Biology subjects

Mukherjee, K.

Publications and source records attributed to Mukherjee, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Biomechanical effects of load-carrying in adolescent idiopathic scoliosis: a subject-specific musculoskeletal modelling study

Load carrying is a common activity during adolescence, yet its biomechanical consequences for the structurally asymmetric spine in adolescent idiopathic scoliosis (AIS) remain poorly understood. This study investigated how load magnitude, carrying height, and side of application influence spinal loading and paraspinal muscle forces in AIS. A subject-specific musculoskeletal model of a 16-year-old female with a 59{degrees} right-convex thoracic curve was used to simulate bilateral and unilateral load carrying at the hand, chest, and above-shoulder levels, with loads corresponding to 5%, 10%, and 15% of body weight. Intervertebral compressive and lateral forces and erector spinae (ES) and multifidus (MF) muscle forces were evaluated. Spinal loading increased progressively with load magnitude and carrying height. At 15% body weight, compressive forces at the curve apex increased from 511-566 N at hand level to 721-831 N above the shoulder. Unilateral carrying produced distinct side-dependent responses: convex-side carrying generated greater compressive forces, whereas concave-side carrying generated greater lateral forces, which were concentrated around the curve apex. Paraspinal muscles also exhibited muscle-specific responses. ES forces primarily reflected the imposed external asymmetry, with unilateral carrying eliciting predominantly contralateral recruitment, whereas MF maintained a characteristic convex-side dominance concentrated around the curve apex. These findings demonstrate that load carrying in AIS produces a coupled biomechanical response governed by both the external loading configuration and the pre-existing structural asymmetry of the spine, highlighting the importance of considering loading direction and muscular adaptation alongside load magnitude when evaluating everyday carrying activities in AIS.

bioengineering↗

bioRxiv2026

Influence of trunk posture on spinal loading and paraspinal muscle forces in adolescent idiopathic scoliosis: a subject-specific musculoskeletal modelling study

Adolescent idiopathic scoliosis (AIS) alters spinal geometry and may influence the biomechanical response of the spine during functional postures. However, posture-dependent changes in spinal loading and paraspinal muscle forces in AIS remain poorly understood. This study investigated the effects of trunk posture on intervertebral loading and paraspinal muscle forces using a subject-specific musculoskeletal model of an adolescent with AIS. The spinal deformity was reconstructed from biplanar radiographs and incorporated into a full-body musculoskeletal model. Flexion, extension, lateral bending, and axial rotation were simulated at three incremental magnitudes, with motion distributed across the thoracolumbar spine. Intervertebral compressive and lateral forces around the curve apex and forces in the erector spinae (ES) and multifidus (MF) muscles were evaluated. Trunk flexion produced the greatest compressive loading, reaching 337 N at the curve apex and 372 N two levels below the apex at 30{degrees} flexion. Lateral bending produced pronounced direction-dependent loading: concave-side bending increased lateral forces, whereas convex-side bending increased compressive forces. Axial rotation produced similar but smaller direction-dependent changes. Paraspinal muscle forces were consistently asymmetric, with concave-side dominance of the ES and convex-side dominance of the MF. Flexion and convex-sided movements generally produced greater muscle imbalance, while increasing posture magnitude amplified spinal loading and muscle forces. These findings demonstrate that trunk posture, movement direction, and magnitude substantially influence the biomechanical environment of the scoliotic spine and should be considered when evaluating spinal mechanics in AIS.

bioengineering↗

bioRxiv2026

Neuropilin-1 functions as a proviral and immunoregulatory host factor during Chikungunya virus infection

Neuropilin-1 (NRP1) is a transmembrane glycoprotein involved in angiogenesis, neurodevelopment, inflammation, cancer driven immune suppression, and immune homeostasis. However, its contribution to virus-induced immune responses is not explored. Chikungunya virus (CHIKV) is a re-emerging arthritogenic alphavirus that causes severe arthralgia, and myalgia, accompanied by heightened inflammatory cytokine responses. The host factors that drive these inflammatory responses, however, remain poorly defined. Here, in this current study, the role of NRP1 in CHIKV infection was investigated using in vitro, and in vivo model systems. Using genetic manipulation, pharmacological, and antibody blockade-mediated approaches in murine and human cellular infection models, it was demonstrated that NRP1 promotes CHIKV infection while restraining the production of proinflammatory cytokines. Furthermore, NRP1 inhibition selectively increased JNK phosphorylation. Hence, inhibiting JNK reduced the elevated cytokine production caused by NRP1 blockade. Moreover, NRP1 interacted with CHIKV-E1 and is involved in multiple phases of CHIKV infection. In addition, it was demonstrated that NRP1 inhibition using EG00229 trifluoroacetate can reduce viral infection in several CHIKV-susceptible cells, human peripheral blood macrophages, and in the in vivo mice model of infection. Together, these findings indicate that NRP1 is an important host factor and a probable therapeutic target during CHIKV infection. IMPORTANCEChikungunya virus (CHIKV) causes acute febrile illness that can progress to debilitating chronic musculoskeletal and occasional neurological complications. The absence of a globally available effective vaccine and the lack of specific antivirals underscore CHIKV as a major burden, especially in endemic tropical regions. There is a growing need to understand host factors that shape CHIKV-driven immune response. The importance of our study lies in understanding the immunoregulatory role of the host receptor Neuropilin-1 (NRP1) during CHIKV infection. We identify NRP1 as a novel host factor of CHIKV infection that also acts as a rheostat to restrict the inflammatory viral immune response. Moreover, we report anti-viral potential of the NRP1 antagonist EG00229 trifluoroacetate in multiple cell lines, primary cells, and mice model. Our findings indicate NRP1 as a probable therapeutic target in CHIKV pathogenesis.

immunology↗

bioRxiv2026

CASK hypomorph mice display cone photoreceptor dysfunction

Variants in the X-linked gene CASK are associated with neurodevelopmental defects. Animal model studies have demonstrated that conditions such as cerebellar hypoplasia, microcephaly, and optic nerve hypoplasia (ONH) are related to loss-of-function (LOF) in the CASK gene. CASK variants are associated with multiple ocular conditions spanning both anterior and posterior segments of the eye including retinopathies. Both Cask heterozygous knockout (+/-) mice and Cask knock-in (KI) mice with reduced Cask expression have been shown to display ONH. Cask (+/-) mice displayed no defects in retinal structure or function. Here, we have systematically examined the Cask (KI) mice. Our results demonstrate that the anterior segment of the eye in Cask (KI) mice does not display any obvious phenotype. Cask (KI) mice however show a reduced visual acuity in optomotor response. The retina of Cask (KI) mice does not exhibit any major changes in their structure, vasculature, or gene expression pattern. We, however, uncovered a specific dysfunction of the cone receptor in Cask (KI) mice using electroretinogram (ERG). Mechanistically this dysfunction arises due to lowered levels of cone-specific opsin (opsin1mw) in Cask (KI) mice. To the best of our knowledge, this is the first description of retinal dysfunction in an animal model with CASK gene suppression. We infer that like ONH and cerebellar hypoplasia, retinopathy also may represent CASK LOF.

neuroscience↗

bioRxiv2026

miRNA Sensor HuR Compartmentalizes Ago2-Uncoupled miRNAs to Lipid Droplets to Buffer miRNA Activity in Mammalian Cells

miRNA activity must be optimized to ensure target gene expression in mammalian cells in response to specific needs. How and when miRNA activity is regulated remains an open question in gene expression regulation, with limited information on how cellular machinery senses miRNA levels to regulate miRNA expression and activity. Because miRNAs are stable molecules that can be reversibly used, the existence of a miRNA-sensing mechanism in mammalian cells has been anticipated. With ectopic expression of miRNAs in mammalian cells, we found a dose-dependent miRNA buffering mechanism in which miRNA export and its storage on lipid droplets are essential for miRNA activity optimization in mammalian cells. We found that the miRNA-binding protein HuR, known for its role in miRNA export, has a dual function in mammalian cells. HuR uncouples miRNAs from Ago2 to facilitate association of lipid droplets with nonfunctional miRNAs, a process that gets augmented in cells with high lipid droplet content and restricted extracellular export. Thus, HuR acts as a miRNA sensor, and the optimal activity and abundance of HuR regulate miRNA storage on lipid droplets or its export to maintain cellular miRNA homeostasis, thereby preventing detrimental effects of an excess miRNA pool in mammalian cells. Thus, targeting miRNA export or lipid droplet association is an important strategy for buffering cellular miRNA levels. ImportanceTo ensure that target gene expression in mammalian cells is appropriately regulated, miRNA activity needs to be carefully fine-tuned. Although miRNAs are stable and can be reused, the precise mechanisms by which their levels are sensed and regulated remain unclear. Our research uncovered a fascinating dose-dependent miRNA buffering process that involves export and storage of miRNAs on lipid droplets--essential steps for precise regulation. We also found that HuR, a protein that facilitates miRNA export, plays a key role by uncoupling miRNAs from Ago2 and promoting their association with lipid droplets in cells with abundant lipid droplets and limited extracellular export capacity. Overall, HuR acts as a miRNA sensor, helping to balance miRNA storage and export to maintain cellular homeostasis and prevent the harmful effects of miRNA overactivity.

cell biology↗

bioRxiv2025

STING and VDAC inhibitors attenuate inflammation and ineffective erythropoiesis caused by an altered metabolome in the Nan (EKLF/E339D) mouse model of neonatal anemia

Erythroid Kruppel-like factor (EKLF/KLF1) is an essential transcriptional regulator of all aspects of erythropoiesis. The mouse neonatal anemia (Nan) mutation is driven by a semi-dominant mutation in one allele of the EKLF second Zn-finger at position E339D. RNA-seq analysis of Nan/+ erythroid cells showed that expression of numerous enzymes associated with metabolic pathways are changed as a result. We assessed and analyzed the effects of this dysregulation by mass spectrometry of embryonic and adult material. Our results show that mono-allelic expression of Nan-EKLF has profound impacts on erythroid cell metabolism: levels of amino acids, nucleotides, and metabolites are altered, more energy is needed for survival and proliferation, and glucose is taken up more rapidly. As a result, mitochondrial morphology is distorted, leading to VDAC1 oligomerization and mtDNA release to the cytosol. This activates the cGAS-STING signaling pathway and induces a type-I IFN response that drives inflammation. Use of STING or VDAC inhibitors alleviates these conditions both ex vivo and in vivo. Mechanistically, treatment restores normal erythroid cell divisions and differentiation, and decreases inflammatory pathways in the bone marrow. Our findings are likely directly relevant to the dyserythropoiesis observed in CDA type IV patients that carry a similar mutation.

molecular biology↗

bioRxiv2025

Isolation and Quantification of mRNAs from Subcellular Phase-Separated Structures from Detergent Permeabilized Brain Cells

Post-transcriptional regulation by RNA processing bodies, also known as P-bodies (PBs), is crucial for mRNA translation, localization, and stability in various animal cells, including neurons and glial cells. PBs facilitate spatial regulation of protein synthesis, influencing differentiation and synaptic function. Understanding mRNA dynamics in PBs is vital and is suspected to be impaired in neurodegenerative disorders. We developed a detergent-based method to isolate phase-separated P-bodies (PBs) free from cytosolic factors and RNAs, which allows us to examine their mRNA content under altered conditions. Using neuronal and glial cell models, we investigated the impact of A{beta}-oligomers on PB-associated mRNAs. In neurons, exposure to amyloid proteins disrupted the release of neuronal differentiation-related mRNAs, hindering their translation. Glial cells exhibited increased levels of cytoplasmic pro-inflammatory cytokine mRNAs after amyloid treatment, as they escaped from RNA processing bodies (PBs), ensuring enhanced translation. These findings underscore the dual role of PBs in controlling mRNA dynamics across cell types and illustrate how amyloid-induced stress may differently affect PB-mediated post-transcriptional control in neurons and astroglia. This method provides a platform for studying the mechanism and quantifying sub-organellar mRNA localization, as well as its effects on altered gene expression caused by amyloid proteins. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=195 HEIGHT=200 SRC="FIGDIR/small/669016v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@335e76org.highwire.dtl.DTLVardef@7ecf8dorg.highwire.dtl.DTLVardef@16c375dorg.highwire.dtl.DTLVardef@1a6c086_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIA detergent-based differential solubilization of RNAs from PBs in brain cells. C_LIO_LIIn neuronal cells, {beta}-Amyloid oligomers target specific neuronal differentiation-related mRNAs to PBs. C_LIO_LIIn astroglia, {beta}-amyloid triggers the escape of inflammatory cytokine mRNAs from PBs. C_LIO_LIAltered mRNAs -protein phase separation connects PBs to neuroinflammation. C_LI

cell biology↗

bioRxiv2025

Change of Guards: ELAVL Proteins Switch miRNA Export Responsibility to Regulate Neuronal Differentiation

ELAVL1 protein HuR controls the stability and activity of miRNAs by disconnecting miRNPs from their target mRNAs and exporting Ago2-uncoupled miRNAs to help hepatic and macrophage cells manage stress. In mammalian neurons, the homolog of HuR, ELAVL4 or HuD, is expressed; however, its role in miRNA regulation remains unknown. PC12, a rat pheochromocytoma cell line, is a well-established model for studying neuronal differentiation that resembles sympathetic neurons. In PC12 cells, HuD levels increase during differentiation, which suppresses HuR expression. Thus, HuD overrides HuRs control of miRNA activity in differentiating cells, promoting differentiation by regulating the activity and levels of specific miRNAs, such as let-7a and miR-125b. When HuD is present, it decreases the activity of these miRNAs by binding to them, thereby facilitating their export and ensuring neuronal differentiation. Overall, there is a shift in miRNA regulation, with HuR being replaced by HuD in controlling miRNA export during neuronal differentiation. This switch in ELAVL-mediated miRNA regulation is essential for the differentiation process.

molecular biology↗

bioRxiv2025

HuR-Dependent Cooperative Export of miRNAs From Activated Macrophages

miRNA export is a regulated process vital for maintaining balanced miRNA levels and target gene expression in metazoan cells. RNA-interacting proteins finely adjust the selectivity and specificity of miRNA export, ensuring context-dependent optimal extracellular export of gene-repressive miRNAs in higher eukaryotes. Our findings reveal that activated macrophage cells export miRNAs in a cooperative manner, where elevated expression of miR-122 can significantly enhance the export of miR-146a and selective others. We predict and observe that the cooperative export of repressive miRNAs achieves synchronized upregulation of pro-inflammatory targets in activated macrophage cells. Exploring the molecular basis of this event, we have noted the co-entry of miRNAs into endosomes for their extracellular export, highlighting the selective and cooperative nature of endosome targeting of miRNAs. HuR, a miRNA-binding protein crucial for selectively exporting specific sets of miRNAs from various cell types, facilitates cooperative miRNA entry into endosomes both in the in vivo and in vitro assay conditions. A catalytic amount of high-affinity miR-122 enhances HuRs binding to low-affinity miR-146a, facilitating the efficient endosomal compartmentalization of both miRNAs for their co-export via extracellular vesicles (EVs).

immunology↗

bioRxiv2025

Influence of simplifications on FE modelling of mandible and TMJ implants

End-stage temporomandibular joint (TMJ) disorders often necessitate joint replacement to restore bilateral mastication. Patient-specific TMJ implants typically rely on detailed in silico modelling derived from subject-specific computed tomography (CT) scans of the mandible. However, generating highly detailed finite element (FE) models is computationally expensive. Although structural simplifications of the mandible are known to influence mechanical behaviour, their quantitative impact on TMJ implant evaluation has not been systematically investigated. This study examines the influence of three modelling simplifications on stress-strain predictions in intact and implanted mandibles: (i) a detailed segmented mandible with tissue-specific material properties (Model 1), (ii) a simplified mandible comprising cortical bone only (Model 2), and (iii) a further simplified mandible excluding dental crowns (Model 3). Both narrow and standard TMJ implants were analysed under osseointegrated and non-osseointegrated conditions, resulting in fifteen FE models. Physiological clenching activities were simulated. Compared with the detailed model, simplified models showed reductions of up to 50% in maximum principal strain in bone and up to 44% in von Mises stress in TMJ implants, while preserving spatial stress-strain trends. These findings indicate that simplified models may be suitable for preliminary implant design, whereas detailed FE modelling remains essential for final pre-clinical evaluation.

bioengineering↗

bioRxiv2025

HuR-Driven Reversible Mitochondrial Shuttling Buffers Cytosolic miRNA Levels in Hepatic Cells

Mitochondria, the "powerhouse" of mammalian cells, also serve as key storage sites for ions, metabolites, and enzymes vital for metabolic regulation. Exploring the regulatory processes that control the activities of miRNAs, the key non-coding RNA in mammalian cells, we found a context-dependent reversible localization of specific miRNAs to the mitochondrial matrix. Our data suggests a de novo role of mitochondria as miRNA sinks in mammalian cells. miR-122 is a key hepatic miRNA regulating metabolic processes in the mammalian liver. In this study, we observed increased mitochondrial targeting of miR-122 in amino acid-starved hepatic cells. Interestingly, when cells were refed with amino acids, mitochondrial miR-122 gets relocalized and reused in the cytosol for the translational repression process. Moreover, this phenomenon is not limited to miR-122 as several mitochondrial miRNAs (mito-miRs) follow similar transient storage inside mitochondria in stressed cells. Remarkably, mitochondria-localized mito-miRs preferentially target mRNAs encoding crucial mitochondrial components related to apoptosis. Hence, hepatic cells regulate apoptosis pathways during the starvation-refeeding cycle by shuttling a specific set of miRNAs to and from mitochondria, thereby balancing cytosolic miRNA content and homeostasis. Stress response miRNA binder ELAVL1 or HuR protein was found to be both necessary and sufficient for transporting the mature mito-miRs to the mitochondrial matrix - a process also controlled by the interaction between mitochondria and the endoplasmic reticulum. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/647748v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@1178f5dorg.highwire.dtl.DTLVardef@1c5578borg.highwire.dtl.DTLVardef@f68555org.highwire.dtl.DTLVardef@ab9c40_HPS_FORMAT_FIGEXP M_FIG C_FIG Key PointsO_LISpecific miRNAs (mito-miRs), including miR-122, are targeted to mitochondria for transient storage in stressed hepatic cells. C_LIO_LIMito-miRs storage in mitochondria allows the expression of apoptosis-related genes in stressed cells. C_LIO_LIMito-miRs relocalization to cytoplasm on stress reversal allows suppression of apoptosis. C_LIO_LIBinding with ELAVL1 protein HuR allows reversible shuttling of mito-miRs to and from mitochondria in hepatic cells. C_LIO_LIER-mitochondrial interaction is key for the mitochondrial localization of miRNAs. C_LI

cell biology↗

bioRxiv2025

Sialylated flagellin from Pseudomonas aeruginosa modulates the process of dendritic cell maturation through Siglec-9 mediated suppression of TLR5 signaling

Sialic acids, a nine carbon acidic sugar, can be detected in Pseudomonas aeruginosa (PA) when it is cultured with any exogenous sialic acids source like serum. Subsequently, several sialoglycoproteins from PA have been identified which includes flagellin. In the current study, the sialylation status of PA flagellin has been further investigated through lectin and Siglecs binding. Siglecs are immunoglobulin-like receptors which can recognize and bind to sialic acids. The sialylated PA flagellin (Fla+Sia) was observed to bind with its cognate receptor TLR5 (Toll-like receptor 5) and also with Siglec-9 on dendritic cell (DC) surface. DCs are potent antigen-presenting phagocytic immune cells which can activate other immune cells through costimulation. Immature DCs undergo maturation upon encountering antigens; which involves changes in the cell morphology, receptors expression, cytokine secretion etc. Here, immature DCs stimulated with Fla+Sia or desialylated-Fla+Sia (ds-Fla+Sia) underwent maturation but exhibited different phenotypic and functional profiles. The Fla+Sia matured DCs showed relatively lower expression of costimulatory molecules, lower pro-inflammatory cytokines secretion, higher phagocytic activity and induced the generation of more Th (T helper) and Treg (regulatory T) cells. The impact of these two antagonistic signaling pathways-TLR5-based immune-activatory and immunosupressive Siglec-9 signaling on DC maturation was further explored in DCs generated from THP-1 cell line. Here, Fla+Sia stimulated DCs showed increased Siglec-9-SHP1 association while ds-Fla-Sia stimulation showed an increased TLR5 association with its interacting partners-MyD88/TRAF-6/IRAK-4. The TLR5/Siglec-9 signaling was disrupted through siRNA transfections or chemical inhibitor treatment which revealed that flagellin-based TLR5 stimulation was crucial for the initiation of robust cell signaling events. However, Fla+Sia treatment activated Siglec-9 signaling, which directly inhibited TLR5 pathway. Interestingly, downregulating Siglec-9 signaling resulted in enhanced TLR5 activation upon Fla+Sia stimulation, along with increased MAP kinase signaling and activation of the NF-{kappa}B pathway. Thus, Siglec-9 silenced DCs responded to Fla+Sia with increased secretion of pro-inflammatory cytokines. Therefore, the altered profile and T cell polarization ability of Fla+Sia matured DCs is caused by the Siglec-9-based disruption of TLR5 signaling.

immunology↗

bioRxiv2024

Biomechanical Evaluation of Femoral Neck Fracture Fixation Based on Finite Element Analysis

Pauwels type III fracture, wherein the fracture plane makes an angle of 50{degrees}-70{degrees} with the transverse plane, is the most unstable femoral neck fracture. Although there are various types of internal fixation devices, including Cannulated cancellous screws (CCS), dynamic hip screw (DHS), dynamic hip screw along with anti-rotation screws (DHS+ARS), and a newly introduced femoral neck system (FNS), patients with Pauwels type III fracture often experience implant failure. There was no study investigating the performance of these internal fixators under physiological musculoskeletal loading. The objective of the present study was to compare the biomechanical performance of CCS, DHS, DHS+ARS and FNS under daily physiological activities like normal walking and stair climbing. The unstable Pauwels type III fracture was virtually induced in a composite femur bone model and was fixed with all four internal fixators. Second-order tetrahedral elements were used to develop the FE models. The stresses, strains, and deformations of intact and reconstructed femur and implant components were compared to understand the biomechanical efficacy. FNS showed the highest inferior axial displacement of the femoral head while DHS+ARS exhibited the least inferior axial displacement. Among the four fracture fixation systems, DHS+ARS offered the highest post-fixation stability in terms of fracture gap opening (normal walking: 0.82mm and stair climbing: 0.95mm) and contact sliding, while the performance of single hole locking plated FNS was the worst (normal walking: 2.65mm, stair climbing: 3.72mm). Based on this computational study, DHS+ARS seems to be a better performing system in Pauwels type III fracture fixation.

bioengineering↗

bioRxiv2024

Dengue Protease-Mediated Activation and Polarization of Macrophages

Controlled activation of macrophages to achieve desired phenotypes in vivo and in vitro could lead to possible treatments for several inflammatory and proliferative diseases. This investigation uniquely established that dengue protease enhances the polarization and activation of human and murine macrophages following extracellular exposure. It was observed that macrophages have a robust response to extracellularly administered purified dengue NS2B/NS3 protease; it stimulated the macrophages in classical M1 directions and enhanced both the mitogen-activated protein kinases (MAPK) and c-Jun N-terminal kinases (JNK). The cells exhibited an increase in the intracellular levels of proinflammatory cytokines such as IL-2, IL-6, IL-12, and IFN-{gamma} and an elevation of phosphorylated versions of Akt, P38 MARK, SAPK, and ERK. In tandem, this investigation also established that the heightened responses of stimulated cells were associated with an increase in the cellular reactive oxygen species (ROS) level and the nuclear translocation of the NF-{kappa}B (P65) protein. The cell viability assay showed that NS2B/NS3 protease exerts no major toxic effect on macrophages after 24 hours of treatment, even at a dosage (20 g/ml) which was four times higher than the effective dose (5 g/ml). Remarkably, we also observed that the native form of the viral protease, which drives its enzyme activities, had no bearing on the antigenic qualities of the enzyme. Thus, our study highlighted the efficacy of dengue viral NS2B/NS3 protease as a non-toxic ex vivo macrophage activating/polarizing agent and may serve a vital role in macrophage-based cell therapy in the near future. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/624958v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@d29cd1org.highwire.dtl.DTLVardef@1357e96org.highwire.dtl.DTLVardef@109cc52org.highwire.dtl.DTLVardef@45536b_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2024

Evolution of g-Type Lysozymes in Metazoa: Insights into Immunity and Digestive Adaptations

Exploring the evolutionary dynamics of lysozymes is critical for advancing our knowledge of adaptations in immune and digestive systems. Here, we characterize the distribution of a unique class of lysozymes known as g-type, which hydrolyze key components of bacterial cell walls. Notably, many basal metazoan groups, including ctenophores, sponges, and choanoflagellates (the sister group of Metazoa), lack g-type lysozymes. We reveal a mosaic distribution of these genes, particularly within lophotrochozoans/spiralians, suggesting the lateral gene transfer (LGT) events from predatory myxobacteria played a role in their acquisition, enabling specialized dietary and defensive adaptations. We further identify two major groups of g-type lysozymes based on their widespread distribution in gastropods. Despite their sequence diversity, these lysozymes maintain conserved structural integrity that is crucial for enzymatic activity, underscoring independent evolutionary pathways where g-type lysozymes have developed functionalities typically associated with different lysozyme types in other species. Specifically, using Aplysia californica as a reference species, we identified three distinct g-type lysozyme genes: two are expressed in organs linked to both feeding and defense, and the third exhibits broader distribution, likely associated with immune functions. These findings advance our understanding of the evolutionary dynamics shaping the recruitment and mosaic functional diversification of these enzymes across metazoans, offering new insights into ecological physiology and physiological evolution as emerging fields.

evolutionary biology↗

bioRxiv2024

Biomechanical Evaluation of Temporomandibular Joint Implants Under Complete Mastication Cycle

To ensure the long-term success of temporomandibular joint (TMJ) implants, it is imperative to understand their biomechanical performances. This study aims to compare the biomechanical performance of two stock implants (narrow and standard) under unilateral and bilateral clenching during both osseointegrated and non-osseointegrated conditions. Finite element models of a human mandible were developed from QCT data, with the left TMJ being replaced by the implants. Six clenching tasks were simulated to evaluate stress and strain distributions in the mandible and implants. Ipsilateral clenching produced higher mandibular strains, while contralateral clenching generated larger implant stresses. Furthermore, intercuspal biting was found to have produced the highest strain (1750-1880 {micro}{varepsilon}) and stress ([~]17 MPa) in the mandible. Osseointegration reduced stresses (up to 0.14 MPa) and strains (up to 30 {micro}{varepsilon}) in mandible as well as stresses in mandibular components (up to 48 MPa) and screws (up to 71 MPa). However, during non-osseointegrated conditions, stresses in cortical bone were higher for standard TMJ implant as compared to narrow implant. This suggests possible preference of narrow implant over standard ones.

bioengineering↗

bioRxiv2024

Amyloid Beta Oligomers Accelerate ATP-Dependent Phase Separation of Ago2 to RNA Processing Bodies

Phase separation to insoluble membrane-less organelles is a major way of activity regulation of specific proteins in eukaryotic cells. miRNA-repressed mRNAs and Ago proteins are known to be localized to RNA-processing bodies, the subcellular structures which are formed due to assembly of several RNA binding and regulatory proteins in eukaryotic cells. Ago2 is the most important miRNA binding protein that by forming complex with miRNA binds to mRNAs having cognate miRNA binding sites and represses protein synthesis in mammalian cells. Factors which control compartmentalization of Ago2 and miRNA-repressed mRNAs to RNA processing bodies are largely unknown. We have adopted a detergent permeabilized cell-based assay system to follow the phase separation of exogenously added Ago2 to RNA processing bodies in vitro. The Ago2 phase separation process is ATP dependent and is influenced by osmolarity and salt concentration of the reaction buffer. miRNA binding of Ago2 is essential for its targeting to RNA processing bodies and the compartmentalization process gets retarded by miRNA binding "sponge" protein HuR. This assay system found to be useful in identification of amyloid beta oligomers as miRNA-activity modulators which repress miRNA activity by enhancing Ago2-miRNP targeting to RNA processing bodies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/584939v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1fe06eeorg.highwire.dtl.DTLVardef@7904b1org.highwire.dtl.DTLVardef@1231746org.highwire.dtl.DTLVardef@cd1405_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LImiRNA bound Ago2 gets phase separated in vitro to RNA processing bodies (PBs) in detergent permeabilized mammalian cells. C_LIO_LIPhase separation of Ago2 to PBs is controlled by presence of ATP and RNA. C_LIO_LIAmyloid beta oligomers retard dynamics of Ago2 bodies to inhibit miRNA function and enhance PB targeting of Ago2 miRNPs. C_LIO_LImicroRNA binding protein HuR can rescue Ago2 miRNP from PBs and inverse the effect of amyloid beta oligomers. C_LI

neuroscience↗

bioRxiv2023

Distinct features of ribonucleotides within genomic DNA in Aicardi-Goutieres syndrome (AGS)-ortholog mutants of Saccharomyces cerevisiae

Ribonucleoside monophosphates (rNMPs) are abundantly found within genomic DNA of cells. The embedded rNMPs alter DNA properties and impact genome stability. Mutations in ribonuclease (RNase) H2, a key enzyme for rNMP removal, are associated with the Aicardi-Goutieres syndrome (AGS), a severe neurological disorder. Here, we engineered two AGS-ortholog mutations in Saccharomyces cerevisiae: rnh201-G42S and rnh203-K46W. Using the ribose-seq technique and the Ribose-Map bioinformatics toolkit, we unveiled rNMP abundance, composition, hotspots, and sequence context in these yeast AGS-ortholog mutants. We found higher rNMP incorporation in the nuclear genome of rnh201-G42S than in wild-type and rnh203-K46W-mutant cells, and an elevated rCMP content in both mutants. Moreover, we uncovered unique rNMP patterns in each mutant, highlighting a differential activity of the AGS mutants towards rNMPs embedded on the leading or on the lagging strand of DNA replication. This study guides future research on rNMP characteristics in human genomic samples carrying AGS mutations.

molecular biology↗