bluuebunny/crossref_metadata_2025 huggingface dataset:
Population analyses reveal heterogenous encoding in the medial prefrontal cortex during naturalistic foraging
Authors: Jeong Ji Hoon , Choi June-Seek
Published: November 2023

Foraging in the wild requires coordinated switching of critical functions, including goal-oriented navigation and context-appropriate action selection. Nevertheless, few studies have examined how different functions are represented in the brain during naturalistic foraging. To address this question, we recorded multiple single-unit activities from the medial prefrontal cortex (mPFC) of rats seeking a sucrose reward in the presence of an unpredictable attack posed by a robotic predator (Lobsterbot). Simultaneously recorded ensemble activities from neurons were analyzed in reference to various behavioral indices as the animal moved freely across the foraging area (F) between the nest (N) and the goal (E) area. An artificial neural network, trained with simultaneously recorded neural activity, estimated the rat’s current distance from the Lobsterbot. The accuracy of distance estimation was the highest in the middle F-zone in which the dominant behavior was active navigation. The spatial encoding persisted in the N-zone when non-navigational behaviors such as grooming, rearing, and sniffing were excluded. In contrast, the accuracy decreased as the animal approached the E-zone, when the activity of the same neuronal ensembles was more correlated with events related to dynamic decision-making between food procurement and Lobsterbot evasion. A population-wide analysis confirmed highly heterogeneous encoding by the region. To further assess the decision-related activity in the E-zone, a naïve Bayesian classifier was trained to predict the success and failure of avoidance behavior. The classifier predicted the avoidance outcome as much as 6 s before the head withdrawal. In addition, two sub-populations of recorded units with distinct temporal dynamics contributed differently to the prediction. These findings suggest that an overlapping population of mPFC neurons may switch between two heterogenous modes, encoding relevant locations for goal-directed navigation or an imminent situational challenge.
Implantable nanophotonic neural probes for integrated patterned photostimulation and electrophysiology recording
Authors: Chen Fu Der , Chameh Homeira Moradi , Movahed Mandana , Wahn Hannes , Mu Xin , Ding Peisheng , Xue Tianyuan , Straguzzi John N. , Roszko David A. , Sharma Ankita , Govdeli Alperen , Jung Youngho , Chua Hongyao , Luo Xianshu , Lo Patrick G. Q. , Valiante Taufik A. , Sacher Wesley D. , Poon Joyce K. S.
Published: November 2023

Optogenetics has transformed neuroscience by allowing precise manipulation of neural circuits with light [1–5]. However, a central difficulty has been to deliver spatially shaped light and record deep within the brain without causing damage or significant heating. Current approaches form the light beam in free space and record the neural activity using fluorescence imaging or separately inserted electrodes [6–9], but attenuation limits optical penetration to around 1 mm of the brain surface [10]. Here, we overcome this challenge with foundry-fabricated implantable silicon neural probes that combine microelectrodes for electrophysiology recordings with nanophotonic circuits that emit light with engineered beam profiles and minimal thermal impact. Our experiments reveal that planar light sheets, emitted by our neural probes, excited more neurons and induced greater firing rate fatigue in layers V and VI of the motor and somatosensory cortex of Thy1-ChR2 mice at lower output intensities than low divergence beams. In the hippocampus of an epilepsy mouse model, we induced seizures, a network-wide response, with light sheets without exceeding the∼1◦C limit for thermally induced electrophysiological responses [11–13]. These findings show that optical spatial profiles can be tailored for optogenetic stimulation paradigms and that the probes can photostimulate and record neural activity at single or population levels while minimizing thermal damage to brain tissue. The neural probes, made in a commercial silicon photonics foundry on 200-mm silicon wafers, demonstrate the manufacturability of the technology. The prospect of monolithically integrating additional well-established silicon photonics devices, such as wavelength and polarization multiplexers, temperature sensors, and optical power monitors, into the probes holds the potential of realizing more versatile, implantable tools for multimodal brain activity mapping.
Parietal alpha stimulation causally enhances attentional information coding in evoked and oscillatory activity
Authors: Lu Runhao , Michael Elizabeth , Scrivener Catriona L. , Jackson Jade B. , Duncan John , Woolgar Alexandra
Published: November 2023

Selective attention is a fundamental cognitive mechanism that allows people to prioritise task-relevant information while ignoring irrelevant information. Previous research has suggested key roles of parietal evoked potentials and alpha oscillatory responses in spatial attention tasks. However, the informational content of these signals is less clear, and their causal effects on the coding of multiple task elements are yet unresolved. Here, we used concurrent TMS-EEG to causally manipulate parietal alpha power and evoked potentials and investigate their roles in coding multiple task features (where to attend,what to attend to, andvisual stimulus) in a selective attention task. First, using EEG-only data, we found that evoked potentials coded all three types of task-relevant information with distinct temporal dynamics, and alpha oscillations carried information regarding both where to attend and what to attend to. Then, we applied rhythmic-TMS (rTMS) at individual alpha frequency over the right intraparietal sulcus (IPS), while concurrently measuring EEG. Compared with control arrhythmic-TMS, alpha rTMS increased alpha power and inter-trial phase coherence and yielded more negative posterior-contralateral evoked potentials. Moreover, alpha rTMS causally and specifically improved multivariate decoding of the information aboutwhere to attend(but notwhat to attend toorfeature information) during task performance, with decoding improvements predicting changes in behavioural performance. These findings illuminate the dynamics with which the complementary aspects of a selective attention task are encoded in evoked and oscillatory brain activity. Moreover, they reveal a specific and causal role of IPS-controlled evoked and oscillatory activity in carrying behaviour-driving information about where to focus attention.
A yeast two-hybrid system to obtain triple-helical ligands from combinatorial random peptide libraries
Authors: Masuda Ryo , Thant Khine Phyu Phyu , Kawahara Kazuki , Oki Hiroya , Kadonosono Tetsuya , Kobayashi Yuji , Koide Takaki
Published: November 2023

Many bioactive proteins interact with collagen, recognizing amino acid sequences displayed on the triple helix. We report here a selection strategy to obtain triple-helical peptides that interact with the proteins from a combinatorial random library constructed in yeast cells. This system enables us to select them using the standard two-hybrid protocol, detecting interactions between triple-helical peptides and target proteins fused to the GAL4-activating and binding domains, respectively. The library was constructed having triple-helical peptides with a “host-guest” design in which host helix-stabilizing regions flanked guest random sequences. Using this system, we selected peptides that bind to pigment epithelium-derived factor (PEDF), a collagen-binding protein that shows anti-angiogenic and neurotrophic activities, from the libraries. Two-step selections from the total random library and subsequently from the second focused library yielded new PEDF-binding sequences that exhibited a comparable affinity to or more potent than that of the native PEDF-binding sequence in collagen. The obtained sequences also contained a variant of the PEDF-binding motif that did not match the known motif identified from the native collagen sequences. This combinatorial library system allows the chemical space of triple-helical peptides to be screened more widely than that found in native collagen, thus increasing the expectation of obtaining more specific and high-affinity peptides.
Acquired temozolomide resistance instructs patterns of glioblastoma behavior in gelatin hydrogels
Authors: Kriuchkovskaia Victoria , Eames Ela K. , Riggins Rebecca B. , Harley Brendan A.C.
Published: November 2023

Acquired drug resistance in glioblastoma (GBM) presents a major clinical challenge and is a key factor contributing to abysmal prognosis, with less than 15 months median overall survival. Aggressive chemotherapy with the frontline therapeutic, temozolomide (TMZ), ultimately fails to kill residual highly invasive tumor cells after surgical resection and radiotherapy. Here, we report a three-dimensional (3D) engineered model of acquired TMZ resistance using two isogenically-matched sets of GBM cell lines encapsulated in gelatin methacrylol hydrogels. We benchmark response of TMZ-resistant vs. TMZ-sensitive GBM cell lines within the gelatin-based extracellular matrix platform and further validate drug response at physiologically relevant TMZ concentrations. We show changes in drug sensitivity, cell invasion, and matrix-remodeling cytokine production as the result of acquired TMZ resistance. This platform lays the foundation for future investigations targeting key elements of the GBM tumor microenvironment to combat GBM’s devastating impact by advancing our understanding of GBM progression and treatment response to guide the development of novel treatment strategies.

Teaser

A hydrogel model to investigate the impact of acquired drug resistance on functional response in glioblastoma.
Cortical acetylcholine dynamics are predicted by cholinergic axon activity and behavior state
Authors: Neyhart Erin , Zhou Na , Munn Brandon R. , Law Robert G. , Smith Cameron , Mridha Zakir H. , Blanco Francisco A. , Li Guochuan , Li Yulong , McGinley Matthew J. , Shine James M. , Reimer Jacob
Published: November 2023

Even under spontaneous conditions and in the absence of changing environmental demands, awake animals alternate between increased or decreased periods of alertness. These changes in brain state can occur rapidly, on a timescale of seconds, and neuromodulators such as acetylcholine (ACh) are thought to play an important role in driving these spontaneous state transitions. Here, we perform the first simultaneous imaging of ACh sensors and GCaMP-expressing axonsin vivo, to examine the spatiotemporal properties of cortical ACh activity and release during spontaneous changes in behavioral state. We observed a high correlation between simultaneously recorded basal forebrain axon activity and neuromodulator sensor fluorescence around periods of locomotion and pupil dilation. Consistent with volume transmission of ACh, increases in axon activity were accompanied by increases in local ACh levels that fell off with the distance from the nearest axon. GRAB-ACh fluorescence could be accurately predicted from axonal activity alone, providing the first validation that neuromodulator axon activity is a reliable proxy for nearby neuromodulator levels. Deconvolution of fluorescence traces allowed us to account for the kinetics of the GRAB-ACh sensor and emphasized the rapid clearance of ACh for smaller transients outside of running periods. Finally, we trained a predictive model of ACh fluctuations from the combination of pupil size and running speed; this model performed better than using either variable alone, and generalized well to unseen data. Overall, these results contribute to a growing understanding of the precise timing and spatial characteristics of cortical ACh during fast brain state transitions.
Flow-field inference from neural data using deep recurrent networks
Authors: Kim Timothy Doyeon , Luo Thomas Zhihao , Can Tankut , Krishnamurthy Kamesh , Pillow Jonathan W. , Brody Carlos D.
Published: November 2023

Computations involved in processes such as decision-making, working memory, and motor control are thought to emerge from the dynamics governing the collective activity of neurons in large populations. But the estimation of these dynamics remains a significant challenge. Here we introduce Flow-field Inference from Neural Data using deep Recurrent networks (FINDR), an unsupervised deep learning method that can infer low-dimensional nonlinear stochastic dynamics underlying neural population activity. Using population spike train data from frontal brain regions of rats performing an auditory decision-making task, we demonstrate that FINDR outperforms existing methods in capturing the heterogeneous responses of individual neurons. We further show that FINDR can discover interpretable low-dimensional dynamics when it is trained to disentangle task-relevant and irrelevant components of the neural population activity. Importantly, the low-dimensional nature of the learned dynamics allows for explicit visualization of flow fields and attractor structures. We suggest FINDR as a powerful method for revealing the low-dimensional task-relevant dynamics of neural populations and their associated computations.
Molecular organization of autonomic, respiratory, and spinally-projecting neurons in the mouse ventrolateral medulla
Authors: Schwalbe Dana C. , Stornetta Daniel S. , Abraham-Fan Ruei-Jen , Souza George M. P. R. , Jalil Maira , Crook Maisie E. , Campbell John N. , Abbott Stephen B. G.
Published: November 2023

The ventrolateral medulla (VLM) is a crucial region in the brain for visceral and somatic control. It also serves as a significant source of synaptic input to the spinal cord. Experimental studies have shown that gene expression in individual VLM neurons is predictive of their function. However, the organizing principles of the VLM have remained uncertain. This study aimed to create a comprehensive dataset of VLM cells using single-cell RNA sequencing. The dataset was enriched with targeted sequencing of spinally-projecting and adrenergic/noradrenergic VLM neurons. Based on differentially expressed genes, the resulting dataset of 114,805 VLM cells identifies 23 subtypes of neurons, excluding those in the inferior olive, and 5 subtypes of astrocytes. Spinally-projecting neurons were found to be abundant in 7 subtypes of neurons, which were validated through in-situ hybridization. These subtypes included adrenergic/noradrenergic neurons, serotonergic neurons, and neurons expressing gene markers associated with pre-motor neurons in the ventromedial medulla. Further analysis of adrenergic/noradrenergic neurons and serotonergic neurons identified 9 and 6 subtypes, respectively, within each class of monoaminergic neurons. Marker genes that identify the neural network responsible for breathing were concentrated in 2 subtypes of neurons, delineated from each other by markers for excitatory and inhibitory neurons. These datasets are available for public download and for analysis with a user-friendly interface. Collectively, this study provides a fine-scale molecular identification of cells in the VLM, forming the foundation for a better understanding of the VLM’s role in vital functions and motor control.
DataSAIL: Data Splitting Against Information Leakage
Authors: Joeres Roman , Blumenthal David B. , Kalinina Olga V.
Published: November 2023

Information Leakage is an increasing problem in machine learning research. It is a common practice to report models with benchmarks, comparing them to the state-of-the-art performance on the test splits of datasets. If two or more dataset splits contain identical or highly similar samples, a model risks simply memorizing them, and hence, the true performance is overestimated, which is one form of Information Leakage. Depending on the application of the model, the challenge is to find splits that minimize the similarity between data points in any two splits. Frequently, after reducing the similarity between training and test sets, one sees a considerable drop in performance, which is a signal of removed Information Leakage. Recent work has shown that Information Leakage is an emerging problem in model performance assessment.

This work presents DataSAIL, a tool for splitting biological datasets while minimizing Information Leakage in different settings. This is done by splitting the dataset such that the total similarity of any two samples in different splits is minimized. To this end, we formulate data splitting as a Binary Linear Program (BLP) following the rules of Disciplined Quasi-Convex Programming (DQCP) and optimize a solution. DataSAIL can split one-dimensional data, e.g., for property prediction, and two-dimensional data, e.g., data organized as a matrix of binding affinities between two sets of molecules, accounting for similarities along each dimension and missing values. We compute splits of the MoleculeNet benchmarks using DeepChem, the LoHi splitter, GraphPart, and DataSAIL to compare their computational speed and quality. We show that DataSAIL can impose more complex learning tasks on machine learning models and allows for a better assessment of how well the model generalizes beyond the data presented during training.
Computational Modeling of Stapled Coiled-Coil Inhibitors Against Bcr-Abl: Toward a Treatment Strategy for CML
Authors: Lima Maria Carolina P. , Hornsby Braxten D. , Lim Carol S. , Cheatham Thomas E.
Published: November 2023

The chimeric oncoprotein Bcr-Abl is the causative agent of virtually all chronic myeloid leukemias (CML) and a subset of acute lymphoblastic leukemias (ALL). As a result of the so-called Philadelphia Chromosome translocation t(9;22), Bcr-Abl manifests as a constitutively active tyrosine kinase which promotes leukemogenesis by activation of cell cycle signaling pathways. Constitutive and oncogenic activation is mediated by an N-terminal coiled-coil oligomerization domain in Bcr (Bcr-CC), presenting a therapeutic target for inhibition of Bcr-Abl activity toward the treatment of Bcr-Abl+ leukemias. Previously, we demonstrated that a rationally designed Bcr-CC mutant, CCmut3, exerts a dominant negative effect upon Bcr-Abl activity by preferential oligomerization with Bcr-CC. Moreover, we have shown conjugation to a leukemia-specific cell-penetrating peptide (CPP-CCmut3) improves intracellular delivery and activity. However, our full-length CPP-CCmut3 construct (81 aa) is encumbered by an intrinsically high degree of conformational variability and susceptibility to proteolytic degradation, relative to traditional small molecule therapeutics. Here, we iterate a new generation of our inhibitor against Bcr-CC mediated Bcr-Abl assembly that is designed to address these constraints through incorporation of all-hydrocarbon staples spanning i, i + 7 positions in helix α2 (CPP-CCmut3-st). We utilize computational modeling and biomolecular simulation to design and characterize single and double staple candidates in silico, evaluating binding energetics and building upon our seminal work modeling single hydrocarbon staples when applied to a truncated Bcr-CC sequence. This strategy enables us to efficiently build, characterize, and screen lead single/double stapled CPP-CCmut3-st candidates for experimental studies and validation in vitro and in vivo. In addition to full-length CPP-CCmut, we model a truncated system characterized by deletion of helix α1 and the flexible-loop linker, which are known to impart high conformational variability. To study the impact of the N-terminal cyclic CPP toward model stability and inhibitor activity, we also model the full-length and truncated systems without CPP, with cyclized CPP, and with linear CPP, for a total of six systems which comprise our library. From this library, we present lead stapled peptide candidates to be synthesized and evaluated experimentally as our next-generation inhibitors against Bcr-Abl.
The histone modifier KAT2A presents a selective target in a subset of well-differentiated microsatellite-stable colorectal cancers
Authors: Kufrin Vida , Seiler Annika , Brilloff Silke , Rothfuß Helen , Schuster Sandra , Schäfer Silvia , Rahimian Elahe , Baumgarten Jonas , Ball Claudia R. , Bornhäuser Martin , Glimm Hanno , Bill Marius , Wurm Alexander A.
Published: November 2023

Background

Lysine acetyltransferase 2A (KAT2A) plays a pivotal role in epigenetic gene regulation across various types of cancer. In colorectal cancer (CRC), upregulation of KAT2A is associated with a more aggressive phenotype. Our study aims to elucidate the molecular underpinnings ofKAT2Adependency in CRC and assess the consequences ofKAT2Adepletion.

Methods

We conducted a comprehensive analysis by integrating CRISPR-Cas9 screening data with genomics, transcriptomics, and global acetylation patterns in CRC cell lines to pinpoint molecular markers indicative ofKAT2Adependency. Additionally, we characterized the phenotypic effect of a CRISPR-Cas9-mediatedKAT2Aknockout and chemical inhibition of KAT2A in CRC cell lines and patient- derived 3D spheroid cultures.

Results

Our findings reveal thatKAT2Adependency is closely associated with a lower mutational burden and increased differentiation grade in CRC cell lines, independent of theKAT2Aexpression levels.KAT2Adependent CRC cell lines display enriched H3K27ac marks at gene loci linked to enterocytic differentiation. Loss ofKAT2Aleads to decreased cell growth and viability, downregulation of proliferation- and stem cell-associated genes, and induction of differentiation markers.

Conclusion

A specific subset of CRCs with a more differentiated phenotype relies on KAT2A. For these CRC cases, KAT2A might represent a promising novel therapeutic target.
From CFTR to a CF signalling network: a systems biology approach to study Cystic Fibrosis
Authors: Najm Matthieu , Martignetti Loredana , Cornet Matthieu , Kelly-Aubert Mairead , Sermet Isabelle , Calzone Laurence , Stoven Véronique
Published: November 2023

Background

Cystic Fibrosis (CF) is a monogenic disease caused by mutations in the gene coding the Cystic Fibrosis Transmembrane Regulator (CFTR) protein, but its overall physio-pathology cannot be solely explained by the loss of the CFTR chloride channel function. Indeed, CFTR belongs to a yet not fully deciphered network of proteins participating in various signalling pathways.

Methods

We propose a systems biology approach to study how the absence of the CFTR protein at the membrane leads to perturbation of these pathways, resulting in a panel of deleterious CF cellular phenotypes.

Results

Based on publicly available transcriptomic datasets, we built and analyzed a CF network that recapitulates signalling dysregulations. The CF network topology and its resulting phenotype was found to be consistent with CF pathology.

Conclusion

Analysis of the network topology highlighted a few proteins that may initiate the propagation of dysregulations, those that trigger CF cellular phenotypes, and suggested several candidate therapeutic targets. Although our research is focused on CF, the global approach proposed in the present paper could also be followed to study other rare monogenic diseases.
Abnormal white matter development during early childhood in autism and developmental disability
Authors: Liu Yuqi , Zhang Jiaying , Rolls Edmund T. , Dai Yuan , Geng Shujie , Deng Lin , Chen Zilin , Zhang Yue , Tao Minyi , Zhang Lingli , Ren Tai , Feng Jianfeng , Cao Miao , Li Fei
Published: November 2023

The abnormal maturation of white matter microstructure in autism spectrum disorder (ASD) compared with typical developing (TD) and developmental delay/intellectual disorder (DD/ID) during early childhood and their associations with clinical implications remain unclear. Here, we characterized spatial and temporal patterns of white matter development in 364 children (including ASD, DD/ID and TD) under 8 years old using neurite orientation dispersion and density imaging. Using neurite density index (NDI), we consistently detected three white matter clusters across all the groups through clustering analysis, indicating the conserved spatial layout in atypical development. Further, three developmental stages with successively lower growth rates were identified in ASD, similar to those in TD but delayed overall. Meanwhile, DD/ID children showed the slowest growth rates and lacked staging features. Finally, for ASD children, the NDI was correlated with cognitive impairments at the fast developmental stage but associated with social deficits during the moderate-to-slow stage.
LPS-Induced Inflammation Reduces GABAergic Interneuron markers and Brain-derived Neurotrophic Factor in Mouse Prefrontal Cortex and Hippocampus
Authors: Rezaei Sara , Prévot Thomas D. , Vieira Erica , Sibille Etienne
Published: November 2023

Inflammation, reduced gamma-aminobutyric acidergic (GABAergic) function and altered neuroplasticity are co-occurring pathophysiologies in major depressive disorder (MDD). However, the link between these biological changes remains unclear. We hypothesized that inflammation induces deficits in GABAergic interneuron markers and that this effect is mediated by brain-derived neurotrophic factor (BDNF). We report here that systemic inflammation induced by intraperitoneal injection of lipopolysaccharide (LPS) (0.125, 0.25, 0.5, 1, 2mg/kg) in the first cohort of C57BL/6 mice (n=72; 9-12 weeks; 50% female) resulted in increased interleukin 1-beta and interleukin-6 in prefrontal cortex (PFC) and hippocampus (HPC), as measured using enzyme-linked immunosorbent assay (ELISA). Quantitative real-time polymerase reaction (qPCR) was used to explore the effect of LPS on the expression of GABAergic interneuron markers. In the PFC of the second cohort (n=39; 9-12 weeks; 50% female), 2mg/kg of LPS decreased the expression of somatostatin (Sst) (p=0.0014), parvalbumin (Pv) (p=0.0257), cortistatin (Cort) (p=0.0003), neuropeptide Y (Npy) (p=0.0033) and cholecystokinin (Cck) (p=0.0041), and did not affect corticotropin-releasing hormone (Crh) and vasoactive intestinal peptide (Vip) expression. In the HPC, 2mg/kg of LPS decreased the expression ofSst(P=0.0543),Cort (p=0.0011),Npy(p=0.0001), andCck(p<0.0001), and did not affectCrh, Pv,andVipexpression. LPS decreased the expression ofBdnfin the PFC (P<0.0001) and HPC (P=0.0003), which significantly correlated with affected markers (Sst, Pv, Cort, Cck,andNpy). Collectively, these results suggest that inflammation may causally contribute to cortical cell microcircuit GABAergic deficits observed in MDD.
A Myelin Map of Trunk Folds in the Elephant Trigeminal Nucleus
Authors: Reveyaz Noémie , Schneeweiß Undine , Heise Olivia , Gerhardt Ben , Gui Andreea M. , Kaufmann Lena V. , Alfken Jette , Reichmann Jakob , Salditt Tim , Hildebrandt Thomas , Brecht Michael
Published: November 2023

Elephants have elaborate trunk skills and large, but poorly understood brains. Here we study trunk representations in elephant trigeminal nuclei, which form large protrusions on the ventral brainstem. These ventral brainstem protrusions have previously been referred to as inferior olive, but a delineation of the olivo-cerebellar tract reveals these (trigeminal) nuclei are not connected to the cerebellum via climbing fibers. In contrast, the olivo-cerebellar tract connects to a large dorsolateral nucleus with a serrated cellular architecture, the putative elephant inferior olive. Dense vascularization and intense cytochrome-oxidase reactivity distinguish several elongated trigeminal putative trunk modules, which repeat in the anterior-posterior direction. We focus on the most anterior and largest of these units, the putative nucleus principalis trunk module. Module neuron density is low and non-neural cells outnumber neurons by ∼108:1. Dendritic trees are elongated along the axis of axon bundles (myelin stripes) transversing the trunk module. Synchrotron X-ray-phase-contrast tomography suggests myelin-stripe-axons transverse the trunk module. We show a remarkable correspondence of trunk module myelin stripes and trunk folds. Myelin stripes show little relation to trigeminal neurons and stripe-axons appear to often go nowhere; we suggest that myelin stripes might serve to separate trunk-fold domains rather than to connect neurons. Myelin-stripes-to-folds mapping allowed to determine neural magnification factors, which changed from 1000:1 proximally to 5:1 in the trunk finger. Asian elephants have fewer (∼640,000) trunk-module neurons than Africans (∼740,000) and show enlarged representations of trunk parts involved in object wrapping. The elephant trigeminal trunk module is exquisitely organized into trunk-fold-related units.
Multiplexed live-cell imaging for drug responses in patient-derived organoid models of cancer
Authors: Colling Kaitriana E. , Symons Emily L. , Buroni Lorenzo , Sumanisiri Hiruni K. , Andrew-Udoh Jessica , Witt Emily , Losh Haley A. , Morrison Abigail M. , Leslie Kimberly K. , Dunnill Christopher J. , De Bono Johann S. , Thiel Kristina W.
Published: November 2023

Patient-derived organoid (PDO) models of cancer are a multifunctional research system that better recapitulates human disease as compared to cancer cell lines. PDO models can be generated by culturing patient tumor cells in extracellular basement membrane extracts (BME) and plating as three-dimensional domes. However, commercially available reagents that have been optimized for phenotypic assays in monolayer cultures often are not compatible with BME. Herein we describe a method to plate PDO models and assess drug effects using an automated live-cell imaging system. In addition, we apply fluorescent dyes that are compatible with kinetic measurements to simultaneously quantitate cell health and apoptosis. Image capture can be customized to occur at regular time intervals over several days. Users can analyze drug effects in individual Z-plane images or a Z Projection of serial images from multiple focal planes. Using masking, specific parameters of interest are calculated, such as PDO number, area, and fluorescence intensity. We provide proof-of-concept data demonstrating the effect of cytotoxic agents on cell health, apoptosis and viability. This automated kinetic imaging platform can be expanded to other phenotypic readouts to understand diverse therapeutic effects in PDO models of cancer.

Patient-derived tumor organoids are a sophisticated model system for basic and translational research. This methods article details the use of multiplexed fluorescent live-cell imaging for simultaneous kinetic assessment of different organoid phenotypes.
Promoting Transparent, Fair, and Inclusive Practices in Grantmaking: Lessons from the Open and Equitable Model Funding Program
Authors: Mercado-Lara Eunice , Tananbaum Greg , McKiernan Erin C.
Published: November 2023

The Open Research Funders Group (ORFG) has been instrumental in promoting open and equitable scholarship to enhance academic research’s transparency and accessibility. In 2020, the ORFG formed the Equity & Open Science Working Group, leading to the launch of the Open & Equitable Model Funding Program in 2021. This program aimed to refine grantmaking processes for broader inclusivity and equitable open scholarship practices.

The program gathered a cohort of 11 funding organizations and focused on applying various proposed interventions within existing funding programs to improve grantmaking practices. The initiative highlighted the importance of targeted intervention selection and the need for delimited goal-setting, revealing challenges in implementation due to limited resources and the complexity of the processes involved.

Participants valued the pilot for its structured approach and opportunities for shared learning despite some facing complexities in fully implementing the interventions. The ORFG’s future approach involves flexible intervention selection, effective resource management, and fostering a collaborative community, aiming for a more inclusive and practical application of open scholarship principles.
Single phage proteins sequester TIR- and cGAS-generated signaling molecules
Authors: Li Dong , Xiao Yu , Xiong Weijia , Fedorova Iana , Wang Yu , Liu Xi , Huiting Erin , Ren Jie , Gao Zirui , Zhao Xingyu , Cao Xueli , Zhang Yi , Bondy-Denomy Joseph , Feng Yue
Published: November 2023

Prokaryotic anti-phage immune systems use TIR (toll/interleukin-1 receptor) and cGAS (cyclic GMP-AMP synthase) enzymes to produce 1’’-3’/1’’-2’ glycocyclic ADPR (gcADPR) and cyclid di-/tri-nucleotides (CDNs and CTNs) signaling molecules that limit phage replication, respectively1–3. However, how phages neutralize these common systems is largely unknown. Here, we show thatThoerisanti-defense proteins Tad14and Tad25both have anti-CBASS activity by simultaneously sequestering CBASS cyclic oligonucleotides. Strikingly, apart from binding Thoeris signals 1’’-3’ and 1’’-2’ gcADPR, Tad1 also binds numerous CBASS CDNs/CTNs with high affinity, inhibiting CBASS systems using these moleculesin vivoandin vitro.The hexameric Tad1 has six binding sites for CDNs or gcADPR, which are independent from two high affinity binding sites for CTNs. Tad2 also sequesters various CDNs in addition to gcADPR molecules, inhibiting CBASS systems using these CDNs. However, the binding pockets for CDNs and gcADPR are different in Tad2, whereby a tetramer can bind two CDNs and two gcADPR molecules simultaneously. Taken together, Tad1 and Tad2 are both two-pronged inhibitors that, alongside anti-CBASS protein 2, establish a paradigm of phage proteins that flexibly sequester a remarkable breadth of cyclic nucleotides involved in TIR- and cGAS-based anti-phage immunity.
Influence of mixed and single infection of grapevine leafroll-associated virus and viral load on berry quality
Authors: Salo Wisam , Considine John A. , Considine Michael J.
Published: November 2023

1

Grapevine leafroll disease (GLD) is a viral disease that affects grapevines (Vitis viniferaL.) and has a severe economic impact on viticulture. In this study, the effect of grapevine leafroll-associated viruses (GLRaV) on berry quality was investigated in clones of cultivar cv. Crimson Seedless table grapes infected with GLRaV. RT-PCR confirmed the identity of the clones: clone 3236, infected only with GLRaV-3 (termed Single); clone 3215, infected with GLRaV-3, GLRaV-4 strain 9 and grapevine virus A (termed Mixed), and a viral free clone of the same genetic background of the infected clones (termed Control). The berry quality indices of size, sugar, acidity, and anthocyanin content were measured at harvest maturity. RT-qPCR was used to determine viral load. The study was repeated over two years. A two-way, multivariate analysis of variance (MANOVA) was applied with clone and season as independent variables and the measured berry quality parameters as a dependent variable. All dependent variables were significantly affected by viral infection (Wilks, λ, [2,33] = 0.033895, p-value < 0.001), while only titratable acidity (TA) was affected by season. Average berry dry mass decreased (p-value < 0.001). The water content of both infected clones was greater than that of the control (p-value < 0.001). Both infected clones displayed reduced sugar content as a fraction of the berry dry mass (p-value < 0.001). The anthocyanin and the phenol content of the infected clones were significantly reduced compared to the control clone (p< 0.001,p< 0.05, clone 3236 and clone 3215, respectively). Finally, the viral load was highly variable, and no quantitative relationship between viral load and berry composition was found.
Cortical spheroids show strain-dependent cell viability loss and neurite disruption following sustained compression injury
Authors: González-Cruz Rafael D. , Wan Yang , Calvao Dominick , Burgess Amina , Renken William , Vecchio Francesca , Franck Christian , Kesari Haneesh , Hoffman-Kim Diane
Published: November 2023

Sustained compressive injury (SCI) in the brain is observed in numerous injury and pathological scenarios, including tumors, ischemic stroke, and traumatic brain injury-related tissue swelling. Sustained compressive injury is characterized by tissue loading over time, and currently, there are fewin vitromodels suitable to study neural cell responses to strain-dependent sustained compressive injury. Here, we present anin vitromodel of sustained compressive neural injury via centrifugation. Spheroids were made from neonatal rat cortical cells seeded at 4000 cells/spheroid and cultured for 14 daysin vitro. A subset of spheroids was centrifuged at 209 or 419 rad/s for 2 minutes. Modeling the physical compression of the spheroids via finite element analyses, we found that spheroids centrifuged at 209 and 419 rad/s experienced pressures of 38 kPa and 149 kPa, respectively, and compressive strains of 18% and 35%, respectively. Quantification of LIVE-DEAD assay and Hoechst 33342 nuclear staining showed that centrifuged spheroids exhibited significantly higher DNA damage than control spheroids at 2, 8, and 24 hours post-injury. Immunohistochemistry of β3-tubulin networks at 2, 8, and 24 hours post-centrifugation injury showed increasing degradation of microtubules over time with increasing compressive strain. Our findings show that cellular injuries occur as a result of specific levels and timings of sustained compressive tissue strains. This experimental compressive injury model provides anin vitroplatform to examine cellular injury to gain insights into brain injury that could be targeted with therapeutic strategies.
Pangenome- and genome-based taxonomic classification inference for the marine bacterial strain KMM 296 producing a highly active PhoA alkaline phosphatase and closely relatedCobetiaspecies
Authors: Nedashkovskaya O.I. , Balabanova L.A. , Otstavnykh N. Y. , Zhukova N.V. , Seitkalieva A.V. , Noskova Yu.A. , Tekutyeva L.A
Published: November 2023

A strictly aerobic, Gram-stain-negative, rod-shaped and motile bacterium, designated strain KMM 296, isolated from the coelomic fluid of musselCrenomytilus grayanus, was investigated in details due to its ability to produce a highly active alkaline phosphatase of the structural family PhoA. A previous taxonomic study placed the strain to the speciesCobetia marina, a member of the familyHalomonadaceaeof the classGammaproteobacteria. However, the comprehensive phylogenetic analysis based on 16S rRNA gene sequencing revealed that the strain KMM 296 is most closely related toCobetia amphilectiNRIC 815Twith the 16S rRNA gene sequence similarity of 100%. The mussel isolate grew with 0.5-19% NaCl and at 4 - 42°C and hydrolysed Tweens 20 and 40, and L-tyrosine. The DNA G+C content was 62.5 mol%. The prevalent fatty acids were C18:1ω7c, C12:03-OH, C18:1ω7c, C12:0and C17:0cyclo. The polar lipid profile was characterized by the presence of phosphatidylethanolamine, phosphatidylglycerol, phosphatidic acid, and unidentified aminolipid, phospholipid, and lipids. The major respiratory quinone was Q-8. According to phylogenetic evidence and similarity in the chemotaxonomic and genotypic properties of the mussel isolate and its nearest neighbors, the strain KMM 296 represents a member of the speciesC. amphilecti. A comparative analysis of the type strains genomes of the speciesC. amphilectiandC. litoralisshowed that they belong to a single species. In addition, a high similarity of the genome sequences ofC. pacificaNRIC 813TandC. marinaLMG 2217Talso allows suggesting the affiliation of these two species to one species. Based on the rules of priority,C. litoralisshould be reclassified as a later heterotypic synonym ofC. amphilecti, andC. pacificais a later heterotypic synonym ofC. marina. The emended descriptions of the speciesC. amphilectiandC. marinaare also proposed.
Investigating the Role of Neck Muscle Activation and Neck Damping Characteristics in Brain Injury Mechanism
Authors: Bahreinizad Hossein , Chowdhury Suman K.
Published: November 2023

Purpose

This study aimed to investigate the role of neck muscle activity and neck damping characteristics in traumatic brain injury (TBI) mechanisms.

Methods

We used a previously validated head-neck finite element (FE) model that incorporates various components such as scalp, skull, cerebrospinal fluid, brain, muscles, ligaments, cervical vertebrae, and intervertebral discs. Impact scenarios included a Golf ball impact, NBDL linear acceleration, and Zhang’s linear and rotational accelerations. Three muscle activation strategies (no-activation, low-to-medium, and high activation levels) and two neck damping levels by perturbing intervertebral disc properties (high: hyper-viscoelastic and low: hyper-elastic) strategies were examined. We employed Head Injury Criterion (HIC), Brain Injury Criterion (BrIC), and maximum principal strain (MPS) as TBI measures.

Results

Increased neck muscle activation consistently reduced the values of all TBI measures in Golf ball impact (HIC: 4%-7%, BrIC: 11%-25%, and MPS (occipital): 27%-50%) and NBDL study (HIC: 64%-69%, BrIC: 3%-9%, and MPS (occipital): 6%-19%) simulations. In Zhang’s study, TBI metric values decreased with the increased muscle activation from no-activation to low-to-medium (HIC: 74%-83%, BrIC: 27%-27%, and MPS (occipital): 60%-90%) and then drastically increased with further increases to the high activation level (HIC: 288%-507%, BrIC: 1%-25%, and MPS (occipital): 23%-305%). Neck damping changes from low to high decreased all values of TBI metrics, particularly in Zhang’s study (up to 40% reductions).

Conclusion

Our results underscore the pivotal role of neck muscle activation and neck damping in TBI mitigation and holds promise to advance effective TBI prevention and protection strategies for diverse applications.
Atom filtering algorithm and GPU-accelerated calculation of simulation atomic force microscopy images
Authors: Amyot Romain , Kodera Noriyuki , Flechsig Holger
Published: November 2023

Simulation atomic force microscopy computationally emulates experimental scanning of a biomolecular structure to produce topographic images that can be correlated with measured images. Its application to the enormous amount of available high-resolution structures, as well as to molecular dynamics modelling data, facilitates the quantitative interpretation of experimental observations by inferring atomistic information from resolution-limited measured topographies. The computation required to generate a simulated AFM image generally includes the calculation of contacts between the scanning tip and all atoms from the biomolecular structure. However, since only contacts with surface atoms are relevant, a filtering method shall highly improve the efficiency of simulation AFM computations. In this report we address this issue and present an elegant solution based on graphics processing unit (GPU) computations that significantly accelerates the computation of simulation AFM images. The method not only allows for visualization of biomolecular structures combined with ultra-fast synchronized calculation and graphical representation of corresponding simulated AFM images (live simulation AFM), but, as we demonstrate, can also reduce the computational effort during automatized fitting of atomistic structures into measured AFM topographies by orders of magnitude. Hence, the developed method will play an important role in post-experimental computational analysis involving simulation AFM. Implementation is realized in our BioAFMviewer software package for simulation AFM of biomolecular structures and dynamics.
Trans-omic analysis reveals opposite metabolic dysregulation between feeding and fasting in liver associated with obesity
Authors: Bai Yunfan , Morita Keigo , Kokaji Toshiya , Hatano Atsushi , Ohno Satoshi , Egami Riku , Pan Yifei , Li Dongzi , Yugi Katsuyuki , Uematsu Saori , Inoue Hiroshi , Inaba Yuka , Suzuki Yutaka , Matsumoto Masaki , Takahashi Masatomo , Yoshihiro Izumi , Bamba Takeshi , Hirayama Akiyoshi , Soga Tomoyoshi , Kuroda Shinya
Published: November 2023

Dysregulation of liver metabolism associated with obesity during feeding and fasting leads to the breakdown of metabolic homeostasis. However, the underlying mechanism remains unknown. Here, we measured multi-omics data in the liver of wild-type and leptin-deficient obese (ob/ob) mice atad libitumfeeding, and constructed a differential regulatory trans-omic network of metabolic reactions. We compared the trans-omic network at feeding with that at 16 h-fasting constructed in our previous study. Intermediate metabolites in glycolytic and nucleotide metabolism decreased inob/obmice at feeding but increased at fasting. Allosteric regulation reversely shifted between feeding and fasting, generally showing activation at feeding while inhibition at fasting inob/obmice. Transcriptional regulation was similar between feeding and fasting, generally showing inhibiting transcription factor regulations, activating enzyme protein regulations inob/obmice. The opposite metabolic dysregulation between feeding and fasting characterizes breakdown of metabolic homeostasis associated with obesity.
Adapting genetic algorithms for artificial evolution of visual patterns under selection from wild predators
Authors: Briolat Emmanuelle S. , Hancock George R. A. , Troscianko Jolyon
Published: November 2023

Camouflage is a widespread and well-studied anti-predator strategy, yet identifying which patterns provide optimal protection in any given scenario remains challenging. Besides the virtually limitless combinations of colours and patterns available to prey, selection for camouflage strategies will depend on complex interactions between prey appearance, background properties and predator traits, across repeated encounters between co-evolving predators and prey. Experiments in artificial evolution, pairing psychophysics detection tasks with genetic algorithms, offer a promising way to tackle this complexity, but sophisticated genetic algorithms have so far been restricted to screen-based experiments. Here, we present methods to test the evolution of colour patterns on physical prey items, under selection from wild predators in the field. Our techniques expand on a recently-developed open-access pattern generation and genetic algorithm framework, modified to operate alongside artificial predation experiments. In this system, predators freely interact with prey, and the order of attack determines the survival and reproduction of prey patterns into future generations. We demonstrate the feasibility of these methods with a case study, in which free-flying birds feed on artificial prey deployed in semi-natural conditions, against backgrounds differing in three-dimensional complexity. Wild predators reliably participated in this experiment, foraging for 11 to 16 generations of artificial prey and encountering a total of 1,296 evolved prey items. Changes in prey pattern across generations indicated improvements in several metrics of similarity to the background, and greater edge disruption, although effect sizes were relatively small. Computer-based replicates of these trials, with human volunteers, highlighted the importance of starting population parameters for subsequent evolution, a key consideration when applying these methods. Ultimately, these methods provide pathways for integrating complex genetic algorithms into more naturalistic predation trials. Customisable open-access tools should facilitate application of these tools to investigate a wide range of visual pattern types in more ecologically-relevant contexts.