critical cellular mechanism underlying learning and memory. Although the forms of synaptic plasticity used by different circuits and cell types vary, a widespread presumption is that the male and female brain has evolved to use the same form of plasticity within the same circuits during performance on the same task. Here, we used complimentary approaches to determine how activity in the mouse frontal cortex supports the extinction of associative memories in a context-dependent manner. While in vivo recordings show that both male and female mice have similar cue-relevant activity patterns and ensemble dynamics in excitatory neurons from the infralimbic cortex (IL) during learning, activity in amygdala-projecting IL neurons was indispensable for extinction memories only in male mice. Likewise, male but not female mice showed evidence for the recruitment of IL by structural remodeling and clustering of dendritic spines on these neurons, and extinction memory impairments were evident only in male mice after projection-specific IL deletion of the glutamate receptor subunit GRIN2B. This work provides strong evidence that synaptic plasticity mechanisms employed during learning and critical for memory retrieval differ between males and females, which undercuts the utility of one-size-fits all therapeutic approaches for mental health conditions in which memory is disrupted.Competing Interest StatementThe authors have declared no competing interest.

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04/09/26 | Adapting upright light sheet fluorescence microscopy for imaging at air-liquid interface
Hobson CM, Izumi K, Aaron JS, Bharathan NK, Ceriani MF, Giang W, Ispizua JI, Kowalczyk AP, Lee RM, Morales EA, Puls OF, Quarles E, Rodriguez-Caron M, Stahley SN, Tassara F, Wang S, Yao S, Tsuchiya T, Chew T
bioRxiv. 2026 Apr 09:. doi: 10.64898/2026.04.07.716945

Light sheet fluorescence microscopy (LSFM) is increasingly appreciated as the gold standard for gentle, volumetric imaging with fast acquisition speeds and/or long imaging durations. However, the often-constrained sample space of these microscopes has precluded a specific class of biological specimens from being studied with these tools: those requiring an air-liquid interface (ALI). Here, we present a device for robust imaging at ALI on an upright light sheet microscope with dipping objectives. We demonstrate the system using three relevant use-cases: ex vivo embryonic mouse salivary glands, human epidermal equivalent cultures, and in vivo adult Drosophila melanogaster brains. While the device presented is engineered for one specific light sheet microscope design, it provides a blueprint for easy adaptation to other systems. In doing so, it can potentially spur the use of LSFM for model systems that have so far been unable to take advantage of this powerful technology.

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04/09/26 | Luminal surface proteome of the brain vasculature uncovers blood-brain barrier regulators.
Zhu Z, Jiang Z, Wang Y, Nguyen K, Zhang Y, Lian CG, Mani DR, Zheng J, Ding L, Gao SM, Xia RA, Kuszpit A, Lindo S, Lopez C, Lindsey C, Groff B, Chen X, Wu J, Xia W, Li W, Liu X, Gradinaru V, Carr SA, Udeshi ND, Li J
Science. 2026 Apr 09;392(6794):eaea2100. doi: 10.1126/science.aea2100

At the blood-tissue interface, vasculature luminal surface is critical for molecular transport, signaling transduction, and cell extravasation. Here, we present a method for proteomic profiling of the vasculature luminal surface in vivo, broadly applicable to any vertebrate. Quantitative mass spectrometry revealed the luminal surface proteome of the mouse brain vasculature and its temporal evolution from development to aging. In vivo genetic perturbation found that the arginine transporter SLC7A1 and the nitric oxide synthase NOS3 are needed for blood-brain barrier integrity in neonatal but not adult mice, whereas the hyaluronan degradation enzyme HYAL2 safeguards the barrier throughout the lifespan. By characterizing the proteomic dynamics of the vasculature luminal surface, the study links the metabolism of nitric oxide and hyaluronan to blood-brain barrier integrity.

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04/09/26 | Time-resolved cryo-EM reveals conformational trajectory of allosteric activation in isocitrate lyase
Taka J, Jung J, Guo S, Jiao W, Kwai BX, de Carvalho LP, McNeil M, Huang EY, Yu Z, Leung IK, Bashiri G
bioRxiv. 2026 Apr 09:. doi: 10.64898/2026.04.08.716820

Isocitrate lyase 2 (ICL2) from Mycobacterium tuberculosis undergoes dramatic conformational rearrangements upon binding to the allosteric effector acetyl-CoA. Time-resolved cryo-EM captured conformational states along the ICL2 activation trajectory, revealing how acetyl-CoA binding at the allosteric sites leads to asymmetric, half-of-site activity at the catalytic centres. These findings support a conformational selection model of allostery, whereby acetyl-CoA binding shifts the pre-existing equilibrium towards an active state of the enzyme.

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Funke Lab
04/07/26 | A multi-resolution imaging and analysis pipeline for comparative circuit reconstruction in insects
Gillet V, Sayre ME, Badalamente GS, Schieber NL, Tedore K, Funke J, Heinze S
eLife. 2026 Apr 7:. doi: 10.7554/elife.110789.1

Connectomics has become essential for the study of brain function, yet for most research groups it remains prohibitively costly in imaging time, data storage, and analysis. Here, we present an imaging, processing, and analysis pipeline for multi-resolution image acquisition and circuit reconstruction. Applied to the central complex of six insect species, we were able to obtain global projectomes at cellular resolution (40-50 nm) with embedded local connectomes describing key computational compartments at synaptic resolution (8-12 nm). We provide standardized protocols for volume EM sample preparation, image acquisition and image alignment, combined with existing methods for µCT block trimming, automatic segmentation, synapse detection, collaborative skeleton tracing with CATMAID, and segmentation proofreading via CAVE. We validated our workflow by reconstructing head direction cells across all six insect species, which revealed deep conservation at the level of cell types, cell numbers and projection patterns, while also revealing circuit level specializations. Overall, our pipeline democratizes comparative connectomics by making this method accessible for small research groups with modest resources.

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04/07/26 | Fatty acid regulation of feeding in <I>Caenorhabditis</I> elegans reveals the potential ancestral origin of a GLP-1-like multiagonist signaling system.
Zhu F, Castillo-Quan JI, Ogawa T, Wu Z, Ding L, Sura M, Watanabe Y, Lentschat H, Fernández-Cárdenas LP, Dag U, Beck-Sickinger A, Wang MC, Kahn CR, Blackwell TK
Proc Natl Acad Sci U S A. 2026 Apr 07;123(14):e2530979123. doi: 10.1073/pnas.2530979123

Regulation of food intake in mammals is complex and controlled by an interplay between hedonic and homeostatic signals, including hormones like leptin, which senses fat storage and suppresses food intake. lack leptin and leptin receptors but still exhibit controlled eating. Here, we show that in eating can be regulated by a balance between saturated and monounsaturated fatty acids interacting with transcriptional pathways regulating lipid synthesis, c-AMP response element binding protein and AMP kinase. This effect is mediated at the endoplasmic reticulum through formation of phospholipids and activation of the IRE-1 sensor in the nervous system, which controls behavior through neuronal serotonin and the G-protein-coupled ligand/receptor pair PDF-1/PDFR-1. We show that this peptide/receptor pair may be an ancestral precursor of the whole family of GLP-1/GIP-related peptides and their receptors. Indeed, administration of a 37 amino acid peptide derived from PDF-1 resulted in a reduction in body weight and improved insulin sensitivity in mice. In worms, signaling through this pathway induced food-leaving behavior on concentrated food and roaming behavior on dispersed food, a state we have termed "food-apathy," paralleling pharmacologic effects of GLP-1/GIP-related peptides in humans. These findings highlight the potential evolutionary origin of this family of hormones and their receptors, and its link to metabolic and neuronal responses in control of feeding behavior.

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04/02/26 | Pearling drives mitochondrial DNA nucleoid distribution.
Landoni JC, Lycas MD, Macuada J, Stepp W, Jaccard R, Obara CJ, Moore AS, Hoffman D, Lippincott-Schwartz J, Marshall W, Sturm G, Manley S
Science. 2026 Apr 02;392(6793):102-109. doi: 10.1126/science.adu5646

The distribution of mitochondrial DNA-containing nucleoids is essential for mitochondrial function and genome inheritance; however, no known mechanisms can explain nucleoid segregation or their regular positioning. In this work, we found that mitochondria frequently undergo a reversible biophysical instability termed "pearling," transforming from a tubular into a regularly spaced beads morphology. Physiological pearling imposed a characteristic length scale and simultaneously mediated nucleoid disaggregation and established internucleoid distancing with high precision. Pearling onset was triggered by calcium influx, whereas the density of lamellar cristae invaginations modulated pearling prevalence and preserved nucleoid spacing following recovery. The dysregulation of mitochondrial calcium influx or inner membrane cristae integrity caused aberrant nucleoid clustering. Our results identify pearling as a mechanism governing nucleoid distribution and inheritance and offer insights into its regulation.

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03/30/26 | Many cells make light work: Self-generated gradients organize <I>Dictyostelium</I> aggregates and neutrophil swarms.
Strickland E, Durel JF, Sgro AE, Weiner OD
Cold Spring Harb Perspect Biol. 2026 Mar 30:. doi: 10.1101/cshperspect.a041739

Cells work together to accomplish complex tasks. For example, both neutrophils and Dictyostelid collectives use self-generated multicellular signaling gradients to coordinate aggregation over large areas through local interactions. However, these aggregation programs occur for different reasons that necessitate different implementations. Dictyostelids are soil-dwelling amoeba that aggregate when starving to facilitate dispersal to new locations. These aggregates do not require specific locations or group sizes. In contrast, neutrophils are innate immune cells that collectively migrate to sites of injury and infection. These swarms need to occur in specific locations and must be constrained in size to avoid collateral damage to the host. Here, we review how these evolutionarily divergent systems sculpt long-range gradients at the molecular and cellular levels, discussing their similarities and differences in light of their distinctive goals. Convergence on self-generated gradients for aggregation despite different goals suggests that it is an optimal strategy to bring individuals together in complex environments.

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