Biology subjects

Krishnan, S.

Publications and source records attributed to Krishnan, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Relaxin-3 neurons of the zebrafish periaqueductal gray mediate behavioral responses evoked by darkness

Ambient illumination influences many aspects of brain function, including responses to threats. One brain region proposed to mediate these effects is the periaqueductal gray (PAG), an evolutionarily conserved midbrain structure that contains multiple subpopulations of peptidergic neurons. Here we ask which cell types in the larval zebrafish PAG respond to changes in ambient illumination. By registering post hoc gene expression to neurons recorded during exposure to sensory stimuli, we show that GABAergic PAG neurons expressing the neuropeptide Relaxin-3 (rln3a+) are persistently activated by darkness, while a neighboring subpopulation of GABAergic PAG neurons expressing penka is not. Zebrafish lacking rln3a show a reduction in locomotion during darkness. We propose that darkness recruits Relaxin-3-releasing PAG neurons to promote vigilance and potentiate defense circuits. These results identify a specific peptidergic population of PAG neurons that are potentially relevant to behavioral state dysregulation associated with excessive darkness.

neuroscience↗

bioRxiv2026

Distributed resonant coupling enables high efficiency power transfer to mm-scale bioelectronics

Miniaturized implantable bioelectronics offer breakthrough potential in disease treatment, biomarker monitoring, and physiological sensing. However, wireless power transfer (WPT) remains a central limitation for millimeter-scale devices, as scaling down the receiver size rapidly decreases coupling efficiency due to tissue attenuation, low quality-factors, reduced mutual inductance, and limited tolerance to spatial and angular displacement. Here, we introduce distributed resonant coupling (DRC), a 3-coil WPT paradigm which enables the receiver (Rx) to actively participate in a strongly coupled resonance, transforming the Rx from a passive energy harvester into an active participant in a strongly coupled regime. By co-designing transmitters (Tx), resonators (Rs), and mm-scale receiver coils (Rx) as fully coupled systems, DRC exhibits simulated maximum power levels of 66%, measured received power transfer efficiencies of [~]56%, and end-to-end DC power transfer efficiencies of 42%, delivering >420 mW to loads at 1 W of transmitted power while maintaining robust performance across a range of practically relevant orientations and tissue media. Systematic theoretical and experimental efforts establish core design rules for DRC systems enabling operation without specialized tuning integrated circuits or components. To illustrate the capabilities of DRC in practical applications in vivo, we demonstrate three technologies that capture a broad application space in bioelectronics: implant localization, rapid wireless battery charging, and ultraminiaturized drug delivery devices compatible with particulate drug formulations. Taken together, these results suggest operational capabilities across a wide range of angular tolerances (up to 60{degrees}), tissue depths and dielectric and scattering media.

bioengineering↗

bioRxiv2026

Striatal activity during contextual word learning is influenced by children's reading ability

Contextual word learning is a fundamental mechanism for vocabulary acquisition during childhood. In adults, successful inference of word meaning from context is intrinsically rewarding, and is associated with greater enjoyment and greater activity in reward-related brain regions. Whether similar reward mechanisms support word learning in children, and whether they differ as a function of ability, remains unknown. We used functional magnetic resonance imaging (fMRI) to examine neural responses during contextual word learning in 25 children aged 11-13 years with typical reading skills and in 20 age-matched children with dyslexia. Neurotypical readers showed enhanced activation in core reward-processing regions, including the ventral striatum, when successfully learning the meanings of novel words. In contrast, children with dyslexia did not exhibit comparable reward-related responses despite performing the same task. Crucially, this group difference was specific to word learning, as no significant group differences were observed in ventral striatal responses during a non-linguistic monetary reward task. In addition, to confirm the behavioural relevance of these neural findings, we examined an age-matched, independent sample of children. We found that stronger reading skills were associated with greater enjoyment during successful word learning. Together, these results suggest that interactions between reward and language systems during contextual word learning is influenced by reading proficiency. Reduced intrinsic reward responses to successful language learning may contribute to differences in reading development and have implications for the design of more engaging and effective reading interventions for struggling readers. Significance statementWe investigated how school-age childrens brains learn new words from context, highlighting the important role of reward systems in this process. We show that ventral striatum, a core region associated with reward processing, is activated when children learn the meaning of new words. This suggests learning the meaning of a new word can be its own reward, driving further learning and engagement. Yet, children with dyslexia showed reduced brain activity in the ventral striatum during language learning, even when they successfully learned words. These findings underscore the importance of understanding the mechanisms through which learning becomes rewarding, with implications for designing more engaging and effective reading interventions

neuroscience↗

bioRxiv2026

Colchicine Directly Targets Aldehyde Dehydrogenase 2 (ALDH2) to Suppress Radiation-Induced Senescence and Atherosclerosis

BackgroundIonizing radiation (IR) accelerates atherosclerosis through induction of cellular senescence, DNA damage, defective efferocytosis, and dysregulation of clonal hematopoiesis (CH) drivers. Although low-dose colchicine reduces ischemic cardiovascular events in coronary artery disease, the precise molecular mechanisms underlying its vasculoprotective effects remain incompletely defined, and whether it mitigates radiation-associated vascular injury is unknown. MethodsBone marrow-derived macrophages (BMDMs) were pretreated with low-dose colchicine and exposed to 2 Gy IR. Molecular effects were assessed by RNA-seq, immunoblotting, and molecular docking. In vivo effects were tested in a partial carotid ligation (PLCL) model using spatial proteomics. Human monocyte-derived macrophages (HMDMs) from thoracic malignancy patients were analyzed before and after radiation therapy (RT). ResultsLow-dose colchicine suppressed IR-induced macrophage senescence signaling while preserving NRF2 activity. In a cell-free assay, colchicine directly activated aldehyde dehydrogenase 2 (ALDH2) in a dose-dependent manner (EC50 1-5 nM), identifying ALDH2 as a direct molecular target of colchicine. Following irradiation, colchicine restored ALDH2, reduced mitochondrial (mt)ROS-dependent p90 ribosomal S6 kinase (p90RSK) activation and lipid peroxidation, preserved TET2 and DNMT3A expression, and rescued impaired efferocytosis while preventing nicotinamide adenine dinucleotide (NAD) and adenosine triphosphate (ATP) depletion. These protective effects were ALDH2-dependent, as they were lost with ALDH2 inhibition or depletion and were mimicked by pharmacologic ALDH2 activation. In vivo, colchicine attenuated radiation-induced atherosclerosis and macrophage senescence-associated stemness (SAS). Consistently, macrophages from patients after RT showed reduced ALDH2 with increased mtROS, lipid peroxidation, and senescence. ConclusionThese findings identify ALDH2 as a previously unrecognized molecular target of colchicine that links mitochondrial redox control to suppression of radiation-induced macrophage senescence and atherosclerosis and may contribute to the efficacy of low-dose colchicine in cardiovascular disease.

cell biology↗

bioRxiv2026

Direct Synthesis of Targeted Nanosized ICG J-aggregate for Photoacoustic Imaging

Indocyanine green (ICG) J-aggregates (JAs) are self-assembled particles characterized by a sharp and strong absorption peak in the near-infrared region ([~]890 nm), enhanced photostability, low fluorescence, and high photothermal conversion efficiency, compared to monomeric ICG. These attributes make ICG-JAs promising contrast agent candidates for photoacoustic imaging (PAI). However, traditional methods for synthesizing ICG-JAs often yield particles without targeting ability, which limit their applications. Thus, to synthesize targeted nanoscale JA, complex and multi-step encapsulation and filtration processes are generally required. To solve this issue, we introduce a robust and rapid strategy for direct synthesis of targeted nanoscale ICG-JA by co-assembling ICG and ICG-azide dyes under optimized formulation conditions that do not require encapsulation. The resulting nanoscale JAAZ particles (nJAAZ) exhibit diameters of [~]120-150 nm and are amenable to direct bio-orthogonal functionalization via copper-free click chemistry for the attachment of virtually any targeting ligands and/or biomolecules. We further demonstrate the strong photoacoustic signal generation of these nJAAZ in vitro and in vivo, highlighting their potential as a modular high-performance contrast agent platform for PAI. This work establishes a scalable and tunable platform for engineering functional JAs, opening new avenues for targeted molecular imaging and theranostic applications.

bioengineering↗

bioRxiv2026

Thermal-Acoustic Activation of Hydrophobic Polystyrene Supports for High-Efficiency Aqueous Solid-Phase Peptide Synthesis

Solid-phase peptide synthesis (SPPS) remains the dominant technique for peptide production. However, its reliance on hazardous organic solvents such as N, N-dimethylformamide (DMF) and dichloromethane (DCM) results in an adverse environmental burden. One potential approach is replacing these organic solvents with water to reduce the hazardous solvent consumption and improve the environmental footprint of peptide production. This has led to the emergence of aqueous solid-phase peptide synthesis (ASPPS) approaches. Although successful, these approaches require specialized hydrophilic resins or modified building blocks, limiting their industrial applicability and scalability. Moreover, conventional hydrophobic polystyrene supports, remain the most widely used solid supports in industrial SPPS due to their high loading capacity, mechanical robustness, and low cost. These resins are generally considered incompatible with aqueous conditions. Here, we demonstrate that industrially relevant 2-chlorotrityl chloride (CTC) polystyrene resin can support efficient peptide coupling under fully aqueous conditions by integrating a precipitate-free 1-Ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC{middle dot}HCl) and Oxyma activation system with a synergistic thermal-acoustic strategy. We posit that heating combined with ultrasonic irradiation likely promotes transient relaxation of the polystyrene matrix and enhances water penetration. This facilitates the diffusion of activated amino acid esters onto the hydrophobic resin required for coupling. The robustness of this aqueous methodology was validated through the synthesis of nine structurally diverse peptide sequences, including aromatic hydrogel-forming peptides, opioid peptides derived from enkephalins, toxin-inspired sequences, and a lipid-interacting fragment of -synuclein. Analytical characterization by HPLC and MALDI-TOF mass spectrometry confirmed successful peptide assembly with high crude purity. We anticipate that this thermal-acoustic aqueous SPPS strategy provides a scalable and accessible pathway toward sustainable peptide manufacturing on classical hydrophobic supports with aqueous chemistry.

biochemistry↗

bioRxiv2026

Scalable genotyping in fixed transcriptomes resolves clonal heterogeneity via single-cell sequencing

Despite the promise of single-cell transcriptomics for understanding cell states in heterogeneous populations, widely used platforms have limited ability to link transcriptional states to somatic mutations within the same cells. Here, we introduce Genotyping in Fixed Transcriptomes (GIFT) for the simultaneous detection of large numbers of targeted genetic variants with whole transcriptome profiles in single cells. The core innovation of GIFT is a rationally designed gapfilling reaction between adjacent single-stranded DNA (ssDNA) probes that barcodes native transcript sequence to enable highly-specific targeted mutation detection. GIFT achieves greater than 99% genotyping accuracy and flexible capture of hundreds of mutations per cell, including in formalin-fixed, paraffin-embedded (FFPE) tissue, enabling clonal lineage tracing in heterogeneous settings. We demonstrate the unique scalability of GIFT by profiling more than 700,000 cells from 35 donors with myeloproliferative neoplasms (MPN), revealing mutation-dependent hematopoietic responses to systemic inflammation associated with the characteristic JAK2V617 mutation, including an allelic dose gradient of interferon-associated transcriptional programs and priming of hematopoietic stem cells that develop into divergent disease states. The technical advantages of GIFT enable direct resolution of genotype-to-phenotype relationships via clonal tracing with comprehensive cell-state measurements at single-cell resolution.

genomics↗

bioRxiv2026

Neural correlates of novel word-form learning in developmental language disorder

Children with developmental language disorder (DLD) have persistent language learning difficulties and often perform poorly on pseudoword repetition, a task that probes phonological, memory, and speech-motor processes that support vocabulary acquisition. Research on the neural basis of pseudoword repetition in DLD is limited. We used whole-brain functional MRI (fMRI) to examine pseudoword repetition and repetition-based learning in 46 children with DLD (ages 10-15 years) and 71 age-matched children with typical language development. During scanning, children heard and repeated pseudowords paired with visual referents, allowing us to track learning-related changes in neural activity across repetitions. Repeated pseudoword production yielded comparable behavioural learning across groups, with faster productions by later repetitions. Post-scan, form-referent recognition was comparable across groups, whereas pseudoword repetition accuracy was lower in DLD. Pseudoword repetition engaged a distributed neural network, including inferior frontal cortex bilaterally (greater on the left), premotor and sensorimotor cortex, and posterior temporal and occipital regions. Group differences emerged primarily in regions where activity was task negative (i.e., below baseline or deactivated): lateral occipito-parietal cortex (posterior angular gyrus), medial parieto-occipital cortex (retrosplenial), and right posterior cingulate cortex. Learning-related decreases in activity were similar across groups, but region-of-interest analyses showed reduced leftward lateralisation of activity in inferior frontal gyrus in DLD. These findings suggest weaker disengagement of the default mode network during a linguistically demanding task in DLD. Although repetition-based pseudoword learning recruited similar neural mechanisms in both groups, these mechanisms may operate less efficiently in DLD, alongside reduced hemispheric specialisation in inferior frontal cortex. HighlightsO_LISimilar repetition-related neural attenuation across groups during pseudoword learning. C_LIO_LIReduced default-mode network suppression during pseudoword repetition in DLD. C_LIO_LIReduced left-hemisphere specialisation of inferior frontal cortex in DLD. C_LIO_LIRepetition-based learning in DLD supported by less efficient neural networks. C_LI

neuroscience↗

bioRxiv2025

Integrative lipidomics of brain and plasma uncovers sex-specific metabolic signatures in Parkinson's disease

Lipid dysregulation is increasingly recognized as a key feature of Parkinsons disease (PD). A central unresolved question, however, is whether lipidomic signatures identified in accessible peripheral biofluids faithfully recapitulate the pathogenic alterations within the central nervous system (CNS). This gap impedes the development of reliable biomarkers and constrains a comprehensive understanding of PD pathophysiology. To address this challenge, we employed a cross-species lipidomic approach. We modeled PD in both male and female mice by injecting human -synuclein preformed fibrils into the substantia nigra. Three months post-injection, lipidomic profiles of the midbrain and plasma were generated and compared. These findings were further validated in plasma from male and female PD patients and age-matched controls, enabling the identification of conserved alterations. We identified shared dysregulation of sphingolipids, glycerophospholipids, and fatty acids in the brains and plasma of diseased mice as well as in plasma from PD patients. Notably, lipids associated with lipid droplet biogenesis, including triacylglycerols and monoacylglycerols, were elevated in diseased mouse brains and patient plasma. These alterations coincided with a marked accumulation of lipid droplets in the mouse midbrain, and were further corroborated by increased lipid droplet abundance in macrophages derived from PD patients. Interestingly, lipid droplet accumulation exhibited sex-specific patterns: male mice displayed greater microglial accumulation, whereas female mice showed enhanced neuronal deposition. Together, these findings demonstrate that peripheral lipidomic signatures reflect CNS pathology in PD, highlighting new opportunities for biomarker discovery and therapeutic intervention. Furthermore, sex-specific lipid droplet accumulation in innate immune cells and neurons implicates these pathways as mechanistic contributors to PD and underscores the necessity of sex-stratified strategies in biomarker discovery and disease modeling.

neuroscience↗

bioRxiv2025

Insights into gallbladder cancer pathogenesis from a living organoid gallbladder cholangiocyte biorepository

Gallbladder cancer (GBC) while rare worldwide has a high prevalence in India. Pathogenesis is unclear and outcomes poor. Gallbladder cholangiocyte organoids (GCOs) or gallbladder carcinoma organoids (GBCOs) were developed and serially propagated from surgically resected gallbladder tissues with benign or malignant diseases, respectively. Patient derived organoids (PDOs) were derived from 15 normal; 58 inflamed; 12 xanthogranulomatous cholecystitis (XGC); 5 pre-invasive neoplasm and 13 invasive malignant gallbladder pathologies. Protocol optimisation achieved 58% (69/119) success in organoid generation and expansion. Organoids maintained tight junction integrity; P-gp pump and enzymatic activity; preserved tissue-specific gene and protein marker expression; histological features and genetic variations. Cryopreserved organoids from 62 patients with primary tissue and high-quality DNA, RNA and protein derivatives have been banked. In gene expression analyses of tissue, XGC samples clustered with malignant subtypes, separate from benign pathologies. Derived XGC organoids showed a similar clustering. Enriched hallmark pathways in XGC support neoplastic change through chronic inflammation. PDOs generated from different gallbladder pathologies are a promising model to investigate the pathogenesis of GBC. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/651639v1_ufig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@465f3dorg.highwire.dtl.DTLVardef@16c5f0org.highwire.dtl.DTLVardef@11d4807org.highwire.dtl.DTLVardef@163d072_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Optical recordings of synaptic vesicle fusion reveal diffusional dispersion

The primary unit of exocytosis, the synaptic vesicle, is replete with proteins which enable vesicle fusion. For maintaining synaptic transmission the vesicle proteins have to be rapidly cleared from the active zone. The immediate fate of the cargo post-fusion and the precise mechanism of its resorting into a readily retrievable pool (RRetP) for endocytosis remains unclear. To address this, we developed a purely presynaptic preparation, the xenapse, presynaptic boutons formed en face directly onto a glass coverslip enabling optical single vesicle recording by total internal reflection microscopy (TIRFM). Electron microscopy showed xenapses contain a few hundred synaptic vesicles (SVs), of which [~]40 SVs are primed (readily releasable pool, RRP), as revealed by single vesicle recordings using the pH-sensitive fluorescent protein pHluorin. Single fusion events synchronous with action potentials could be localized with [~]20 nm precision and rapid post-fusion diffusional dispersion of vesicular proteins observed with diffusion constants in the order of 0.1 {micro}m2/s. Unroofing of xenapses revealed numerous Clathrin-coated structures, enriched for vesicle cargo and numerically equivalent to about twice the measured RRP size. In this way SV proteins are rapidly cleared from the release site into this RRetP of pre-assembled pits to allow for rapid re-docking and re-priming at vacated release sites in synapses tuned for high-fidelity fast signaling.

neuroscience↗

bioRxiv2025

Non-canonical role for ATPase HSC70 in driving Clathrin remodeling during compensatory endocytosis in synapse

Neurons use Clathrin-mediated endocytosis to retrieve synaptic vesicle (SV) proteins during compensatory endocytosis after presynaptic SV fusion. We have shown SV cargo to be re-sorted and pre-assembled outside the active zone into Clathrin-coated structures (CCS) of variable size and curvature, constituting a readily retrievable pool. During compensatory endocytosis CCS of the readily retrievable pool must be remodeled swiftly into spherical vesicles within 10 seconds at physiological temperature. How this is achieved remains elusive. Here we performed live-cell imaging on intact as well as scanning electron microscopy on unroofed hippocampal Xenapses, TIRFM-amenable presynaptic boutons formed en-face on microstructured and functionalized coverslips. While CCS can slowly remodel into spherical pits in unroofed Xenapses within tens of minutes, this process is highly accelerated in intact Xenapses, as evidenced by the rapid (< 10 seconds) exchange of EGFP-labelled Clathrin and AP2 adaptor after photo-bleaching. This fast remodeling of CCS was observed in the absence of stimulation and cannot be explained by constitutive endocytosis. Hence, this process must be driven by cytosolic factors which are lost during unroofing. Using membrane-permeant interfering peptides we identify Hsc70, the ATPase which along with Auxilin drives uncoating of endocytosed Clathrin-coated vesicles, to have an additional role in driving curvature of invaginating CCS.

neuroscience↗

bioRxiv2025

Slow scission of single synaptic vesicles by Dynamin at physiological temperature

Compensatory endocytosis is crucial for the presynapse to maintain a functional pool of fusion-competent vesicles. Slow Clathrin-mediated endocytosis has been widely regarded as the primary mechanism of retrieval but this has been challenged by competing Clathrin-independent endocytic models, most notably sub-second ultra-fast endocytosis, reported to be predominant at physiological temperature. Here, we sought to resolve the salience of the respective endocytic modes by using a purely presynaptic preparation, the Xenapse, amenable to total internal reflection fluorescence microscopy (TIRFM). While the role of Clathrin is in dispute, Dynamin is widely acknowledged to figure as the scission protein at the invaginated vesicle neck. Hence, we labelled the endogenous Dynamin I with EGFP by CRISPR-Cas9 techniques and visualized single synaptic Dynamin-mediated scission events at very high temporal resolution. This revealed only a single slow mode of Dynamin-dependent retrieval with a half time of [~] 9 seconds at physiological temperature. Cross-correlational analysis with fluorescently labelled Clathrin confirmed these Dynamin events to be Clathrin-dependent. We thereby affirm Clathrin-mediated endocytosis as the primary mode of compensatory retrieval.

neuroscience↗

bioRxiv2024

Sensing of extracellular L-Proline availability by the integrated stress response determines the outcome of cell competition.

Cell competition is a quality control acting from development to the adult that eliminates cells that are less-fit than their neighbours. How winner cells induce the elimination of losers during this process is poorly understood. Here, we address this question by studying the onset of differentiation in mouse, where cell competition eliminates 35% of embryonic cells. These loser cells have mitochondrial dysfunction, and we find that this causes amino-acid deprivation and activation of the integrated stress response (ISR), a pathway essential for their survival. We show that L-Proline is a key amino-acid sensed by the ISR and that in a competitive environment, winner cells induce increased L-Proline uptake in loser cells. This causes ISR repression and their elimination. Our results imply that cell competition is acting as a nutrient sensor, eliminating dysfunctional cells when amino acids are plentiful but sparing them in nutrient poor environments.

developmental biology↗

bioRxiv2024

A contextual fear conditioning paradigm in head-fixed mice exploring virtual reality.

Contextual fear conditioning is a classical laboratory task that tests associative memory formation and recall. Techniques such as multi-photon microscopy and holographic stimulation offer tremendous opportunities to understand the neural underpinnings of these memories. However, these techniques generally require animals to be head-fixed. There are few paradigms that test contextual fear conditioning in head-fixed mice, and none where the behavioral outcome following fear conditioning is freezing, the most common measure of fear in freely moving animals. To address this gap, we developed a contextual fear conditioning paradigm in head-fixed mice using virtual reality (VR) environments. We designed an apparatus to deliver tail shocks (unconditioned stimulus, US) while mice navigated a VR environment (conditioned stimulus, CS). The acquisition of contextual fear was tested when the mice were reintroduced to the shock-paired VR environment the following day. We tested three different versions of this paradigm and, in all of them, observed an increased conditioned fear response characterized by increased freezing behavior. This was especially prominent during the first trial in the shock-paired VR environment, compared to a neutral environment where the mice received no shocks. Our results demonstrate that head-fixed mice can be fear conditioned in VR, discriminate between a feared and neutral VR context, and display freezing as a conditioned response, similar to freely behaving animals. Furthermore, using a two-photon microscope, we imaged from large populations of hippocampal CA1 neurons before, during, and following contextual fear conditioning. Our findings reconfirmed those from the literature on freely moving animals, showing that CA1 place cells undergo remapping and show narrower place fields following fear conditioning. Our approach offers new opportunities to study the neural mechanisms underlying the formation, recall, and extinction of contextual fear memories. As the head-fixed preparation is compatible with multi-photon microscopy and holographic stimulation, it enables long-term tracking and manipulation of cells throughout distinct memory stages and provides subcellular resolution for investigating axonal, dendritic, and synaptic dynamics in real-time.

animal behavior and cognition↗

bioRxiv2024

Unraveling Honey Bee's Waggle Dances in Natural Conditions with Video-Based Deep Learning

O_LIWild and managed honey bees, crucial pollinators for both agriculture and natural ecosystems, face challenges due to industrial agriculture and urbanization. Understanding how bee colonies utilize the landscape for foraging is essential for managing human-bee conflicts and protecting these pollinators to sustain their vital pollination services. To understand how the bees utilize their surroundings, researchers often decode bee waggle dances, which honey bee workers use to communicate navigational information of desirable food and nesting sites to their nest mates. This process is carried out manually, which is time-consuming, prone to human error and requires specialized skills. C_LIO_LIWe address this problem by introducing a novel deep learning-based pipeline that automatically detects and measures waggle runs, the core movement of the waggle dance, under natural recording conditions for the first time. We combined the capabilities of the action detector YOWOv2 and the DeepSORT tracking method, with the Principal Component Analysis to extract dancing bee bounding boxes and the angles and durations within waggle runs. C_LIO_LIThe presented pipeline works fully automatically with videos taken from wild Apis dorsata colonies in its natural environment, and can be used for any honey bee species. Comparison of our pipeline with analyses made by human experts revealed that our procedure was able to detect 93% of waggle runs on the testing dataset, with a run duration Root Mean Squared Error (RMSE) of less than a second, and a run angle RMSE of 0.14 radians. We also assessed the generalizability of our pipeline to previously unseen recording conditions, successfully detecting 50% of waggle runs performed by Apis mellifera bees from a colony managed in Tokyo, Japan. In parallel, we discovered the most appropriate values of the models hyperparameters for this task. C_LIO_LIOur study demonstrates that a deep learning-based pipeline can successfully and automatically analyze the waggle runs of Apis dorsata in natural conditions and generalize to other bee species. This approach enables precise measurement of direction and duration, enabling the study of bee foraging behavior on an unprecedented scale compared to traditional manual methods contributing to preserving biodiversity and ecosystem services. C_LI

ecology↗

bioRxiv2024

A comparison between full-length 16S rRNA Oxford Nanopore sequencing and Illumina V3-V4 16S rRNA sequencing in head and neck cancer tissues

IntroductionDescribing the microbial community within the tumour has been a key aspect in understanding the pathophysiology of the tumour microenvironment. In head and neck cancer (HNC), most studies on tissue samples have only performed 16S ribosomal RNA (rRNA) short-read sequencing (SRS) on V3-V5 region. SRS is mostly limited to genus level identification. In this study, we compared full-length 16S rRNA long-read sequencing (FL-ONT) from Oxford Nanopore Technology (ONT) to V3-V4 Illumina SRS (V3V4-Illumina). To date, this is the largest study using HNC tissues samples to perform FL-ONT of the 16S rRNA using ONT. MethodsSequencing of the full-length and the V3-V4 16S rRNA region was conducted on tumour samples from 26 HNC patients, using ONT and Illumina technologies respectively. Paired sample analysis was applied to compare differences in diversities and abundance of microbial communities. Further validation was also performed using culture-based methods in 16 bacterial isolates obtained from 4 patients using MALDI-TOF MS. ResultsWe observed similar alpha diversity indexes between FL-ONT and V3V4-Illumina technologies. However, beta-diversity was significantly different between techniques (PERMANOVA - R2 = 0.083, p < 0.0001). At higher taxonomic levels (Phylum to Family), all metrics were more similar among sequencing techniques, while lower taxonomy displayed more discrepancies. At higher taxonomic levels, correlation in microbial abundance from FL-ONT and V3V4-Illumina were higher, while this correlation decreased at lower levels. Finally, FL-ONT was able to identify more isolates at the species level that were identified using MALDI-TOF MS (81.3% v.s. 62.5%). ConclusionsFL-ONT was able to identify lower taxonomic levels at a better resolution as compared to V3V4-Illumina 16S rRNA sequencing. Depending on application purposes, both methods are suitable for identification of microbial communities, with FL-ONT being more superior at species level.

microbiology↗

bioRxiv2023

Reward Expectation Reduces Representational Drift in the Hippocampus

Spatial memory in the hippocampus involves dynamic neural patterns that change over days, termed representational drift. While drift may aid memory updating, excessive drift could impede retrieval. Memory retrieval is influenced by reward expectation during encoding, so we hypothesized that diminished reward expectation would exacerbate representational drift. We found that high reward expectation limited drift, with CA1 representations on one day gradually re-emerging over successive trials the following day. Conversely, the absence of reward expectation resulted in increased drift, as the gradual re-emergence of the previous days representation did not occur. At the single cell level, lowering reward expectation caused an immediate increase in the proportion of place-fields with low trial-to-trial reliability. These place fields were less likely to be reinstated the following day, underlying increased drift in this condition. In conclusion, heightened reward expectation improves memory encoding and retrieval by maintaining reliable place fields that are gradually reinstated across days, thereby minimizing representational drift.

neuroscience↗