Biology subjects

Rai, S.

Publications and source records attributed to Rai, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Dose-Response Immunomodulatory Effects of Mesenchymal Stem Cells-Derived Culture-Conditioned Media in Acute Graft-versus-Host-Disease

BackgroundMesenchymal stem cell-based therapy faces challenges that have driven interest in MSCs-derived culture-conditioned media (CCM) as a cell-free alternative. Our study aims to optimize the dose, and collection timing of CCM to enhance its therapeutic efficacy in aGVHD, while also standardizing co-culture conditions for CD3+ T-cell interaction with CCM. Material and MethodsHuman MSCs were isolated from BM and WJ and subsequently preconditioned under hypoxic conditions (1% O2) for 24 hours in a tri-gas incubator. Culture-conditioned media (CCM) was collected from both naive and hypoxia-preconditioned MSCs at 24, 48, and 72 hours and filtered using a 0.2 m membrane filter. CD3+ T-cell were isolated from PBMNCs derived from aGVHD patients. These T-cell were co-cultured at varying densities (2*106, 5*106, and 10*106 cells/ml) with different concentrations of CCM (25%, 50%, and 100%), and cell proliferation was assessed using the MTS assay. Furthermore, CD3+ T-cell proliferation and activation status were evaluated in a 2D co-culture model of CD3+ T-cell and CCM using flow cytometry. ResultsOur findings revealed that CCM collected at 48 hours, at a 50% concentration, exerted the most pronounced inhibitory effect on CD3+ T-cell proliferation, particularly at a density of 5*106 cells/ml, irrespective of the MSCs source. Hypoxia preconditioning significantly enhanced the immunomodulatory effects, with WJ-MSCsHYP-CCM demonstrating superior efficacy in suppressing T-cell proliferation, increasing the CD4+/CD8+ T-cell ratio, and reducing CD4+ T-cell activation compared to BM-MSCsHYP-CCM. ConclusionThese results emphasize the critical role of optimizing CCM collection timing and concentration to maximize therapeutic potential. Our study paves the way for the development of standardized, scalable, and effective cell-free therapies for aGVHD. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=198 HEIGHT=200 SRC="FIGDIR/small/640019v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@16ecc48org.highwire.dtl.DTLVardef@12591dborg.highwire.dtl.DTLVardef@18af4beorg.highwire.dtl.DTLVardef@1c9e8c9_HPS_FORMAT_FIGEXP M_FIG C_FIG Optimum conditions for CCM dose, collection time point, and CD3+ T-cell dose for effective immunomodulatory effect of MSCs-derived CCM in aGVHD. (created using Biorender.com)

immunology↗

bioRxiv2025

Consistency in floral volatiles impacts plant-pollinator interactions in the face of environmental change in the Eastern Himalayas

Floral scents are an important mediator of many plant-pollinator interactions. However, environmental and ecological change could affect the synthesis and emission of volatile chemicals that constitute floral scents, potentially influencing pollinator perception of scents. We investigated the effects of elevation and warming on the floral scents of multiple co-occurring alpine meadow plant species along an elevational gradient in the Eastern Himalayas (3000 - 4000 masl). We also investigated pollinator responses in the same locations using 3-D printed floral models that replicated the differing volatile constituents. Finally, we assessed how pollinator preferences changed with variations in elevation, flowering season and location. We found that elevation and in-situ warming using Open Top Chambers (OTC) led to significant intraspecific variation in the composition of floral scents, both in terms of quality and quantity of volatiles released. Nevertheless, conspecific floral scents across elevations were more similar to each other than to other species. Cafeteria assays using artificial floral models revealed that pollinator preferences were driven by a small number of volatiles (p-cymene, 2-pentylfuran and -pinene), but these preferences were abolished in a novel plant-pollinator community where the same floral volatiles were not detected. Our results suggest that the local odourscape established by the floral community present plays a key role in plant-pollinator interactions. This emphasizes the need to incorporate ecological impacts such as changes in community into climate change analyses to understand the long-term impacts of human activity on co-evolutionary relationships like pollination. Significance StatementFloral scents are important for most plant-pollinator interactions, and can be affected by environmental factors like elevation and temperature. Our study shows that elevation and simulated in situ warming change the composition of floral scents, yet scents from the same species were more similar to each other across elevations and temperatures than to other species. Further, pollinator preferences to these scents replicated in artificial models persisted in spite of variation in temperature and elevation, but not in a novel plant-pollinator community containing floral species not releasing those volatiles. This emphasizes the need to incorporate factors such as floral community composition into our understanding of the long-term impacts of climate change and human activity on co-evolutionary relationships like pollination.

ecology↗

bioRxiv2025

Divergent modulation of dopaminergic neurons by hypocretin/orexin receptors-1 and -2 shapes dopaminergic cell activity and socio-emotional behavior

BACKGROUNDMany neuropsychiatric disorders involve dysregulation of the dopaminergic (DA) input to the forebrain. Of particular relevance are DA projections stemming from the midbrain ventral tegmental area (VTA). A key neuromodulatory influence onto DAVTA neurons arises from lateral hypothalamic area hypocretin/orexin (OX) neurons. Despite being a major input, the differential action of orexin peptides A and B (OXA and OXB) on orexin receptors 1 and 2 in DA cells is poorly understood. We recently identified profoundly divergent functions of OX1R vs OX2R in DA cells in regulating sleep/wake architecture, brain oscillations and cognitive behaviors. OX2R, but not OX1R, loss dramatically increased time in EEG theta-rich (alert) wakefulness, reward-driven learning and attentional skills, but impaired inhibitory control. METHODSUsing genetically engineered mice whose DA cells selectively lack OX input via Hcrtr1 (DAOx1R-KO) or Hcrtr2 (DAOx2R-KO), we assessed intrinsic excitability and electrophysiological responses of DAVTA neurons and evaluated behavioral phenotypes across multiple domains. RESULTSWe uncover previously unrecognized effects of OX peptides on DAVTA cell response. In WT and control mice, we show that while OXA enhances, OXB diminishes DAVTA neuronal excitability. OX1R-deficient DA cells lose OXA responding and OX2R-deficient DA cells lose OXB responding. DA Ox1R loss generates anxiety-like behavior and context-dependent hyperactivity. In contrast, OX2R loss decreases sociability and, despite exhibiting enhanced reward-driven learning, mice show highly compromised aversion-driven learning. CONCLUSIONSWe evidence strikingly distinct functions of OX1R vs OX2R signaling in modulating the intrinsic excitability of DAVTA neurons and influencing DA-related behaviors. These data implicate OX[->]DA signaling pathways in neuropsychiatric endophenotypes relevant to obsessive-compulsive, attention-deficit/hyperactivity, and autism spectrum disorders, and raise important considerations for the development of OXR-targeted therapeutics.

neuroscience↗

bioRxiv2025

Hypoxia-Mediated Molecular Interactions of Tissue-Specific Mesenchymal Stem Cells Drive Metabolic Reprogramming and Immunomodulation in Acute Graft-versus-Host Disease

BackgroundMesenchymal stem cells (MSCs) mediate immunomodulation through various mechanisms, including apoptosis, efferocytosis, and mitochondrial transfer. Our study investigates the impact of hypoxia preconditioning on the immune metabolic reprogramming and immunomodulatory potential of MSCs in acute graft-versus-host disease (aGVHD). Additionally, we explored the differential immunomodulatory effects of tissue-specific MSCs, specifically bone marrow (BM) and Whartons Jelly (WJ), and elucidated the mechanisms underlying variability in their therapeutic efficacy. MethodsMSCs were isolated from BM and WJ and subjected to hypoxia preconditioning. Their immunometabolic programming potential was assessed by evaluating T-cell proliferation, regulatory T-cell (Treg) induction, effector T-cell differentiation toward Th2, Th9 phenotypes, and macrophage polarization, T-cell bioenergetics in the direct co-culture systems. ResultsWJ-MSCsHYP exhibited superior immunomodulatory properties compared to BM-MSCsHYP, by inhibiting T-cell proliferation, enhancing Treg induction, and promoting anti-inflammatory macrophage polarization. WJ-MSCsHYP demonstrated enhanced mitochondrial transfer to T-cell, improving mitochondrial health, reducing ROS, and promoting oxidative phosphorylation, leading to immune homeostasis. Unlike BM-MSCs, WJ-MSCs exhibited higher rates of apoptosis, which facilitated immune modulation through mechanisms independent of efferocytosis. ConclusionOur findings highlight that WJ-MSCsHYP is a superior candidate for aGVHD by utilizing apoptosis, mitochondrial transfer, and metabolic reprogramming to achieve immune regulation.

immunology↗

bioRxiv2024

High-Throughput Targeted Drug Screening for NF1-associated High-Grade Gliomas with ATRX Deficiency

Neurofibromatosis type 1 (NF1)-associated high-grade gliomas (HGGs) harboring ATRX mutations exhibit an aggressive clinical phenotype, driven by heightened genomic instability and metabolic reprogramming. Existing therapies, including chemotherapy and radiotherapy, are limited by resistance mechanisms and formation of secondary malignancy, underscoring the need for novel therapeutic strategies. Here, we report the results of a high-throughput screening of 10,000 small molecules aimed at identifying compounds selectively targeting vulnerabilities associated with concurrent ATRX and NF1 loss. Among the screened compounds, K784-6195 (ChemDiv ID) emerged as a promising candidate, exhibiting marked selective cytotoxicity in NF1-associated glioma cell lines with ATRX deficiency (IC50 = 4.84 {micro}M). In comparison, wild-type ATRX sporadic glioma cell lines (U251) exhibited significantly reduced sensitivity to K784-6195 (IC50 = 37.03 {micro}M). However, ATRX knockout U251 glioma cells recapitulating concurrent ATRX and NF1 loss exhibited heightened susceptibility to K784-6195 (IC50 = 20-23 {micro}M) compared to their wild-type counterpart. Metabolomic analysis revealed that K784-6195 treatment impairs metabolic pathways, including the pentose phosphate pathway, glutamine metabolism, and redox homeostasis, leading to oxidative stress and impaired cell survival. These findings highlight K784-6195 as a promising candidate for therapeutic development, offering a targeted approach for the treatment of NF-1 associated HGGs with ATRX deficiency.

cancer biology↗

bioRxiv2024

EEG data quality in large scale field studies in India and Tanzania

There is a growing imperative to understand the neurophysiological impact of our rapidly changing and diverse technological, social, chemical, and physical environments. To untangle the multidimensional and interacting effects requires data at scale across diverse populations, taking measurement out of a controlled lab environment and into the field. Electroencephalography (EEG), which has correlates with various environmental factors as well as cognitive and mental health outcomes, has the advantage of both portability and cost-effectiveness for this purpose. However, with numerous field researchers spread across diverse locations, data quality issues and researcher idle time due to insufficient participants can quickly become unmanageable and expensive problems. In programs we have established in India and Tanzania, we demonstrate that with appropriate training, structured teams, and daily automated analysis and feedback on data quality, non-specialists can reliably collect EEG data alongside various survey and assessments with consistently high throughput and quality. Over a 30-week period, research teams were able to maintain an average of 25.6 subjects per week, collecting data from a diverse sample of 7,933 participants ranging from Hadzabe hunter-gatherers to office workers. Furthermore, data quality, computed on the first 2,400 records using two common methods, PREP and FASTER, was comparable to benchmark datasets from controlled lab conditions. Altogether this resulted in a cost per subject of under $50, a fraction of the cost typical of such data collection, opening up the possibility for large-scale programs particularly in low- and middle-income countries. Significance StatementWith wide human diversity, a rapidly changing environment and growing rates of neurological and mental health disorders, there is an imperative for large scale neuroimaging studies across diverse populations that can deliver high quality data and be affordably sustained. Here we demonstrate, across two large-scale field data acquisition programs operating in India and Tanzania, that with appropriate systems it is possible to generate high throughput EEG data of quality comparable to controlled lab settings. With effective costs of under $50 per subject, this opens new possibilities for low- and middle-income countries to implement large-scale programs, and to do so at scales that previously could not be considered.

neuroscience↗

bioRxiv2024

Vocal species are more central in Eastern Himalayan Mixed-Species bird flocks

Mixed-species flocks (MSF) represent an important form of social organisation in bird communities worldwide. Despite its likely importance in flock formation and cohesion, the role of vocal communication in the formation and maintenance of MSF in birds is hitherto understudied. In this study, we examine if a species centrality within a mixed-species flock is influenced by its vocal behaviour during the dawn chorus, i.e., the time of MSF formation. Using acoustic sampling and field observations, we studied the bird species found in MSF in the Eastern Himalayas. Our results show differential vocal activity patterns among MSF-forming bird species and suggest a positive correlation between calling rates and closeness centrality (species importance in a flock) in understory MSFs. We also found a more synchronised vocalisation pattern in the understory MSFs, with a consistent peak in vocal activity in the early morning hours, whereas no consistent vocal pattern was found for canopy flocks. Overall, our results suggest a potential mechanism that drives MSF formation wherein the vocal activity of central species precedes and likely attracts participation from other attendant species.

ecology↗

bioRxiv2024

Social isolation reduces metabolic rate and social preference in Wild-type Zebrafish (Danio rerio)

Group living is a common feature of many animals and serves a variety of functions, including predator avoidance, collective foraging, and reproduction. Individuals from group-living species may face isolation from their social group in their natural environment. Prior research has shown that social isolation in zebrafish (Danio rerio), a highly social fish, results in physiological and behavioural changes, including reduced locomotor activity and loss of interest in their environment. We investigated whether social isolation was associated with differences in dissolved oxygen consumption rate, movement speed, and social preference in adult zebrafish. We subjected fish to one month of visual and olfactory social isolation, and measured metabolic rate via dissolved oxygen consumption rate before and after social isolation. A control group was not subjected to any form of social isolation but held in comparable housing. We measured movement speed and social interaction before and after social isolation using a social preference assay. We found that socially isolated fish show a significant decrease in oxygen consumption rate compared to Day 0 isolation baseline levels, whereas control fish did not show this decrease. After a month of social isolation fish also showed lower social preference, and lower movement speed. These findings could suggest reduced energy expenditure in the context of social isolation in this species. This work enhances our understanding of the physiological and behavioural consequences of isolation in social animals.

ecology↗

bioRxiv2024

A Comparative assessment of T-Cell response of Healthy donors and Acute Graft-versus-Host-Disease Patients: Customizing immune monitoring platform

BackgroundT-cell activation and proliferation are critical for understanding immune responses in both healthy and pathological conditions such as acute graft-versus-host disease (aGVHD). Phytohemagglutinin (PHA) and interleukin-2 (IL-2) are commonly used in in vitro assays to study T-cell responses. In view of the discrete response of T cells from aGvHD patients cohorts, our study optimized PHA / IL-2 based T-cell response among healthy individuals versus aGVHD patients. MethodsPeripheral blood was collected from age- and sex-matched healthy individuals (n=10) and aGVHD patients (n=10). CD3+ T-cell were isolated and stimulated with varying concentrations of PHA (1-10g/ml) and IL-2 (50-500 IU/ml). Cell proliferation was assessed using MTS and CFSE assays, while their apoptosis was evaluated with Annexin V/7-AAD staining. ResultsWe observed enhanced proliferation of healthy individuals at higher PHA concentrations (5-10g/ml), whereas aGVHD patients exhibited heightened proliferation even at lower PHA concentrations (1-2.5g/ml) at 48 hours. Prolonged exposure of T cells from GvHD patients to PHA led to decreased proliferation while it increased in the T cells from healthy donors.IL-2 supplementation (50 IU/ml) of T-cells from healthy donors significantly enhanced their proliferation and survival, with the optimal concentration supporting robust proliferation over extended culture periods. ConclusionOur study optimized PHA and IL-2 concentrations required for T-cell proliferation studies among healthy individuals and aGVHD patients. and underscored experimental conditions required for studying T-cell behavior/dysregulation in aGVHD condition. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/611044v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@ab3c47org.highwire.dtl.DTLVardef@2786forg.highwire.dtl.DTLVardef@30c698org.highwire.dtl.DTLVardef@3e4821_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights of the studyO_LILower doses of PHA (1.0g/ml) and IL-2 (50IU/ml) are optimum conditions for aGVHD patients derived CD3+ T-cell proliferation under in vitro conditions. C_LIO_LIThe maximum T-cell proliferation in healthy individuals occurs with 7.5g/ml PHA and 50IU/ml IL-2. C_LIO_LIHigher doses of PHA induce cytotoxicity in both cohorts. C_LIO_LIIL-2 significantly enhances T-cell survival, with 50IU/ml maintaining robust proliferation over extended periods. C_LI

immunology↗

bioRxiv2024

Plant U-Box 4 regulates chloroplast stress signaling and programmed cell death via Salicylic acid modulation

BackgroundIn response to environmental stresses, chloroplasts generate reactive oxygen species, including singlet oxygen (1O2), an excited state of oxygen that regulates chloroplast-to-nucleus (retrograde) signaling, chloroplast turnover, and programmed cell death (PCD). Yet, the central signaling mechanisms and downstream responses remain poorly understood. The Arabidopsis thaliana plastid ferrochelatase two (fc2) mutant conditionally accumulates 1O2 and Plant U-Box 4 (PUB4), a cytoplasmic E3 ubiquitin ligase, is involved in propagating 1O2 signals for chloroplast turnover and cellular degradation. Thus, the fc2 and fc2 pub4 mutants are useful genetic tools to elucidate these signaling pathways. Previous studies have focused on the role of 1O2 in promoting cellular degradation in fc2 mutants, but its impact on retrograde signaling from mature chloroplasts (the major site of 1O2 production) is poorly understood. ResultsTo gain mechanistic insights into 1O2 signaling pathways, we compared transcriptomes of adult wt, fc2, and fc2 pub4 plants. The accumulation of 1O2 in fc2 plants broadly repressed genes involved in chloroplast function and photosynthesis, while inducing genes and transcription factors involved in abiotic and biotic stress, the biosynthesis of jasmonic acid (JA) and salicylic acid (SA), microautophagy, and senescence. Elevated JA and SA levels were observed in 1O2-stressed fc2 plants. pub4 reversed most of this 1O2-induced gene expression and reduced the JA content in fc2 plants. The pub4 mutation also blocked JA-induced senescence pathways in the dark. However, fc2 pub4 plants maintained constitutively elevated levels of SA even in the absence of bulk 1O2 accumulation. ConclusionsTogether, this work demonstrates that in fc2 plants, 1O2 leads to a robust retrograde signal that may protect cells by downregulating photosynthesis and ROS production while simultaneously mounting a stress response involving SA and JA. The induction of microautophagy and senescence pathways indicate that 1O2-induced cellular degradation is a genetic response to this stress, and the bulk of this transcriptional response is modulated by the PUB4 protein. However, the effect of pub4 on hormone synthesis and signaling is complex and indicates that an intricate interplay of SA and JA are involved in promoting stress responses and programmed cell death during photo-oxidative damage.

plant biology↗

bioRxiv2024

Synergistic Hypoxia and Apoptosis Conditioning Unleashes Superior Mesenchymal Stem Cells Efficacy in Acute Graft-versus-Host-Disease

Mesenchymal stem cells (MSCs) have emerged as promising candidates for immune modulation in various diseases that are associated with dysregulated immune responses like Graft-versus-Host-Disease (GVHD). MSCs are pleiotropic and the fate of MSCs following administration is a major determinant of their therapeutic efficacy. In this context, we here demonstrate that hypoxia preconditioned apoptotic MSCs [bone marrow (BM), Whartons Jelly (WJ)] bear more immune programming ability in a cellular model of acute Graft-versus-Host-Disease (aGVHD). To this purpose, we programmed MSCs by exposing them to hypoxia and inducing apoptosis both sequentially as well as simultaneously. Our findings demonstrated that WJ MSCs that were conditioned with indicated approaches simultaneously induced the differentiation of CD4+T-cell towards Tregs, enhanced Th2 effector, and concomitantly mitigated Th1 and Th17, with polarization of M1 effector macrophages towards their M2 phenotype, and more interestingly enhanced efferocytosis by macrophages indicated Th2 programming ability of MSCs programmed by conjunctional approaches Overall, our study highlights the potential of WJ-MSCs conditioned with hypoxia and apoptosis concurrently, as a promising therapeutic strategy for aGVHD and underscores the importance of considering MSC apoptosis in optimizing MSCs-based cellular therapy protocols for enhanced therapeutic efficacy in aGvHD. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=123 HEIGHT=200 SRC="FIGDIR/small/588248v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@92c102org.highwire.dtl.DTLVardef@bd895forg.highwire.dtl.DTLVardef@185e041org.highwire.dtl.DTLVardef@45ef0f_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2023

Bamboozling Interactions: Interspecific associations within mixed-species bird flocks in bamboo in the Eastern Himalayas

O_LIBamboo, although widespread, is a globally understudied habitat, but supports significant biodiversity, including specialist bird species. Mixed-species bird flocks (flocks) are an important and regular feature of forest bird communities worldwide and have been well-studied. However, how and why flocks might differ between bamboo and non-bamboo habitats is unknown. C_LIO_LIWe studied flocks and their arthropod prey in rainforest and bamboo stands across two seasons in the Eastern Himalaya. Using network analysis, we compared interspecific associations within flocks, and asked if resource availability (arthropod abundance) drives flocking. C_LIO_LIBamboo and rainforest flocks were significantly different, with bamboo flocks being more cohesive, less modular and their species more interconnected. Further, bamboo flocks were more consistent in their composition across seasons whereas rainforest flocks partially disintegrated in spring, probably because of increased arthropod abundance. In bamboo, the loss of arthropods in an entire substrate and the increase in other substrates was potentially insufficient to cease flocking in spring. C_LIO_LIResource availability and the unique foraging behaviour of the bamboo specialists likely drive flocking in the Eastern Himalaya bamboo. Our study is among the few to describe bamboo flocks and we emphasise conserving bamboo stands to ensure persistence of this unique flock in the Eastern Himalaya. C_LI

ecology↗

bioRxiv2023

Limb regeneration is blastema dependent in a ladybird beetle, Cheilomenes Sexmaculata (Fabricius)

Holometabolous insects undergoes metamorphosis which involves an intercalated pupal stage between larva and adult. The body plan of the adult is established during pupal stage and larval systems are de-differentiated and reorganized in insects undergoing complete metamorphosis. In ladybird beetles, limbs amputated in larval stages are regenerated in adults. This occurs during pupation. Given that changes in pupa are akin to embryogenesis, does the lost limbs are redeveloped as a part of metamorphosis or has some pre-patterning initiated prior pupation? To study this we hypothesised that limb regeneration in a holometabolous ladybird beetles, Cheilomenes sexmaculata is the result of the recapitulation of the embryonic gene programs in the pupa. To test this, we exposed third larval stages of C. sexmaculata to amputation and prior to amputation the tissues on the amputated site was scraped off every 24hrs. It was found that limb regeneration does not occur in the treatment where scrapping was done. Assuming that these epidermal cells correspond to blastema, for limb regeneration in ladybird beetles blastema is essential and does not occur in its absence.

developmental biology↗

bioRxiv2023

IL-1β promotes MPN disease initiation by favoring early clonal expansion of JAK2-mutant hematopoietic stem cells

JAK2-V617F is the most frequent somatic mutation causing myeloproliferative neoplasm (MPN). However, JAK2-V617F can also be found in healthy individuals with clonal hematopoiesis of indeterminate potential (CHIP) with a frequency much higher than the prevalence of MPN. The factors controlling the conversion of JAK2-V617F CHIP to MPN are largely unknown. We hypothesized that IL-1{beta} mediated inflammation is one of the factors that favors this progression. We examined mono- or oligoclonal evolution of MPN by performing bone marrow transplantations at limiting dilutions with only 1-3 JAK2-mutant HSCs per recipient. Genetic loss of IL-1{beta} in JAK2-mutant hematopoietic cells or inhibition by a neutralizing anti-IL-1{beta} antibody restricted the early clonal expansion of these JAK2-mutant HSCs resulting in a reduced frequency of a CHIP-like state and a lower rate of conversion to MPN. The MPN disease-promoting effects of IL-1{beta} were associated with damage to sympathetic innervation leading to loss of nestin-positive mesenchymal stromal cells and required the presence of IL-1R1 on bone marrow stromal cells. The anti-IL-1{beta} antibody protected these mesenchymal stromal cells from IL-1{beta} mediated damage and limited the expansion of the JAK2-mutant clone. Our results identify IL-1{beta} as a potential therapeutic target for preventing the transition from JAK2-V617F CHIP to MPN. Brief summaryIn a mouse model of oligo-clonal myeloproliferative neoplasm (MPN), IL-1{beta} produced by JAK2-mutant cells favored expansion of sub-clinical JAK2-V617F clones and initiation of MPN disease.

cancer biology↗

bioRxiv2023

Peanut Shell Carbon Nanocellulose Preparation, Analysis and Plausible Role in Regenerative Medicine Using Mesenchymal Stem Cell Line C3H10t1/2

Peanut Shell is a major agro industry waste. Cellulose, the most abundant crystalline component of naturally porous peanut shell biomass. Nanomaterial science has actively used peanut shell as a source of nanocellulose. However, there are few reports on the biocompatibility of cellulose nanocrystal based nanocomposites from agro on mesenchymal cell lines. To evaluate how mesenchymal stem cells behave onto this scaffold in vitro, cellulose nanocrystals (CNCs) made from peanut shells were combined with polyvinyl alcohol (PVA) to create tissue engineering scaffolds. SEM images illustrated that for PVA/CNC nanocomposites and clean PVA respectively, increasing the CNC concentration was accompanied with pore size enlargement. The nanocomposites three-dimensional porous structure conveyed uneven and intertwined pore structures in additionto the pore distribution. The highest relative crystallinity was observed at 10 wt% of CNCs, according to X-ray diffraction, which also showed that the relative crystallinity of the PVA with 0 and 5 wt% of CNCs was lower than that of neat PVA. In order to confirm the modifications in chemical functional groups, Fourier transform infrared spectroscopy was utilized. The non-cytotoxicity of PVA/CNC_10% was measured for cell viability during an in vitro cytotoxicity test. Additionally, the acquired PVA/biocompatibility CNCs with the Murine Mesenchymal cell line (C 3H 10T 1/2) demonstrated good cell spreading and adherence to the material surfaces. These results suggest that future research into the in vitro integration of mesenchymal cells with a PVA/CNC scaffold can prove to be a promising candidate for regenerative purposes.

bioengineering↗

bioRxiv2023

Bird communities in a selectively logged tropical montane forest are dominated by small, low-elevation species

Tropical montane forests are critical centres of terrestrial biodiversity and endemism, and face a range of threats, including selective logging and climate change. However, few studies have explored the joint influence of these threats, particularly in tropical mountains, despite how crucial it is to understand the cumulative impact of forest loss and climate change on biodiversity. We used mist-netting and bird ringing data from a long-term (10-year) community and population monitoring program to examine how the composition of the mid-elevation Eastern Himalayan understorey bird community changed in the mid-elevation primary and logged forest. Because logged forest is warmer than primary forest, we hypothesised that the bird community would shift towards lower elevation species, with a faster transition in logged forest. Further, because logged forest has lower arthropod abundance, we hypothesised that the primary forest community would have larger species than the logged forest community. Our study shows that the bird community in the logged forest shifted towards lower-elevation species than in the primary forest (although this was not statistically significant). Moreover, we found that smaller species were better able to colonise warmer logged forest, whereas larger species reached higher densities in primary forest. These trends are likely to be driven by climate change causing upslope range shifts and logged forest selecting for species that are likely to tolerate the consequently altered abiotic (higher temperatures) and biotic (lower resources) environment. These findings have significant implications for understanding the impacts of forest loss and climate change on biodiversity, particularly in tropical montane forests.

ecology↗

bioRxiv2023

Understanding inter-individual social networks in mixed-species bird flocks

Mixed-species flocks (MSFs) are an important form of social organisation in forest bird communities worldwide. MSFs provide participants with the benefits of reduced predation risk and/or enhanced foraging efficiency. Recent work has shown that participation in MSFs confers long-term survival benefits in the face of anthropogenic change. However, our understanding of MSFs mainly comes from studies that examine species-level networks, where each node is a unique species and the edges or connections between nodes are associations/interactions between species. While valuable, such approaches might not allow us to understand and investigate the mechanisms that drive MSF formation and structure because social interactions and their effects occur at the individual-level. Empirical studies on multi-species, individual-level MSF social networks have seldom been undertaken due to the various complexities and logistical challenges involved. In this study, we use mist-netting and colour-ringing followed by a standardised observation protocol to construct individual-level social networks in MSFs at 2000m ASL in Eaglenest Wildlife Sanctuary, Arunachal Pradesh, Eastern Himalaya, India. First, we found two separate flocktypes at our study site, comprising two distinct sets of understorey species. The mechanisms contributing to individual-level co-occurrences are likely to differ between these flocktypes, and with MSFs in the Neotropics. The Rusty-fronted Barwing (the nuclear species of one flocktype) shows spatially disjunct territories for each flock while the Yellow-throated Fulvetta (nuclear species of the other flocktype) shows large spatial overlap in its MSF networks, which is likely driven by non-individual-specific benefits such as predation risk dilution. Further, the addition of associating individuals to the social networks has opposite impacts on the two networks. The addition of Coral-billed Scimitar Babblers to the barwing networks greatly reduces network modularity because the associating individuals bridge two modules of barwings (both spatially and in the social network). On the contrary, territorial Rufous-capped Babblers and Grey-cheeked Warblers increase the modularity of the spatially overlapping fulvetta network. Our study provides novel insights into flock formation mechanisms in the Eastern Himalaya, likely applicable to other multi-species flock systems in the Old World.

ecology↗

bioRxiv2022

Impact of clonal architecture on clinical course and prognosis in patients with myeloproliferative neoplasms

Myeloproliferative neoplasms (MPNs) are caused by a somatic gain-of-function mutation in one of three "disease driver" genes JAK2, MPL or CALR. About half of MPN patients also carry additional somatic mutations that modify the clinical course. The order of acquisition of these gene mutations has been proposed to influence the phenotype and evolution of the disease. We studied 50 JAK2-V617F-positive MPN patients who carried at least one additional somatic mutation and determined the clonal architecture of their hematopoiesis by sequencing DNA from single cell derived colonies. In 22 of these patients we also side-by-side applied Tapestri single-cell DNA sequencing (scDNAseq) with cells from the same blood sample. The clonal architectures derived by the two methods showed good overall concordance. scDNAseq showed higher sensitivity for mutations with low variant allele fraction, but had more difficulties distinguishing between heterozygous and homozygous mutations. By unsupervised analysis of clonal architecture data from all 50 MPN patients we defined 4 distinct clusters that differed by the order of acquisition of the mutations, and the complexity of the subclonal structure. Cluster 4, characterized by more complex subclonal structure without a preferred order of acquisition, correlated with reduced overall survival, and in multivariate analysis represented a risk factor independent of the MPN subtype or the age at diagnosis. Our results suggest that deciphering the clonal architecture in patients with MPN that carry multiple gene mutations can improve the molecular prognostic stratification that until now was primarily based on the number and type of gene mutations.

cancer biology↗