Biology subjects

BANERJEE, S.

Publications and source records attributed to BANERJEE, S..

7 recordsLinked to original sources

bioRxiv2025

Metagenomic characterisation of fungal communities associated with Scots pine bark beetles: mechanisms of selective antagonism and monoterpene tolerance

Bark beetle-associated fungi contribute to beetle nutrition, detoxification, and interactions with conifer hosts; however, their composition and function across development and environments remain poorly understood. We characterised fungal communities of two pine-feeding Ips bark beetles, I. sexdentatus and I. acuminatus, in larval, pupal, and adult stages, and in wild versus laboratory populations, using high-throughput ITS2 amplicon sequencing combined with qPCR and functional assays. Both beetles harboured a stable core mycobiome dominated by Kuraishia, Ogataea, Ophiostoma, Graphilbum and Cyberlindnera, while adults showed species-specific differences and wild beetles, especially I. acuminatus, exhibited greater diversity than laboratory populations. Beetles shared more taxa with unfed control wood than with gallery wood, indicating acquisition during feeding and concurrent restructuring of the wood mycobiome. Monoterpene bioassays on beetle-associated yeasts revealed that mixtures of -pinene, 3-carene and terpinolene suppressed growth more strongly than single compounds, suggesting synergistic inhibition. Yeasts selectively antagonised entomopathogenic fungi and expressed complementary cell-wall-lytic and digestive activities, consistent with combined roles in pathogen suppression and plant-polymer deconstruction. Our results show that Ips mycobiomes are conserved yet dynamic across life stages and environments, and emphasise the importance of multi-terpene and interaction assays for understanding bark beetle-fungus-conifer interactions. ImportanceOur study reveals that pine-feeding bark beetles co-evolved in close association with a stable core mycobiota that supports nutrient acquisition, detoxification, and chemical signalling, while additional fungal partners shift in response to beetle development, environment, and host context. By demonstrating higher mycobiome diversity in beetle larvae and wild populations, substantial overlap between beetle- and wood-associated fungi, differential sensitivity to monoterpene blends and selective antagonism of yeasts towards entomopathogenic fungi, our study unravels key ecological and mechanistic principles shaping beetle-fungus assemblages under conifers, paving the way for more in-depth functional investigations.

microbiology↗

bioRxiv2025

Exploring Brain State Changes Through Reaction Time in a Simultaneity Judgment Task: A Pilot Study on Multisensory Integration

Problem statementMultisensory Integration (MSI), the brains ability to merge information from different sensory modalities, relies on the Temporal Binding Window (TBW)--the interval during which stimuli are most likely to be perceived as simultaneous. Beyond its role in perception, MSI may also reflect changes in brain state as task difficulty evolves. In this pilot study, we aimed to explore whether behavioral metrics, particularly reaction time (RT), can capture these brain state changes during a Simultaneity Judgment (SJ) task. Understanding this relationship is critical for developing adaptive Brain-Computer Interfaces (BCIs) that rely on real-time cognitive and perceptual feedback. ApproachTo assess how temporal alignment influences both perception and underlying brain state, we employed a Two-Alternative Forced Choice (2AFC) SJ task using audiovisual stimuli. After estimating individual simultaneity thresholds, we implemented an adaptive task that gradually increased difficulty by manipulating the stimulus onset asynchrony (SOA) closer to the TBW. We hypothesized that as perceptual uncertainty increased, RTs would reflect evolving cognitive states, serving as an observable indicator of underlying neural activity shifts. Materials and MethodsTwo participants were tested with consistent auditory (500 Hz tone) and visual (faded white circle) stimuli. The TE phase used a staircase procedure to determine personalized TBWs. In the subsequent adaptive test phase, SOAs were progressively modulated around these thresholds to induce varying levels of perceptual ambiguity. Behavioral responses were analyzed using psychometric curve fitting, confusion matrices, and detailed RT evolution across trials. Results and DiscussionParticipant 1 showed clear RT modulation near the TBW, suggesting heightened cognitive load and decision uncertainty--a potential signature of brain state transitions. In contrast, Participant 2 exhibited less sensitivity, possibly due to suboptimal thresholding. These preliminary findings suggest that RT holds promise as a behavioral correlate of perceptual state; however, further refinement and standardization of the task are needed before it can be reliably scaled to larger and more controlled studies of MSI-linked brain dynamics.

neuroscience↗

bioRxiv2025

Pulmonary Hypertension Promotes Neuroinflammation and Neurodegeneration

IntroductionPulmonary arterial hypertension (PAH) is associated with neurocognitive deficits and abnormal brain MRI. Little is known about the mechanisms underlying these clinical observations. TDP-43 is a proteinopathy associated with frontotemporal lobar degeneration (FTLD), Alzheimers Disease, and Amyotrophic Lateral Sclerosis (ALS). In this study, we hypothesize PAH will result in gliosis, reduced neuronal density, and increased TDP-43 mislocalization. MethodsSprague Dawley rats were randomly assigned to receive Vehicle (DMSO) Monocrotaline, or Sugen/Hypoxia to induce PH. Right heart catheterization was used to confirm PAH. Brain tissue was fixed and probed for microglia (Iba1), astrocytes (GFAP), neurons (NeuN), and TDP-43. Human PH vs control brain tissue was also probed for NeuN and TDP-43. Results and ConclusionsWe identify an increase in microglia and astrocyte density in the frontal cortex along with reduced neuronal density and neuronal TDP-43 mislocalization in rat models of PH. In addition, human PH frontal cortex demonstrated neuronal TDP-43 mislocalization. This is the first evidence of TDP-43 proteinopathy in PH.

physiology↗

bioRxiv2025

AP-3 complex sorts preferential cargo to govern dense core vesicle function in neuroendocrine cells

This study reveals new insights into the role of the Adaptor protein (AP-3) complex in dense core vesicle function. Despite numerous studies, an existing knowledge lacuna in the role of AP-3 in DCV function prompted us to delve deeper. Advanced microscopy and biochemical analysis revealed compromised DCV exocytosis in AP-3-depleted PC12 cells and C. elegans. AP-3 depletion altered the size and positioning of DCVs. Golgi defects and RUSH (Retention under Selective Hook) substantiated the role of AP-3 in trans-Golgi DCV budding. Proteomics revealed the loss of specific known and putative novel DCV proteins, which were mislocalized and rerouted to lysosomes in AP-3-depleted cells. Bioinformatics, Proximity ligation assays and Co-immunoprecipitation identified interactions of mislocalized proteins with AP-3 subunit. These findings corroborated with functional defects in granule maturation, release modes, Zinc and neurotransmitter mobilisation. Our study highlights the complexity of the AP-3 complex in regulating DCV function and its importance in vesicle transport in neurons and neuroendocrine cells. SummaryThis work reveals the critical role of AP-3 complex in DCV function, highlighting its impact on DCV exocytosis, positioning, and trans-Golgi budding. This study identifies Dlk1 as a novel DCV cargo.

cell biology↗

bioRxiv2024

Cross Modal Correspondence based MultisensoryIntegration: A pilot study showing how HAV cues can modulate the reaction time.

We live in a multisensory world, where all our senses work together for giving us a fulfilling experience of the environment that we are in or during our use of immersive technologies. For gaining more insight into the temporal scale understanding of the integration phenomenon EEG based BCI can give us the understanding of the transient changes in the brain. In this study, we investigated the potential of incorporating haptics into crossmodal correspondence based research to induce MSI effect through either the active touch users feedback or crossmodal correspondences with visual and auditory modalities, such as Kiki Bouba effect. We designed two experiments: O_LIVisual stimuli were presented on a standard computer monitor, and auditory stimuli were delivered through computer dynamics. Participants responded using left or right hand by pressing either CapsLock or Enter buttons respectively. Visual cue consisted of a red circle displayed randomly either on the left or on the right side of the screen. Auditory cue was a brief high tone presented through left or right headphones for 500 ms. Text stimuli that appeared on the screen instructed participants to respond with their left or right hand. Before each trial there was a fixation central cross displayed for 500 ms. C_LIO_LIThis experiment was inspired by previous studies on Kiki-Bouba correspondence. Visual stimuli consisted of 4 shapes - circle, triangle, polygon with 6 vertices, and star - presented on a computer screen. Locations of the visual stimuli were randomized. Auditory stimuli were generated using the Online Tone Generator website (https://onlinetonegenerator.com/). 2 sets of sounds were used: the first set included sine, triangle, square, and sawtooth waveforms, each at a frequency of 500 Hz; the second set included sawtooth waveforms at frequencies of 50 Hz, 300 Hz, 600 Hz, and 2000 Hz (summarised in Table 2). C_LI O_TBL View this table: org.highwire.dtl.DTLVardef@4b63fdorg.highwire.dtl.DTLVardef@191b6cborg.highwire.dtl.DTLVardef@177e6f4org.highwire.dtl.DTLVardef@dba414org.highwire.dtl.DTLVardef@1f13b3c_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 2:C_FLOATNO O_TABLECAPTIONVisual and auditory stimuli used in Experiment 2 C_TABLECAPTION C_TBL Results suggested that it is indeed possible to achieve this type of integration without relying on complex haptic devices. Introducing haptics into BCI technologies through feedback touch or crossmodal correspondances holds potential to improve the user experience and information transfer rate (ITR). Participants, as expected, showed the lowest reaction times in congruent sequential test and the highest - in incongruent HAV cues based test. This indicates the importance preference for sequential cue presentation over simultaneous one. The time was significantly higher in case of Incongruent Haptic cues.

animal behavior and cognition↗

bioRxiv2021

Designing peptide drug with archaeal antimicrobial peptides against multidrug resistant bacterial biofilms and human diseases: an in silico approach

Novel peptide therapeutics have been the cardinal part of modern-day research. Such therapies are being incorporated to prevent the adverse effects of globally emerging multi-drug resistant bacteria and various chronic human diseases which pose a great risk to the present world. In this study, we have designed a novel peptide therapy involving archaeal antimicrobial peptides. In silico predictions assign the peptide construct to be antigenic, non-allergenic, non-toxic and having stable physicochemical properties. The secondary and tertiary structures of the construct were predicted. The tertiary structure was refined for improving the quality of the predicted model. Computational tools predicted intracellular receptors in Escherichia coli, Klebsiella pneumoniae and the human body to be possible binding targets of the construct. In silico docking of modelled peptide with predicted targets, showed prominent results against targets for complex human diseases and that of bacterial infections. The stability of those docked complexes was confirmed with computational studies of conformational dynamics. Certainly, the designed peptide could be a potent therapeutic against multi-drug resistant bacteria as well as several human diseases.

bioinformatics↗

bioRxiv2020

How young is your Muscle? A Machine Learningframework for motor functional assessment with ageingby NMF based analysis of HD-sEMG signal.

ObjectiveWith ageing, there are various changes in the autonomic nervous system and a simultaneous decline in the motor functional abilities of the human body. This study falls within the framework improvement of the clinical tools dedicated to the robust evaluation of motor function efficiency with ageing. MethodAnalysis of HD-sEMG signals recorded from 32 channels during Sit To Stand (STS) test are used for the functional assessment of body muscles. For this purpose, five primary characteristic features, iEMG, ARV, RMS, Skewness, Kurtosis, are employed for the study. A channel clustering approach is proposed based on the parameters using Non Negative Matrix Factorization (NMF). ResultsThe NMF based clustering of the HD-sEMG channels seems to be sensitive toward modifications of the muscle activation strategy with ageing during STS test. ConclusionThis manuscript provides a framework for the assessment of Motor Functional Age(MFA) of subjects having a range of chronological from 25 yrs to 75 yrs. The groups were made a decade apart and it was found that the MFA varies with the level of activeness of the muscle under study and a premature ageing is observed according to the change in activation pattern of the HD-sEMG grid.

bioengineering↗