bluuebunny/crossref_metadata_2025 huggingface dataset:
Vortex light field microscopy: 3D spectral single-molecule imaging with a twist
Authors: Zhang Boya , Daly Sam , Zhu Chengxi , Lenz Martin O. , Weiss Lucien E. , Needham Lisa-Maria , Peters Ruby , Lee Steven F. , O’Holleran Kevin
Published: July 2024

We introduce vortex light field microscopy (VLFM), a novel method for snapshot 3D spectral single-molecule localization microscopy. Inspired by the azimuthal phase profile of optical vortices, we place an azimuthally oriented prism array immediately after the microlens array in a Fourier light field microscope (FLFM). This innovative arrangement causes the axial position and spectral peak for a point emitter to be encoded in the radial and azimuthal displacement of point-spread-function (PSF) respectively. This enables simultaneous detection of 3D position and emission peak of individual fluorophores with 25 nm spatial precision and 3 nm spectral precision over a 4μm depth of field (DOF). We illustrate the spectral scalability of our method by performing four-color 3D single particle tracking of freely diffusing fluorescent beads, and two-color 3D dSTORM imaging of microtubules and mitochondria in fixed COS-7 cells, without the need for spectrally distinct fluorophores.
Association between genetic clades and cancer prevalence suggested by French-wide study of oncogenic small ruminant beta-retroviruses diversity
Authors: Benjamin Riocreux-Verney , Marie Verneret , Rémi Diesler , Christine Dolmazon , Barbara Gineys , Jean-Luc Cadoré , Jocelyn Turpin , Caroline Leroux
Published: July 2024

ENTV (Enzootic Nasal Tumor Virus) and JSRV (Jaagsiekte Sheep Retrovirus) are β-retroviruses responsible for respiratory cancers in sheep and goats. In this study, we analyzed the genetic features of the sheep and goat β-retrovirus (29 JSRV and 24 ENTV strains) circulating in France to identify molecular signatures associated with disease severity in flocks. We developed a highly specific PCR to amplify and sequence exogenous targeted regions or near full length proviruses based on limited discriminating motifs along their genomes. The phylogenetic reconstructions based on the LTR andenvregions suggest that one major strain is circulating on the French territory for ENTV-1 and ENTV-2 while not clustering with already published Spanish, Canadian or Chinese strains. JSRV strains circulating in French sheep flocks were distributed in 2 distinct genetic clades clustering with sequences originating from North America, Africa and United-Kingdom. JSRV clade I was found to be associated with a higher incidence of cancer in French flocks. Specific motifs spanning the entire JSRV genome particularly in the LTRs and in the intracytoplasmic domain of the envelope were detected between the two genetic subtypes.

This work represents the first nationwide study describing the circulation of the three closely related β-oncogenic retrovirus JSRV, ENTV-1 and ENTV-2 in French sheep and goat flocks. Better characterization of strain genetics is a critical step in monitoring circulating β retrovirus, especially those associated with higher cancer incidence in small ruminants.
Ru(II)-Photoactive Agents for Targeting ER Stress and Immunogenic Cell Death
Authors: Denison Madeline , Ullrich Alexander , Herroon Mackenzie K. , Mecca Shane , Turro Claudia , Podgorski Izabela , Gibson Heather , Kodanko Jeremy J.
Published: July 2024

Immunotherapy has emerged as a promising avenue for cancer treatment by bolstering the immune system’s ability to recognize and attack cancer cells. Photodynamic therapy shows potential in enhancing antitumor immunity, though the mechanisms behind its success are not fully understood. In this manuscript, we investigate two previously reported green light activated PCT/PDT agents where compound2- [Ru(tpy)(Me2bpy)(3)]2+, (tpy = 2,2’:6’,2’’- terpyridine, Me2bpy = 6,6’-dimethyl-2,2’-bipyridine,3= pyridyl-BODIPY-I2,) - shows remarkable photoselectivity in assays containing both 2D cancer cells and 3D cocultures containing BALB/c macrophages and 4T1 murine breast cancer cells. Through flow cytometry and protein analysis, we found complex2displays superior evidence of induced endoplasmic reticulum (ER) stress markers and indicators of immunogenic cell death (ICD) compared to its ligand3, despite its weaker photoselectivity. Most importantly, these results were supported byin vivostudies where2produced anti-tumor immunity against the 4T1 tumor model in BALB/c mice. Complete tumor elimination was achieved in 2/8 mice, and these mice were both protected against a subsequent contralateral rechallenge and showed increasedex vivoperipheral tumor antigen-specific recall, suggesting memory T cells are induced by2. Signatures of M1 macrophage polarization were also evident in tumor tissue from the remaining 6/8 mice treated with2compared to untreated tumors.

These findings demonstrate Ru(II) complexation plays a critical role in ER targeting which triggers ICD, highlighting the potential of Ru(II) agents as futurein situtumor vaccines.
The cGAS-STING Pathway Is Essential in Acute Ischemia-Induced Neutropoiesis and Neutrophil Priming in the Bone Marrow
Authors: Zhu Jiankun , Ruan Xinjia , Mangione MariaSanta C , Parra Pablo , Su Xiaoping , Luo Xiang , Cao Dian J
Published: July 2024

Acute myocardial ischemia triggers a rapid mobilization of neutrophils from the bone marrow to peripheral blood, facilitating their infiltration into the infarcted myocardium. These cells are critical for inducing inflammation and contributing to myocardial repair. While neutrophils in infarcted tissue are better characterized, our understanding of whether and how ischemia regulates neutrophil production, differentiation, and functionality in the bone marrow remains limited. This study investigates these processes and the influence of the cGAS-STING pathway in the context of myocardial infarction. The cGAS-STING pathway detects aberrant DNA within cells, activates STING, and initiates downstream signaling cascades involving NFKB and IRF3. We analyzed neutrophils from bone marrow, peripheral blood, and infarct tissues using MI models generated from wild-type,Cgas-/-, andSting-/-mice. These models are essential for studying neutropoiesis (neutrophil production and differentiation), as it involves multiple cell types. RNA sequencing analysis revealed that ischemia not only increased neutrophil production but also promoted cytokine signaling, phagocytosis, chemotaxis, and degranulation in the bone marrow before their release into the peripheral blood. Inhibition of the cGAS-STING pathway decreased neutrophil production after MI and down-regulated the same pathways activated by ischemia. Neutrophils lacking cGAS or STING were less mature, exhibited reduced activation, and decreased degranulation. Deletion of cGAS and STING decreased the expression of a large group of IFN-stimulated genes and IFIT1+ neutrophils from peripheral blood and the infarct tissue, suggesting that cGAS-STING plays an essential role in neutrophils with the IFN-stimulated gene signature. Importantly, transcriptomic analysis ofCgas-/-andSting-/-neutrophils from bone marrow and MI tissues showed downregulation of similar pathways, indicating that the functionality developed in the bone marrow was maintained despite infarct-induced stimulation. These findings highlight the importance of neutropoiesis in dictating neutrophil function in target tissues, underscoring the critical role of the cGAS-STING pathway in neutrophil-mediated myocardial repair post-ischemia.
Lipid droplet surface promotes three-dimensional morphological evolution of non-rhomboidal cholesterol crystals
Authors: Lee Hyun-Ro , Kang Seunghan , Choi Siyoung Q.
Published: July 2024

Cholesterol crystals, which cause inflammation and various diseases, predominantly grow in a platy, rhomboid structure on the plasma membranes but exhibit an uneven three-dimensional architecture intracellularly. Here, we demonstrate how cholesterol crystallizes in a non-rhomboidal shape on the surface of lipid droplets and develops into three-dimensional sheet-like agglomerates using anin vitrolipid droplet reconstitution system with stereoscopic fluorescence imaging. Our findings reveal that interfacial cholesterol transport on the lipid droplet surface and unique lipid droplet components significantly influence the nucleation-and-growth dynamics of cholesterol crystals, leading to crystal growth in various polygonal shapes. Furthermore, cholesterol crystals readily agglomerate to form large, curved sheet structures on the confined, spherical surfaces of lipid droplets. This discovery enhances our understanding of the volumetric morphological growth of intracellular cholesterol crystals.
Phase transition of WTAP regulates m6A modification of interferon-stimulated genes
Authors: Cai Sihui , Zhou Jie , Luo Xiaotong , Zhang Chenqiu , Jin Shouheng , Ren Jian , Cui Jun
Published: July 2024

N6-methyladenosine (m6A) is the most prevalent modification of mRNA which controls diverse physiological processes. Although m6A modification is reported to regulate type I interferon (IFN) responses by targeting the mRNA of IFN-β and the interferon stimulated genes (ISGs), the detailed mechanism of how m6A methyltransferase complex (MTC) responses quickly to conduct the modification on nascent mRNA co-transcriptionally during IFN-β stimulation remains largely unclear. Here, we demonstrate that WTAP, the adaptor protein of m6A MTC, goes through dephosphorylation regulated phase transition from aggregates to liquid droplets under IFN-β stimulation. Phase transition of WTAP mediates the m6A modification of a subset of ISGs mRNA to restrict their expression. In mechanism, we found that formation of aggregates prevents WTAP from binding on the promoter region of ISGs or conducting m6A modification on mRNA in untreated cells. while IFN-β induced WTAP droplets interacts with nucleus-translocated transcriptional factor STAT1 and recruits MTC on the promoter region of ISGs, directing the co-transcriptional m6A modification on ISGs mRNA. Collectively, our findings reveal a novel regulatory role of WTAP phase transition under viral infection to orchestrate dynamic m6A modification with the cooperation of transcriptional factors and MTC, and precisely manipulate signaling pathway.
Positive and negative selective assortment in pairwise interactions
Authors: Izquierdo Segismundo S. , Izquierdo Luis R. , Hauert Christoph
Published: July 2024

In populations subject to evolutionary processes, the assortment of players with different genes or strategies can have a large impact on players’ payoffs and on the expected evolution of each strategy in the population. Here we consider assortment generated by a process of partner choice known asselective assortment. Under selective assortment, players looking for a mate can observe the strategies of a sample of potential mates or co-players, and select one of them to interact with. This selection mechanism can generate positive assortment (if there is a preference for players using the same strategy), or negative assortment. We study the impact of selective assortment in the evolution and in the equilibria of a population, providing results for different games under different evolutionary dynamics (including the replicator dynamics).
Circulating Myeloid-Derived Suppressor Cell load and disease severity are associated to an enhanced oligodendroglial production in a murine model of multiple sclerosis
Authors: Serrano-Regal Mari Paz , Camacho-Toledano Celia , Alonso-García Inmaculada , Ortega María Cristina , Machín-Díaz Isabel , Lebrón-Galán Rafael , García-Arocha Jennifer , Calahorra Leticia , Clemente Diego
Published: July 2024

Background

Multiple sclerosis (MS) is a chronic, inflammatory and demyelinating disease of the central nervous system (CNS) that is highly heterogeneous in terms of disease severity and tissue damage extent. Improving myelin restoration is essential to prevent neurodegeneration and the associated disability in MS patients. However, remyelinating therapies are failing in clinical trials, in part, due to the absence of classifying biomarkers of different endogenous regenerative capacities amongst enrolled patients. We previously reported that circulating monocytic myeloid-derived suppressor cells (M-MDSCs) at the onset of the murine model of MS experimental autoimmune encephalomyelitis (EAE) are associated with milder disease courses and less degree of demyelination and axonal damage in spinal cord lesions, while at peak are indicative of a better symptom recovery. Moreover, M-MDSCs are able to promotein vitrooligodendrocyte precursor cell (OPC) proliferation and differentiation towards mature oligodendrocytes (OLs) through the release of the soluble factor osteopontin.

Results

Here, we show a relationship between disease severity and a gradient of OPCs between the rim and the core in mixed active-inactive lesions of MS patients, along with a positive correlation between M-MDSC density and OPC abundance in the same lesions. We also show that EAE disease severity negatively influences the density of total and newly generated OPCs found associated to the demyelinated lesions of the spinal cord at the peak of the disease. In addition, disease severity also impacts the abundance of newly generated OLs originated either during the effector phase or during the early recovery phase. We also demonstrate the positive association between infiltrated M-MDSCs and the abundance of OPCs in the periplaque of demyelinating lesions at the peak of EAE. Interestingly, circulating M-MDSCs at EAE onset and peak of the disease are directly associated to a higher density of newly generated OLs in the plaque and periplaque, respectively.

Conclusion

Disease severity clearly impacts oligodendrocyte generation during a neuroinflammatory insult like EAE. Our results set the basis for further studies on M-MDSCs as a promising new biomarker that identify a CNS prone to the generation of new OLs that may contribute to restore myelin.
CB-1 receptor agonist drastically changes oscillatory activity, defining active sleep
Authors: Topchiy Irina , Kocsis Bernat
Published: July 2024

Brain oscillations in different behavioral states are essential for cognition, and oscillopathies contribute to cognitive dysfunction in neuro-psychiatric diseases. Cannabis-1 receptor (CB1-R) activation was reported to suppress theta and fast gamma activities in rats during waking exploration, and here, we show that cannabis fundamentally alters network activity during sleep, as well. Prominent theta rhythm is present in rapid eye movement sleep (REMS), whereas fast oscillations appear as regular sequences of sleep spindles during intermediate sleep (IS) - both implicated in dreaming and memory consolidation. The CB1-R agonist disrupted these mechanisms, restructuring IS-REMS episodes; IS lengthened 6-fold and intruded REMS, where on-going theta was drastically reduced. The spindle architecture was also affected; its amplitude increased, and its peak frequency down-shifted into the theta range. Cannabis is known to induce psychotic-like conditions and cognitive deficits; thus, our results may help understanding the dual effect of cannabis on cognitive states and the role of network oscillations in psychiatric pathology.
LCSkPOA: Enabling banded semi-global partial order alignments via efficient and accurate backbone generation through extended LCSk++
Authors: Weerakoon Minindu , Saunders Christopher T , Heaton Haynes
Published: July 2024

Background

Most multiple sequence alignment and string-graph alignment algorithms focus on global alignment, but many applications exist for semi-global and local string-graph alignment. Long reads require enormous amounts of memory and runtime to fill out large dynamic programming tables. Effective algorithms for finding the backbone and thus defining a band of an alignment such as the longest common subsequence with kmer matches (LCSk++) exist but do not work with graphs. This study introduces an adaptation of the Longest Common Subsequence with kmer matches (LCSk++) algorithm tailored for graph structures, particularly focusing on Partial Order Alignment (POA) graphs. POA graphs, which are directed acyclic graphs, represent multiple sequence alignments and effectively capture the relationships between sequences. Current state of the art methods like ABPOA and SPOA, while improving POA, primarily focus on global alignment and thus are limited in local and semi-global banding scenarios. Our approach addresses these limitations by extending the LCSk++ algorithm to accommodate the complexities of graph-based alignment.

Results

Our extended LCSk++ algorithm integrates dynamic programming and graph traversal techniques to detect conserved regions within POA graphs, termed the LCSk++ backbone. This backbone enables precise banding of the POA matrix for local and semi-global alignment, significantly enhancing the construction of consensus sequences. Compared to unbanded semi-global POA, our method demonstrates substantial memory savings (up to 98%) and significant run-time reductions (up to 37-fold), particularly for long sequences. The method maintains high alignment scores and proves effective across various string lengths and datasets, including synthetic and PacBio HiFi reads. Parallel processing further enhances runtime efficiency, achieving up to 150x speed improvements on conventional PCs.

Conclusion

The extended LCSk++ algorithm for graph structures offers a substantial advancement in sequence alignment technology. It effectively reduces memory consumption and optimizes run times without compromising alignment quality, thus providing a robust solution for local and semi-global alignment in POA graphs. This method enhances the utility of POA in critical applications such as multiple sequence alignment for phylogeny construction and graph-based reference alignment.
Sex-Specific Changes in Cardiac Function and Electrophysiology During Progression of Adenine-Induced Chronic Kidney Disease in Mice
Authors: Dargam Valentina , Sanchez Anet , Kolengaden Aashiya , Perez Yency , Arias Rebekah , Cabrera Ana M Valentin , Chaparro Daniel , Tarafa Christopher , Coba Alexandra , Yapaolo Nathan , Todd Emily A. , Williams Monique M. , Shehadeh Lina A. , Hutcheson Joshua D.
Published: July 2024

BACKGROUND

Chronic kidney disease (CKD) and cardiovascular disease (CVD) often co-exist and interact; however, notable sex-dependent differences are observed in how these conditions manifest and progress in parallel, despite men and women sharing similar risk factors. Identifying sex-specific diagnostic markers of cardiac structure and function throughout CKD progression could elucidate why the development and progression of these diseases differ by sex.

METHODS AND RESULTS

Adult, C57BL/6J male and female mice were subjected to a high-adenine (0.2%) diet throughout 12-weeks to induce CKD. Control mice were fed a normal chow diet. Every three weeks, electrocardiogram (ECG) and echocardiogram-based markers of cardiac physiology were evaluated. Adenine-induced CKD showed markers of left ventricular (LV) hypertrophy in male mice only. CKD males had markers indicative of LV systolic and diastolic dysfunction throughout regimen duration, worsening as disease progressed. Adenine males had a prolonged QTc and STc intervals when compared to Adenine females and Control males. Sex-dependent differences in the duration of the Speak-J marker, measured via ECG, was identified, with Adenine males showing increases in duration earlier than Adenine females compared to their Control counterparts.

CONCLUSIONS

In this study, we identified sex-dependent differences in cardiac structure, function, and electrophysiology in a mouse model of CKD-induced CVD throughout disease progression. We found that male mice are more prone to developing LV hypertrophy, systolic dysfunction, and diastolic dysfunction, with significant increases in ECG markers indicative of ventricular dysfunction observed in adenine-treated males at late stages of the disease. Additionally, we identified a new ECG parameter, Speak-J duration, that highlights sex-specific cardiac electrophysiological changes, demonstrating the model’s utility in studying sex-dependent cardiac differences.
Systemic inflammation is a minor contributor to remnant cholesterol atherogenicity
Authors: Kraaijenhof Jordan M. , Kerkvliet Marije J. , Nurmohamed Nick S. , Grefhorst Aldo , Kroon Jeffrey , Wareham Nicholas J. , Hovingh G. Kees , Stroes Erik S.G. , Boekholdt S. Matthijs , Reeskamp Laurens F.
Published: July 2024

Background

Both plasma levels of remnant cholesterol and low-density lipoprotein cholesterol (LDL-C) levels are independent risk factors for atherosclerotic cardiovascular disease. However, only remnant cholesterol has consistently been associated with systemic inflammation. The extent to which inflammation mediates the effect of remnant cholesterol on major adverse cardiovascular events (MACE) remains unclear.

Methods and Results

This study included 16,445 participants without prior atherosclerotic cardiovascular disease from the EPIC-Norfolk cohort, with a mean age of 58.8±9.1 years, of which 9,357 (56.9%) were women. Every 1 mmol/L higher remnant cholesterol was associated with 29.5% higher hsCRP levels (95% Confidence Interval (CI): 22.1, 37.4, p<0.001), whereas LDL-C was not significantly associated with hsCRP levels in the fully adjusted model. Additionally, each 1 mmol/L higher remnant cholesterol was associated with a hazard ratio (HR) of 1.31 (95% CI: 1.14, 1.50, p<0.001) for MACE, compared to a HR of 1.21 (95% CI: 1.13, 1.31, p<0.001) for LDL-C. Mediation analysis showed that hsCRP mediated 5.9% (95% CI: 1.2, 10.6%, p<0.001) of the effect of remnant cholesterol on MACE, whereas hsCRP did not mediate the effect of LDL-C.

Conclusions

Plasma remnant cholesterol levels are independently associated with systemic inflammation and cardiovascular events. Inflammation, as measured with hsCRP, contributed minorly to the association between remnant cholesterol and MACE. This underscores the need to address both remnant cholesterol and systemic inflammation separately in the clinical management of cardiovascular disease.

Graphical abstract:

The study assessed the relationship between remnant cholesterol, systemic inflammation, and MACE risk in 16,445 participants free from atherosclerotic cardiovascular disease from the EPIC-Norfolk cohort. Every 1 mmol/L higher remnant cholesterol was associated with 29.5% higher hsCRP levels (95% CI: 22.1, 37.4, p<0.001), while LDL cholesterol was not significantly associated with hsCRP levels. Additionally, each 1 mmol/L higher remnant cholesterol was associated with a HR of 1.31 (95% CI: 1.14, 1.50, p<0.001) for MACE, compared to a HR of 1.21 (95% CI: 1.13, 1.31, p<0.001) for LDL-C. hsCRP mediated 5.9% (95% CI: 1.2, 10.6%, p<0.001) of the effect of remnant cholesterol on MACE, while it did not mediate the effect of LDL cholesterol. LDL: low-density lipoprotein cholesterol, HR: hazard ratio, CI: confidence interval, MACE: major adverse cardiovascular events.
The Origin of Cognitive Modules for Face Processing: A Computational Evolutionary Perspective
Authors: Liu Jirui , Wang Xuena , Liu Jia
Published: July 2024

Despite extensive research, understanding how cognitive modules emerge remains elusive due to the complex interplay of genetic, developmental, and environmental factors. Computational modeling, however, provides a means of exploring their origins by directly manipulating these factors. Here we aimed to investigate the emergence of cognitive modules by developing the Dual-Task Meta-Learning Partitioned (DAMP) model, whose plastic architecture facilitates automatic structure optimization through a genetic algorithm that emulates natural selection by iteratively selecting for efficient learning fitness. We found that a specialized module for face identification robustly emerged in the DAMP model. Critically, the emergence of the face module was not influenced by the demands of cognitive tasks (identification versus categorization) or the type of stimuli (faces versus non-face objects). Instead, it was determined by the structural constraint of sparse connectivity within the network, suggesting that the face module may arise as an adaptation strategy to challenges posed by sparse connections in neural networks, rather than being an information processor required by certain stimuli or tasks. These findings provide a new evolutionary perspective on the formation of cognitive modules in the human brain, highlighting the pivotal role of the structural properties of neural networks in shaping their cognitive functionality.
Clinical Response to Azacitidine in Myelodysplastic Neoplasms is Associated with Distinct DNA Methylation Changes in Haematopoietic Stem and Progenitor cellsin vivo
Authors: Thoms Julie A.I. , Yan Feng , Hampton Henry R. , Davidson Sarah , Joshi Swapna , Saw Jesslyn , Sarowar Chowdhury H. , Lim Xin Ying , Nunez Andrea C. , Kakadia Purvi M. , Bhuyan Golam Sarower , Zou Xiaoheng , Nguyen Mary , Ghodousi Elaheh S. , Koch Forrest C. , Vafaee Fatemeh , Pickford Russell , Raftery Mark J. , Hough Sally , Buckland Griselda , Bailey Michelle , Ghodke Yuvaraj , Absar Noorul , Vaughan Lachlin , Pasalic Leonardo , Fong Chun Y. , Kenealy Melita , Hiwase Devendra K. , Stoddart Rohanna I. , Mohammed Soma , Lee Linda , Passam Freda H. , Larsen Stephen R. , Spring Kevin J. , Skarratt Kristen K. , Rebeiro Patricia , Presgrave Peter , Stevenson William S. , Ling Silvia , Tiley Campbell , Fuller Stephen J. , Roncolato Fernando , Enjeti Anoop K. , Hoenemann Dirk , Lemech Charlotte , Jolly Christopher J. , Bohlander Stefan K. , Curtis David J. , Wong Jason W H , Unnikrishnan Ashwin , Hertzberg Mark , Olivier Jake , Polizzotto Mark N. , Pimanda John E.
Published: July 2024

Hypomethylating agents are used as frontline therapy for myelodysplastic neoplasms (MDS), but clinical response is unpredictable. To determine whether response was associated within vivodynamics of DNA hypomethylation, we conducted a phase 2 trial for MDS using both injection and oral azacitidine (AZA). We established that global DNA methylation levels in peripheral blood and bone marrow mononuclear cells were comparable in AZA responders and non-responders during their course of treatment. However, there were distinct baseline and early drug induced differences in CpG methylation in haematopoietic stem and progenitor cells (HSPCs) in responders compared to non-responders that overlapped with regulatory regions of genes associated with tissue patterning, cell migration and myeloid differentiation. Following six cycles of therapy when clinical response typically manifests, differential hypomethylation in responder HSPCs pointed to marrow adaptation as a driver of enhanced haematopoiesis. Taken together, CpG methylation differences in HSPCs may explain variable response to AZA.
Live-cell imaging of pathogenic fungal hyphae reveal dynamic cellular responses to clinical antifungals
Authors: Thomson Darren David , Inman Rebecca , Bignell Elaine
Published: July 2024

Antifungal susceptibility testing quantifies end-point fungal biomass in liquid cultures initiated from non-invasive yeast or spore morphologies. However, end-point analyses obscure informative spatio-temporal responses to drug exposures. In the major fungal pathogens Aspergillus fumigatus and Candida albicans we used microfluidic-coupled, fluorescence-mediated live-cell imaging to capture the real-time responses of fungal hyphae to clinical concentrations of AmBisome or Caspofungin. In both fungi, AmBisome exposure caused rapid growth arrest, extensive hyphal vacuolation and membrane blebbing. Responses to Caspofungin exposure were slower with initial lytic effects occurring after 1.5 or 4 hours in A.fumigatus and C.albicans, respectively. Whilst C.albicans hyphae undergo unsalvageable hyphal lysis in response to Caspofungin, A.fumigatus exhibit several compensatory growth behaviours, including a novel resuscitative growth form, that circumvent lytic events to maintain apical and sub-apical hyphal growth. This study reveals how the differing biologies of the two pathogens affected outcomes and contributes to the highly disparate rates of antifungal efficacy amongst commonly used drugs, where spore/yeast-derived inhibitory doses may underestimate the dose required to arrest/kill the invasive hyphal morphotypes of fungal pathogens in vitro.
Correlated spontaneous activity sets up multi-sensory integration in the developing higher-order cortex
Authors: Dwulet JaeAnn M. , Zabouri Nawal , Kirchner Jan H. , Wosniack Marina E. , Raspanti Alessandra , Kong Deyue , Houwen Gerrit J. , Maldonado Paloma P. , Lohmann Christian , Gjorgjieva Julijana
Published: July 2024

To perceive and navigate complex sensory environments, animals combine sensory information from multiple modalities in specialized brain circuits. Known as multisensory integration, this process typically depends on the existence of co-aligned topographic connections from several sensory areas to downstream circuits exhibiting multimodal representations. How such topographically co-aligned connectivity necessary for multisensory integration gets set up in early stages of development is still unknown. Inspired by the role of spontaneous activity in refining topographic connectivity between early sensory circuits, here we investigated the potential of such spontaneous activity to also guide the co-alignment of multiple sensory modalities in RL, a higher-order associative cortical area rostro-lateral to V1. Analyzing spontaneous activity simultaneously recorded in primary visual and somatosensory cortex and area RL at different developmental ages before sensory experience, we identify candidate features of this activity to guide the emergence of co-aligned topographic multisensory projections with somatosensory leading the visual projection. We confirm this hypothesis using a computational model of activity-dependent circuit refinement, and show that the correlation of spontaneous activity between the visual and somatosensory primary cortex can establish an optimal fraction of multisensory neurons in RL for stimulus decoding. Our model provides an exciting new computational perspective of the role of spontaneous activity in the emergence of topographically co-aligned multimodal sensory representations in downstream circuits, specialized for the processing of rich sensory environments.
Novel verbal instructions recruit abstract neural patterns of time-variable information dimensionality
Authors: Pena Paula , Palenciano Ana F. , González-García Carlos , Ruz María
Published: July 2024

Human performance is endowed by neural representations of information that is relevant for behavior, some of which are also activated in a preparatory fashion to optimize later execution. Most studies to date have focused on highly practiced actions, leaving largely unaddressed the novel re-configuration of information to generate unique whole task-sets. Using electroencephalography (EEG), this study investigated the dynamics of the content and geometry reflected on the neural patterns of control representations during re-configuration of information. We designed a verbal instruction paradigm where each trial involved novel combinations of multi-component task information. By manipulating three task-relevant factors in a sample of 40 participants (26 females, 14 males), we observed complex coding schemes throughout the trial, during both preparation and implementation stages. The temporal profiles were consistent with a hierarchical structure: whereas task information was active in a sustained manner, the coding of more concrete stimulus features was more transient. Data showed both high dimensionality and abstraction, particularly during instruction encoding and target processing. Our results suggest that whenever task content could be recovered from neural patterns of activity, there was evidence of abstract coding, with an underlying geometry that favored generalization. During target processing, where potential interference across stimulus and response factors increased, orthogonal configurations also appeared. Overall, our findings uncover the dynamic manner with which control representations operate during novel recombination unique scenarios, with changes in dimensionality and abstraction adjusting along processing stages.

Significance Statement

The neural mechanisms that support task performance in novel contexts have been largely overlooked. Cognitive control is thought to enable complex behavior through the active maintenance of task sets, containing essential information for execution. However, how novel whole combinations of information are organized in neural patterns and their temporal dependencies remain unknown. Here, using a novel complex instruction paradigm, we observed that coding of informational content and its underlying geometry followed a dynamic temporal pattern. Our results reveal varying dimensionality and abstraction throughout the trial, with neural codes generally structured in a geometry favoring generalization of relevant information across task demands. These findings provide a first glimpse into the temporal computations engaged by the brain when encountering novel recombination settings.
Modelling genetic risk of β-cell dysfunction in human induced pluripotent stem cells from patients carrying theMTNR1Brisk variant
Authors: Singh T. , Kalamajski S. , Cunha J.P.M.C.M. , Hladkou S. , Roberts F. , Gheibi S. , Soltanian A. , Yektay Farahmand K. , Ekström O. , Mamidi A. , Franks P.W. , Rosengren A. , Semb H. , Mulder H. , Fex M.
Published: July 2024

Disruptions in circadian rhythm, partly controlled by the hormone melatonin, increase the risk of type 2 diabetes (T2D). Accordingly, a variant of the gene encoding the melatonin receptor 1B (MTNR1B) is robustly associated with increased risk of T2D. This single nucleotide polymorphism (SNP; rs10830963; G-allele) is an expression quantitative trait locus (eQTL) in human pancreatic islets, conferring increased expression ofMTNR1B, which is thought to perturb pancreatic β-cell function. To understand this pathogenic mechanism in detail, we utilized human induced pluripotent stem cells (hiPSC), derived from individuals with T2D carrying theMTNR1BG-allele. Patient-derived fibroblasts were reprogrammed to hiPSC and single-base genome editing by CRISPR/Cas9 was employed to create isogenic lines of either the C/C or G/G genotypes (non-risk and risk, respectively). In addition, the human embryonic stem cell (hESC) line (HUES4) was subjected to genome editing to create isogenic lines of either the C/C or G/G genotypes. hiPSC and hESC were differentiated into β-cells, using a 50-day 2D protocol. Single-base genome editing generated cells with the desired genotype at a success rate of >90%. Expression of stage-specific markers confirmed differentiation of both hiPSC and hESC into β-cells.MTNR1BmRNA levels were consistently low in differentiated β-cells, precluding quantitative analysis of gene expression. However, Western blot analysis showed higher levels of MTNR1B in differentiated β-cells carrying the risk allele, consistent with rs10830963 (G-allele) being an eQTL in β-cells. Insulin secretion in response to glucose and IBMX was similar between the genotypes, whereas addition of melatonin reduced secretion in G-allele carriers. We conclude that the stem cell-derived β-cells are not sufficiently mature to allow determination of eQTL status at the mRNA level. However, we did observe increased MTNR1B protein and increased sensitivity of β-cells from risk allele carriers (G-allele) to melatonin with regard to insulin secretion, thus supporting a functional role for the rs10830963 SNP in β-cell dysfunction.
Adaptive Safety Coding in the Prefrontal Cortex
Authors: Tashjian Sarah M. , Cussen Joseph , Deng Wenning , Zhang Bo , Mobbs Dean
Published: July 2024

Pivotal to self-preservation is the ability to identify when we are safe and when we are in danger. Previous studies have focused on safety estimations based on the features of external threats and do not consider how the brain integrates other key factors, including estimates about our ability to protect ourselves. Here we examine the neural systems underlying the online dynamic encoding of safety. The current preregistered study used two novel tasks to test four facets of safety estimation:Safety Prediction,Meta-representation,Recognition, andValue Updating. We experimentally manipulated safety estimation changing both levels of external threats and self-protection. Data were collected in two independent samples (behavioralN=100; fMRIN=30). We found consistent evidence of subjective changes in the sensitivity to safety conferred through protection. Neural responses in the ventromedial prefrontal cortex (vmPFC) tracked increases in safety during all safety estimation facets, with specific tuning to protection. Further, informational connectivity analyses revealed distinct hubs of safety coding in the posterior and anterior vmPFC for external threats and protection, respectively. These findings reveal a central role of the vmPFC for coding safety.
Hysteresis and noise floor in gene expression optimised for persistence against lethal events
Authors: Bokes Pavol , Singh Abhyudai
Published: July 2024

Bacterial cell persistence, crucial for survival under adverse conditions like antibiotic exposure, is intrinsically linked to stochastic fluctuations in gene expression. Certain genes, while inhibiting growth under normal circumstances, confer tolerance to antibiotics at elevated expression levels. The occurrence of antibiotic events lead to instantaneous cellular responses with varied survival probabilities correlated with gene expression levels. Notably, cells with lower protein concentrations face higher mortality rates. This study aims to elucidate an optimal strategy for protein expression conducive to cellular survival. Through comprehensive mathematical analysis, we determine the optimal burst size and frequency that maximise cell proliferation. Furthermore, we explore how the optimal expression distribution changes as the cost of protein expression to growth escalates. Our model reveals a hysteresis phenomenon, characterised by discontinuous transitions between deterministic and stochastic optima. Intriguingly, stochastic optima possess a noise floor, representing the minimal level of fluctuations essential for optimal cellular resilience.
Interactions between weather, ungulates and geese create opportunities for wood-pasture cycles
Authors: Kramer Koen , Cornelissen Perry , Groot Bruinderink Geert W.T.A. , Kuiters Loek , Lammertsma Dennis , Vulink J. Theo , van Wieren Sip E. , Prins Herbert H.T.
Published: July 2024

Managing nature reserves to achieve coexistence of ungulate species and vegetation heterogeneity is challenging in small reserves. A central question is whether spatial heterogeneity is maintained or restored through occasional natural disturbances. This is the premise of the wood-pasture hypothesis, which asserts that natural disturbances, such as winter severity, are sufficiently significant to sustain the long-term coexistence of ungulate species and provide opportunities for the establishment of shrubs and trees, thereby enhancing vegetation heterogeneity. Testing the wood-pasture hypothesis under field conditions necessitates long-term time series of both vegetation and herbivore dynamics. Therefore, we employed a modeling approach to test this hypothesis.

The study area was the Oostvaardersplassen, a nature reserve in the Netherlands characterized by rich and productive clay soil. This area hosts an assemblage of Heck cattle, Konik horses, and red deer. Additionally, large numbers of geese frequent this reserve, competing for the same food resources. The Oostvaardersplassen is one of the few areas in Europe where neither the populations of coexisting herbivore species nor the vegetation have been managed and its development was monitored for several decades. This provides unique insights into natural herbivore-vegetation interactions that can be applied to the management of other nature reserves.

The results indicate that weather variability and the presence of both geese and large ungulates are essential factors in creating a heterogeneous landscape. The general pattern is that weather variability induces fluctuations in ungulate numbers, and geese reduce the numbers of ungulates. Coexistence of the three ungulate species remains possible regardless of weather variability and the presence of geese. However, the presence of the largest ungulate, cattle, is threatened when weather is highly variable and geese numbers are high. The vegetation is likely evolving towards a predominantly open landscape with occasional opportunities for the establishment of spiny shrub species. Nature reserves managed with an assemblage of ungulate species, which numbers are controlled by food supply, winter severity and competition, should thus focus on the substantial presence of a few species (“biomassality,” e.g., for migratory birds) rather than achieving the highest species diversity in a small area (“biodiversity”).
Olfactory cortical outputs recruit and shape distinct brain-wide spatiotemporal networks
Authors: Ma Teng , Wang Xunda , Lin Xuehong , Wen Junjian , Xie Linshan , Khong Pek-Lan , Cao Peng , Wu Ed X. , Leong Alex T. L.
Published: July 2024

Odor information is transmitted from the olfactory bulb to several primary olfactory cortical regions in parallel, including the anterior olfactory nucleus (AON) and piriform cortex (Pir). However, the specific roles of the olfactory bulb and cortical outputs in wider interactions with other interconnected regions throughout the brain remain unclear due to the lack of suitable in vivo techniques. Furthermore, emerging associations between olfactory-related dysfunctions and neurological disorders underscore the need for examining olfactory networks at the systems level. Using optogenetics, fMRI, and computational modeling, we interrogated the spatiotemporal properties of brain-wide neural interactions in olfactory networks. We observed distinct downstream recruitment patterns. Specifically, stimulation of excitatory projection neurons in OB predominantly activates primary olfactory network regions, while stimulation of OB afferents in AON and Pir primarily orthodromically activates hippocampal/striatal and limbic networks, respectively. Temporally, repeated OB or AON stimulation diminishes neural activity propagation brain-wide in contrast to Pir stimulation. Dynamic causal modeling analysis reveals a robust inhibitory effect of AON outputs on striatal and limbic network regions. In addition, experiments in aged rat models show decreased brain-wide activation following OB stimulation, particularly in the primary olfactory and limbic networks. Modeling analysis identifies a dysfunctional AON to Pir connection, indicating the impairment of this primary olfactory cortical circuit that disrupts the downstream long-range propagation. Our study for the first time delineates the spatiotemporal properties of olfactory neural activity propagation in brain-wide networks and uncovers the roles of primary olfactory cortical, AON and Pir, outputs in shaping neural interactions at the systems level.
Power-law adaptation in the presynaptic vesicle cycle
Authors: Mikulasch Fabian A. , Georgiev Svilen V. , Rudelt Lucas , Rizzoli Silvio O. , Priesemann Viola
Published: July 2024

After synaptic transmission, fused synaptic vesicles are recycled, enabling the synapse to recover its capacity for renewed release. The recovery steps, which range from endocytosis to vesicle docking and priming, have been studied individually, but it is not clear what their impact on the overall dynamics of synaptic recycling is, and how they influence signal transmission. Here we model the dynamics of vesicle recycling and find that the multiple timescales of the recycling steps are reflected in synaptic recovery. This leads to multi-timescale synapse dynamics, which can be described by a simplified synaptic model with ‘power-law’ adaptation. Using cultured hippocampal neurons, we test this model experimentally, and show that the duration of synaptic exhaustion changes the effective synaptic recovery timescale, as predicted by the model. Finally, we show that this adaptation could implement a specific function in the hippocampus, namely enabling efficient communication between neurons through the temporal whitening of hippocampal spike trains.
Programmable Editing of Primary MicroRNA Switches Stem Cell Differentiation and Improves Tissue Regeneration
Authors: Truong Vu Anh , Chang Yu-Han , Tu Yi , Nguyen Thi Kieu Nuong , Pham Ngoc Nam , Chang Chin-Wei , Chang Yi-Hao , Ngo Thi Kim Dung , Pham Huu Dang , Tu Jui , Dang Thuc Quyen , Truong Anh Vy , Hu Yu-Chen
Published: July 2024

Programmable RNA editing is harnessed for modifying mRNA. Besides mRNA, miRNA also regulates numerous biological activities, but current RNA editors have yet to be exploited for miRNA manipulation. To engineer primary miRNA (pri-miRNA), the miRNA precursor, we present a customizable editor REPRESS (RNA Editing of Pri-miRNA for Efficient Suppression of miRNA) and characterize critical parameters. The optimized REPRESS is distinct from other mRNA editing tools in design rationale, hence enabling editing of pri-miRNAs that are not editable by other RNA editing systems. We edited various pri-miRNAs in different cells including adipose-derived stem cells (ASCs), hence attenuating mature miRNA levels without disturbing host gene expression. We further developed an improved REPRESS (iREPRESS) that enhances and prolongs pri-miR-21 editing for at least 10 days, with minimal perturbation of transcriptome and miRNAome. iREPRESS reprograms ASCs differentiation, promotes in vitro cartilage formation and augments calvarial bone regeneration in rats, thus implicating its potentials for engineering miRNA for many applications such as stem cell engineering and tissue regeneration.
The kinesin Kip2 promotes microtubule growth using a bipartite polymerase module to deliver tubulin to microtubule plus-ends
Authors: Nadalis Simos , Neyret Aymeric , Abrieu Ariane , Drechsler Hauke , Liakopoulos Dimitris , Portran Didier
Published: July 2024

Kinesin molecular motors are essential for fundamental cellular processes such as chromosome segregation or vesicular transport. To fulfil their function, some kinesins promote microtubule growth, but the molecular mechanism underlying this activity remains unclear. One of the motors with the strongest microtubule growth-promoting activity is Kip2, a kinesin that is required for astral microtubule integrity and spindle positioning in yeast. Here we show that the ability of Kip2 to polymerize microtubules is coupled to binding and transport of free tubulin. We report that the Kip2 N-terminus is required to promote microtubule elongationin vitroandin vivo. Kip2 binds free tubulin through this unstructured, basic domain and delivers it to microtubule plus-ends. In addition to the N-terminus, we find that ATP hydrolysis and motor activity is also required for microtubule polymerisation. Finally, transfer of the Kip2 N-terminus to kinesin-1, a kinesin that lacks polymerase activity, transforms kinesin-1 into a tubulin-transporting microtubule polymerase. We propose that motor-driven tubulin delivery to microtubule plus-ends is an efficient mechanism used by kinesins to promote microtubule polymerization.
Robust and Memoryless Median Estimation for Real-Time Spike Detection
Authors: Burman Ariel , Solé-Casals Jordi , Lew Sergio E.
Published: July 2024

We propose a novel moving median estimator specifically designed for online detection of threshold crossings in multi-channel signals, such as extracellular neural recordings. This estimator offers two key advantages: a reduced sensitivity to outliers and the elimination of memory requirements for storing arrival times. Furthermore, its design facilitates parallel implementation on FPGAs, making it ideal for real-time processing of multi-channel recordings.