Novel insights into non-coding RNAs and their role in hydrocephalus

A large body of evidence has highlighted the role of non-coding RNAs in neurodevelopment and neuroinflammation. This evidence has led to increasing speculation that non-coding RNAs may be involved in the pathophysiological mechanisms underlying hydrocephalus, one of the most common neurological conditions worldwide. In this review, we first outline the basic concepts and incidence of hydrocephalus along with the limitations of existing treatments for this condition. Then, we outline the definition, classification, and biological role of non-coding RNAs. Subsequently, we analyze the roles of non-coding RNAs in the formation of hydrocephalus in detail. Specifically, we have focused on the potential significance of non-coding RNAs in the pathophysiology of hydrocephalus, including glymphatic pathways, neuroinflammatory processes, and neurological dysplasia, on the basis of the existing evidence. Lastly, we review the potential of non-coding RNAs as biomarkers of hydrocephalus and for the creation of innovative treatments.

Update on the correlation between mitochondrial function and osteonecrosis of the femoral head osteocytes

Mitochondrial health is maintained in a steady state through mitochondrial dynamics and autophagy processes. Recent studies have identified healthy mitochondria as crucial regulators of cellular function and survival. This process involves adenosine triphosphate (ATP) synthesis by mitochondrial oxidative phosphorylation (OXPHOS), regulation of calcium metabolism and inflammatory responses, and intracellular oxidative stress management. In the skeletal system, they participate in the regulation of cellular behaviors and the responses of osteoblasts, osteoclasts, chondrocytes, and osteocytes to external stimuli. Indeed, mitochondrial damage or dysfunction occurs in the development of a few bone diseases. For example, mitochondrial damage may lead to an imbalance in osteoblasts and osteoclasts, resulting in osteoporosis, osteomalacia, or poor bone production, and chondrocyte death and inflammatory infiltration in osteoarthritis are the main causes of cartilage degeneration due to mitochondrial damage. However, the opposite exists for osteosarcoma, where overactive mitochondrial metabolism is able to accelerate the proliferation and migration of osteosarcoma cells, which is a major disease feature. Bone is a dynamic organ and osteocytes play a fundamental role in all regions of bone tissue and are involved in regulating bone integrity. This review examines the impact of mitochondrial physiological function on osteocyte health and summarizes the microscopic molecular mechanisms underlying its effects. It highlights that targeted therapies focusing on osteocyte mitochondria may be beneficial for osteocyte survival, providing a new insight for the diagnosis, prevention, and treatment of diseases associated with osteocyte death.

Association between renal function and memory-related disease: evidence from the China Health and Retirement Longitudinal Study

BACKGROUND

Previous studies have reported that renal function is associated brain structure and cognitive dysfunction. However, the association between renal function and memory-related disease was not well characterized.

METHODS

Altogether, 5,282 individuals were included in this study based on China Longitudinal Study of Health and Retirement. Four estimated glomerular filtration rate indicators (eGFR), including CG, CKD-EPIscr, CKD-EPIscr-cys, and CKD-EPIcys were used to evaluate the association between renal function and memory-related disease.

RESULTS

The multivariable-adjusted HRs (95% CIs) of the memory-related disease in the low eGFR group (eGFR < 90 mL/min/1.73m2) were 1.56 (1.13-2.16) for CG, 1.56 (1.19-2.06) for CKD-EPIscr, 1.45 (1.06-1.99) for CKD-EPIscr-cys and 1.27 (0.91-1.77) for CKD-EPIcys, respectively. Similarly, each SD increase of eGFR was associated with reduced risk of memory-related disease on continuous analyses. Subgroup analyses further confirmed these associations. Moreover, the addition of eGFR to conventional risk factors improved the predictive power for memory-related disease (net reclassification improvement: 13.90% for CG, 19.83% for CKD-EPIscr and 30.65% for CKD-EPIscr-cys).

CONCLUSIONS

In conclusion, impaired renal function was associated with the increasing risk of memory-related disease, indicating that renal function may be a potential indicator for memory-related disease. Further studies from other races and populations are needed to replicate our findings and to clarify the potential mechanisms.

Translation elongation: measurements and applications

Translation converts genetic information in mRNAs into functional proteins. This process occurs in four major steps: initiation, elongation, termination and ribosome recycling; each of which profoundly impacts mRNA stability and protein yield. Over recent decades, regulatory mechanisms governing these aspects of translation have been identified. In this review, we focus on the elongation phase, reviewing the experimental methods used to measure elongation rates and discussing how the measurements shed light on the factors that regulate elongation and ultimately gene expression.

The E3 ligase RAD18-mediated ubiquitination of henipavirus matrix protein promotes its nuclear-cytoplasmic trafficking and viral egress

The nuclear-cytoplasmic trafficking of matrix proteins (M) is essential for henipavirus budding, with M protein ubiquitination playing a pivotal role in this dynamic process. Despite its importance, the intricacies of the M ubiquitination cascade have remained elusive. In this study, we elucidate a novel mechanism by which Nipah virus (NiV), a highly pathogenic henipavirus, utilizes a ubiquitination complex involving the E2 ubiquitin-conjugating enzyme RAD6A and the E3 ubiquitin ligase RAD18 to ubiquitinate the virus's M protein, thereby facilitating its nuclear-cytoplasmic trafficking. We demonstrate that RAD18 interacts with RAD6A, enabling the latter to supply ubiquitins for the RAD18-mediated transfer of ubiquitin to M through RAD18-M interactions. Specifically, M is ubiquitinated by the RAD6A-RAD18 complex at lysine (K) 258 through a K63-linked ubiquitination, a modification crucial for M's function. This ubiquitination drives M's relocation to the cytoplasm, directing it to plasma membranes for effective viral egress. Conversely, disrupting the RAD6A-RAD18-M axis, mutating RAD18's E3 ligase activity, or inhibiting RAD6A activity with TZ9 (a RAD6-ubiquitin thioester formation inhibitor) impairs M ubiquitination, resulting in defective nuclear export and budding of NiV. Significantly, live NiV and Hendra virus infection is attenuated in RAD18 knockout cells or in cells treated with TZ9, highlighting the critical physiological role of RAD6A-RAD18-mediated M ubiquitination in the henipavirus life cycle. Our findings not only reveal how NiV manipulates a nucleus-localized ubiquitination complex to promote virus's M protein ubiquitination and nuclear export, but also suggest that the small molecule inhibitor TZ9 could serve as a potential therapeutic against henipavirus infection.

Influences of physical stimulations on the migration and differentiation of Schwann cells involved in peripheral nerve repair

Peripheral nerve injury repair has always been a research concern of scientists. At the tissue level, axonal regeneration has become a research spotlight in peripheral nerve repair. Through transplantation of autologous nerve grafts or other emerging biomaterials functional recovery after facial nerve injury is not ideal in clinical scenarios. Great strides have been made to improve facial nerve repair at the micro-cellular level. Physical stimulation techniques can trigger Schwann cells (SCs) to migrate and differentiate into cells required for peripheral nerve repair. Classified by the sources of physical stimulations, SCs repair peripheral nerves through galvanotaxis, magnetotaxis and durotaxis. This article summarized the activation, directional migration and differentiation of SCs induced by physical stimulations, thus providing new ideas for the research of peripheral nerve repair.

Temperature vaulting: A method for screening of slow- and tight-binding inhibitors that selectively target kinases in their non-native state

A polypeptide folds into its protein tertiary structure in the native state through a folding intermediate in the non-native state. The transition between these states is thermodynamically driven. A folding intermediate of dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) autophosphorylates intramolecularly, whereas DYRK1A in the native state no longer catalyzes this reaction. The alteration in substrate specificity suggests a conformational transition of DYRK1A during its folding process. Consistent with this hypothesis, we identified FINDY (1), which inhibits the intramolecular autophosphorylation but not the intermolecular phosphorylation, suggesting that DYRK1A in the non-native state possesses an alternative inhibitor-binding site. Meanwhile, it remains an issue that the methods for approaching the alternative binding site require an intricate assay tailored to the individual target. Here we show a method, designated as "temperature vaulting," for inhibitor screening that targets the non-native state. Transient heating of recombinant DYRK1A protein drove the reversible transition between the native state and the non-native state targeted by FINDY (1). At physiological temperature, FINDY (1) slowly bound to the DYRK1A protein. These results indicate that transient heating accelerates the slow-binding process by assisting the protein to overcome the high-energy barrier leading to the target non-native state. The energy barrier also slowed down the dissociation, resulting in tight binding between DYRK1A and FINDY (1). Structure-activity relationship revealed that both the methoxy group and the alkyne moiety underlie the selectivity of FINDY (1) toward DYRK1A in the non-native state. Furthermore, this study suggests that the dissociation rate underlies the inhibition selectivity of FINDY (1) between DYRK1A and its family kinase DYRK1B. This method could leverage conventional assays to identify slow- and tight-binding inhibitors.

P-Pev: micelle-like complexes transformed from tumor extracellular vesicles by PEG-PE for personalized therapeutic tumor vaccine

The clinical benefits of personalized therapeutic tumor vaccines are mainly challenged by the need to identify immunogenic neoantigens promptly, given the rapid pace of tumor mutations. An increasing body of literature addresses the potential of tumor-derived extracellular vesicles (TEVs) as an anti-tumor "cell-free" vaccine due to their substantial presence of neoantigens. However, their immunosuppression and limited presentation efficiency of dendritic cells (DCs) restrict their further application. Here, we have developed a novel tumor-personalized vaccine, termed P-Pev, based on remodeled TEVs by polymeric surfactant polyethylene glycol-phosphatidyleolamine (PEG-PE) and adjuvant monophosphoryl lipid A (MPLA). Our results show that PEG-PE transforms TEVs into micelle-like complexes by disrupting the original structure, facilitating antigens delivery to the cytoplasm, and cross-presentation by DCs. P-Pev particularly prevents the immunosuppressive impacts of TEVs on the ability of DCs to prime CD8+ T cells and eliminates the potency of TEVs to promote lung metastasis through their membrane-bound PD-L1. Finally, the P-Pev effectively induces neoantigen-specific cytotoxic T lymphocytes (CTLs) responses and exhibits excellent therapeutic effects in various murine tumor models. Also, the P-Pev induces neoantigen-specific antibodies, suggesting the involvement of humoral immunity in its anti-tumor effects. More importantly, it has been shown that P-Pev prepared by mutated tumor cells can retard these mutated tumor cell-established syngeneic tumors better than P-Pev prepared by original tumor cells, indicating the feasibility that leverages TEVs to prepare personalized tumor vaccines, and it is synergistically enhanced by PD-1 mAb combination. Collectively, we present a general strategy that offers a streamlined, cost-effective, and time-consuming approach to preparing personalized therapeutic tumor vaccines.

Pyroptosis, ferroptosis, and autophagy in spinal cord injury: regulatory mechanisms and therapeutic targets

Regulated cell death is a form of cell death that is actively controlled by biomolecules. Several studies have shown that regulated cell death plays a key role after spinal cord injury. Pyroptosis and ferroptosis are newly discovered types of regulated cell deaths that have been shown to exacerbate inflammation and lead to cell death in damaged spinal cords. Autophagy, a complex form of cell death that is interconnected with various regulated cell death mechanisms, has garnered significant attention in the study of spinal cord injury. This injury triggers not only cell death but also cellular survival responses. Multiple signaling pathways play pivotal roles in influencing the processes of both deterioration and repair in spinal cord injury by regulating pyroptosis, ferroptosis, and autophagy. Therefore, this review aims to comprehensively examine the mechanisms underlying regulated cell deaths, the signaling pathways that modulate these mechanisms, and the potential therapeutic targets for spinal cord injury. Our analysis suggests that targeting the common regulatory signaling pathways of different regulated cell deaths could be a promising strategy to promote cell survival and enhance the repair of spinal cord injury. Moreover, a holistic approach that incorporates multiple regulated cell deaths and their regulatory pathways presents a promising multi-target therapeutic strategy for the management of spinal cord injury.

Engineering adeno-associated viral vectors for CRISPR/Cas based in vivo therapeutic genome editing

The recent approval of the first gene editing therapy for sickle cell disease and transfusion-dependent beta-thalassemia by the U.S. Food and Drug Administration (FDA) demonstrates the immense potential of CRISPR (clustered regularly interspaced short palindromic repeats) technologies to treat patients with genetic disorders that were previously considered incurable. While significant advancements have been made with ex vivo gene editing approaches, the development of in vivo CRISPR/Cas gene editing therapies has not progressed as rapidly due to significant challenges in achieving highly efficient and specific in vivo delivery. Adeno-associated viral (AAV) vectors have shown great promise in clinical trials as vehicles for delivering therapeutic transgenes and other cargos but currently face multiple limitations for effective delivery of gene editing machineries. This review elucidates these challenges and highlights the latest engineering strategies aimed at improving the efficiency, specificity, and safety profiles of AAV-packaged CRISPR/Cas systems (AAV-CRISPR) to enhance their clinical utility.

Quantitative analysis of trace-level bleomycin in complex matrices: Application to in vitro electrochemotherapy

Bleomycin, a cytotoxic antibiotic, poses substantial challenges for mass spectrometry-based analysis due to its extreme polarity, chelating properties, heterogeneity of fractions, and propensity to form multiple charged species during electrospray ionization. As one of the few effective drugs used in electrochemotherapy, the ability to quantify trace levels of bleomycin is critical for evaluating treatment efficacy, often requiring sensitivity beyond the capabilities of existing analytical methods. Such precise quantification would facilitate the evaluation of electrochemotherapy efficacy, such as comparing the in vitro effects of nanosecond electric pulses with conventional microsecond pulses. To address these challenges, we integrated cell viability assays with a robust chemical analytical approach. This approach employed solid-phase extraction for sample preparation, combined with HILIC-LC-MS/MS, achieving exceptional sensitivity with LLOQ of 0.075 µg/L and overcoming analyte and matrix complexity. Although a significant reduction in cell survival was confirmed when combining nanosecond pulses (25 × 400 ns) with bleomycin, chemical analysis revealed discrepancies, underscoring the complex interaction between electric pulse parameters and drug action. These findings highlight the need for further refinement of treatment protocols and the development of advanced analytical techniques.

Self-packed size-exclusion columns enable versatile high-throughput native, top-down, and ion mobility-mass spectrometry studies on proteins and complexes

Native MS (nMS) is a key structural biology technique that makes it possible to study intact proteins and their interactions. Unfortunately, non-volatile salts are incompatible with nMS, which demands a laborious desalting procedure. Non-denaturing size-exclusion chromatography (SEC) allows both rapid desalting and separation and has previously been explored for nMS automation. However, SEC at conventional scale requires rather large sample amounts as well as harsh ESI conditions, which can cause protein unfolding. Capillary LC allows softer conditions; however, the few commercially available SEC columns appropriate for this flow rate are prohibitively expensive for many laboratories. Existing protocols for packing buffer exchange columns rely on specialized equipment and/or result in columns that have limited capacity for size-based protein separation. Here, we present self-packed miniaturized SEC columns with different stationary phases and customizable dimensions. The columns, produced via slurry packing with an ordinary LC pump were used across a range of samples in several applications including nMS, top-down MS (TDMS), ligand screening, and ion mobility (IM)-MS. Native separation allowed acquisition of data from samples containing more than one protein. We acquired native TDMS data of 3 proteins in 12 min, with up to 47 % sequence coverage. IM-MS of alpha-synuclein at different charge states was measured in ca. 60 min (including calibrants), with results that match the literature. Finally, we used SEC-nMS to rapidly screen proteolysis-targeting chimera candidates and performed collision-induced unfolding (CIU) of a PROTAC-induced ternary complex. Through this work, we highlight the potential of SEC to support developments in structural MS.

Modulating nanopore size and ion transport using (Anti)-Polyelectrolyte effects inspired by the nuclear pore complex

This study explores the modulation of nanopore size and ion transport through (anti)-polyelectrolyte effects, which is inspired by the nuclear pore complex. We aimed to control ionic selectivity and rectification by applying these effects to synthetic nanopores. Single bicylindrical nanopores were fabricated on the PET membranes and functionalized with PEI/HA or PLL/PAA polyelectrolyte layers. Varying the structural and charge characteristics under different pH levels and ionic strengths revealed that at low salt concentrations, charge density and surface charge polarity significantly impacted ion selectivity and transport. At higher concentrations, conformational changes in the polyelectrolytes influenced the conductance via volume expansion or compaction. Our findings highlight the distinct roles of charge inversion and molecular expansion in nanopore transport, which can be modulated by pH and ionic environment. This work provides insights for developing highly selective ion channels with potential applications in filtration, biosensing, and nanofluidics, where precise ion transport and selective rectification are essential.

Cornel iridoid glycosides exerted neuroprotective effects against cerebral ischemia/reperfusion injury in rats via inhibiting TLR4/MyD88/NF-κB pathway

Inflammatory response plays a key role in the pathophysiological process of Ischemic stroke. Cornel iridoid glycosides (CIG), the primary components of Cornus officinalis Sieb. et Zucc., have demonstrated a wide range of anti-inflammatory pharmacological activities. This study aimed to investigate the neuroprotective effect of CIG against cerebral ischemia/reperfusion injury and to explore its anti-inflammatory mechanisms. Sprague-Dawley rats were pre-treated with CIG at doses of 1.25, 2.5, and 5 mL/kg and then subjected to transient middle cerebral artery occlusion/re-perfusion (tMCAO/R). The effectiveness of prevention was determined based on neurological function, cerebral infarction, edema, histological changes, microglia aggregation, and induction of inflammation cytokines using hematoxylin-eosin staining, TUNEL staining, and real-time quantitative PCR. Proteins involved in the canonical nuclear factor kappa B (NF-κB) signaling pathway were analyzed using immunofluorescence, western blot, and molecular docking analysis. The results showed that CIG could dose-dependently reduce the neurological deficit score, cerebral infarction and edema, and brain cells apoptosis caused by tMCAO/R injury. Additionally, CIG significantly inhibited the aggregation of microglia and decreased levels of tumor necrosis factor-α, interleukin-1β and interleukin-6 in a dose-dependent manner. Furthermore, the tMCAO/R rats pre-treated with CIG displayed inhibition of NF-κB nuclear translocation and down-regulations on TLR4, MyD88, TRAF6, and inhibitory kappa B. Molecular docking analysis revealed that the CIG components (morroniside, loganin, and cornuside I) exhibited good affinities with protein TLR4, MyD88, and TRAF6. CIG could alleviate cerebral ischemia/reperfusion injury by inhibiting microglia aggregation and reducing the neuroinflammatory response, which targets the TLR4/MyD88/NF-κB signaling pathway. Therefore, CIG might potentially serve as a new medicine candidate for the prevention of ischemic stroke.

Glucose-regulated protein 94 (Grp94/gp96) in viral pathogenesis: Insights into its role and therapeutic potentials

Glucose-regulated protein 94 (Grp94/gp96) is endoplasmic reticulum (ER) resident form of the 90 kDa heat shock protein 90 (Hsp90) that is responsible for folding, maturation and stabilization of more than 400 client proteins. Grp94 has been implicated for various diseases including metastatic cancer, primary open-angle glaucoma, and infectious diseases. In fact, Grp94 plays critical roles in different stages of viral infection cycle. It chaperones receptor proteins and viral glycoproteins that are necessary for viral entry and replication. Beyond its role in protein homeostasis, Grp94 modulates host cellular processes such as apoptosis and immune responses, which are often exploited by viruses to sustain infection. This work provides an overview of the roles of Grp94 in viral pathogenesis across various viruses and its involvement in immune modulation with the development of Grp94-selective inhibitors and their potential as anti-viral therapeutics.

Roxadustat pre-conditioning and cyclic uniaxial stretching improve tenogenic differentiation potential of human adipose derived mesenchymal stromal cells

Tendon injuries represent a significant challenge to treat owing to their limited intrinsic reparative capacity. The use of mesenchymal stem cells (MSC) offers promising alternative therapeutic option to augments tendon repair. It is hypothesised that the activation of hypoxia inducible factor-1 alpha (HIF-1α), could facilitate the tendon repair process by promoting the proliferation and tenogenic differentiation of MSCs. To demonstrate this, a study was conducted incorporating the use of Roxadustat, a specific hypoxia mimetic mediator and cyclic uniaxial stretching at a frequency of 1 Hz and 8 % strain on adipose derived-mesenchymal stromal cells (ADMSCs).

METHODS

Cellular morphology, proliferation rate, tenogenic protein and gene expression levels from 8 different treatment groups were compared. These groups include untreated ADMSCs (Control), Roxadustat pre-conditioned ADMSCs (ROX), ADMSCs subjected CAY10585 treatment only (CAY), Roxadustat pre-conditioned ADMSCs with CAY10585 inhibition (ROX+CAY), ADMSCs subjected to uniaxial stretching only (S), Roxadustat pre-conditioned ADMSCs with uniaxial stretching (ROX+S), ADMSCs subjected CAY10585 with uniaxial stretching (CAY+S) and primary tenocytes (Tenocytes).

RESULTS

ROX+S group exhibited the highest expression of HIF-1α and demonstrated a significant up-regulation of collagen I and III expressions, increasing by 4.9 and 5.6-fold compared to ROX group, respectively. There is a significant increase of SCX, TNC, TNMD, COLI and COLIII expression in this combination treatment group; (SCX= 9.9, TNC= 12.6, TNMD= 7.0, COLI= 8.0 and COLIII= 10.0-fold). Conversely, the expression of the markers markedly reduced with HIF-1α inhibitor CAY10585. However, uniaxial stretching effectively counteracted the inhibitory effects of CAY10585 in the CAY+ S group, resulting in a 3.9-fold increase in SCX expression compared to CAY treatment alone.

CONCLUSION

HIF-1α accumulation promotes superior tenogenic differentiation of ADMSCs, suggesting that the combination of Roxadustat and cyclic uniaxial stretching may be a potential therapeutic mediator in tendon repair strategies.

Application of pulsed electric field (PEF) as a strategy to enhance aminoglycosides efficacy against Gram-negative bacteria

In this study, two aminoglycosides (AGs), Kanamycin and Gentamicin, with similar modes of action and molecular weights, were combined with PEF treatment to enhance the inactivation of E. coli cells. Various PEF strengths were applied to assess the combined effect. To compare the inactivation efficacy of different AGs, bacterial growth measurements in suspension were performed at 3 and 10 h intervals over a 10-h period after PEF treatment. Interestingly, it was found that the additive effect of PEF treatment on E. coli growth inhibition was significantly greater with Kanamycin (IC50) than with Gentamicin (IC50). Further analysis revealed that the combined treatment with Kanamycin (IC50) was most effective within a timeframe of around 3 h. Our findings suggest that PEF treatment can significantly enhance the efficacy of AGs against Gram-negative bacteria; however, the extent of the additive effect varies depending on the specific antibiotic and the intensity of the applied PEF treatment.

Diffusion of sodium ions based on the interactions between gum arabic and oral mucin: Effects from the molecular weight of gum arabic

Diffusion behaviors of sodium ions in mucin layers plays an important role in saltiness perception. The influence of mucin-gum arabic interactions on the diffusion behaviors of sodium ions was investigated, in which the gum arabic was hydrolyzed to change its molecular weight. Results showed that the hydrolysis of gum arabic led to its structural changes, showing a lower zeta-potential. Gum arabic hydrolysates with lower molecular weight increased the diffusion of sodium ions through the mucin layer, which might be related to the conformation changes of mucin chains and the swelling expansion of mucin network. This mechanism was further confirmed by transmission electron microscopy, and a more swelling and looser structure of mucin layer was revealed, which contributed to the high diffusion rate of sodium ions. This work can improve our understanding of mucin network affects the penetration and perception of sodium ions, which may be useful for other molecular tastants.

Bystander effect of metal byproducts released from electroporated cells after electroporation in vitro

Electrodes dissolution during electroporation releases metal ions into the medium, altering the microenvironment of electroporated cells and allowing metal ions to penetrate cell membrane. During cell membrane repair, homeostasis restoration or activation of cell death pathways, cells eliminate excess metals from the cytoplasm and membrane. This study assessed the effects of post-electroporation metal byproducts on untreated (non-electroporated) cells in vitro. CHO and HCT116 cells were electroporated with three pulse protocols (unipolar: 100 μs, 5 ms; bipolar: 2 μs) using either aluminum or stainless-steel electrodes. After electroporation, cells were transferred to fresh growth medium and incubated for 2 or 4 h. Incubation period allowed either cell recovery or the activation of cell death pathways, leading to the accumulation of metal byproducts in the incubation medium. Stainless-steel electrodes with the 5 ms pulse protocol caused a considerable increase in iron, chromium and nickel ions in incubation medium compared to aluminum electrodes or other protocols. Metal ions in incubation medium caused toxicity in non-electroporated cells, disrupting cell cycle function or inducing cell death. The observed toxicity results from combined effects of metal ions on cellular functions and the mechanisms the cells use to protect themselves from metal overload.

Numerical modeling of giant pore formation in vesicles under msPEF-induced electroporation: Role of charging time and waveform

Giant unilamellar vesicle is the closest prototypical model for investigating membrane electrodeformation and electroporation in biological cells. This work employs numerical simulations to investigate the effect of membrane charging time on vesicle electroporation under milli-second pulsed-electric-field (msPEF) of different waveforms. Our numerical approach, which implements the effect of electric stretching on membrane tension and precise calculation of pore energy, successfully predicts the formation of giant pores of O(1)μm size as observed in previous experiments. The poration zone is found to extend up to certain angles as measured from the poles, termed critical angles. An increase in charging time delays pore formation, decreases the pore density, and trims down the poration zone. Counterintuitively, this effect promotes significant pore growth. Moreover, there exists a cut-off charging time above which pore formation is completely inhibited. This phenomenon is particularly pronounced with square bipolar pulses. Comparisons with the previous experimental results reveal that electrodeformation-poration-induced membrane surface area variation and that induced only by electroporation evolves in a similar fashion. Therefore, although the agreements are qualitative, the present electroporation model can be used as the simplest tool to predict the evolution of vesicles under electric pulses in laboratory experiments.

Biophysical insights into osmolytes-driven enhancements in urate oxidase activity and stability

The thermal instability of pharmaceutical enzymes such as uricase or urate oxidase (UOX) in liquid solutions is a major problem. Notably, compatible osmolytes are a specific class of osmolytes that can preferentially stabilize the folded state of proteins. However, the detailed molecular interactions that enable them to affect protein stability are still not completely elucidated. This study aimed to investigate how the enzyme environment could be altered using osmolytes to improve its catalytic activity and stability. Initially, experimental conditions were optimized using response surface methodology (RSM). Then, kinetic and thermodynamic properties, as well as structural changes of urate oxidase, were assessed using spectroscopic and computational techniques in the presence and absence of mixed osmolytes. Kinetic parameters indicated an improvement in the catalytic function of urate oxidase and the results of thermodynamic analysis indicated that the van der Waals forces and hydrogen bonding network played a crucial role in the UOX-osmolytes interactions. Fluorescence measurements suggested that osmolyte-UOX interactions alter the enzyme's structure. The data revealed a complex quenching mechanism between the enzyme and osmolyte. Molecular dynamics (MD) simulations showed an increase in stability and structural compactness of the enzyme in the presence of mixed osmolytes. Furthermore, it depicted an increase in the abundance of secondary structure contents of the enzyme, which in turn maintained the integrity of its active site. Also, the molecular docking analysis further supported the experimental results. These findings revealed mechanisms by which binary-compatible osmolytes could have relevant effects on the catalytic function and stability of urate oxidase.

A supported lipid bilayer to model solid-ordered membrane domains

Membrane models are widely used to mimic the behaviour of native plasma membranes and to simulate interactions occurring at their interface. Such models can be built up with different molecular compositions, ranging from single phospholipids to more complex, heterogeneous mixtures of phospho- and sphingo-lipids, possibly enriched with cholesterol and proteins. In particular, mixing different lipids and cholesterol is instrumental to promote the formation of phase-separated, ordered domains, which resemble the structure of lipid rafts, specialized functional domains of real membranes. According to the specific lipid composition, physical characteristics of the rafts can be tuned, such as fluidity, strongly related to membrane biological activity. Here, we introduce a novel three-component membrane model constituted by the mixing of a saturated phospholipid, 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), sphingomyelin and cholesterol to mimic the presence of solid ordered rafts and to study their behaviour. Differential scanning calorimetry, neutron reflectometry, and atomic force microscopy were synergistically applied to gain information on the membrane's transverse and lateral organization, as well as on its thermotropic behaviour. The membrane model benefits from the use of DMPC, a lipid (i) characterized by an accessible transition temperature; (ii) saturated; (iii) fluid at physiological temperature and (iv) commercially available in both protiated and deuterated forms. The proposed model, along with the wide range of biophysical techniques employed, constitutes an ideal system to study the molecular mechanisms and the physical properties that govern membrane functions, such as molecular signalling and membrane trafficking.

Development of novel plant protein with low gelation concentration from Torreya grandis nuts: Effect and mechanism of metal cations on its thermal gelation behavior

High protein concentrations were often required for thermally induced gelation, posing challenges in cost and resource efficiency. This study investigates the effects and mechanisms of metal cations (Na+, K+, Mg2+, Ca2+, 0-0.4 mol/L) on the thermal gelation behavior of Torreya grandis nut protein (TGNP) with a low gelation concentration (3 %-6 %). However, the addition of metal cations induced structural unfolding and an increase in particle size of TGNP from 358 to 3205 nm, leading to a decrease in TGNP solubility by an average of 8 %, which reduced TGNP gel properties, including modulus, hardness, and water-holding capacity. Furthermore, the presence of metal cations decreased the native β-sheet and disulfide bond content and increased the surface hydrophobicity of the TGNP gels, resulting in a loose structure and poorer stability. Overall, this study provides novel insights for the formulation and application of TGNP in edible delivery gels such as plant-based milk.

Immune cells in dorsal root ganglia are associated with pruritus in a mouse model of allergic contact dermatitis and co-culture study

The interaction between the neuroimmune system plays a crucial role in itch sensation, yet most research has focused on immune cells within the skin. Our study seeks to explore the presence and functions of immune cells within the dorsal root ganglia (DRG) in the context of allergic contact dermatitis (ACD). Immunofluorescence and histological staining techniques were employed to identify immune cells, including T-cells, basophils, mast cells, and dendritic cells (DCs), within the DRG of BALB/c mice sensitized and challenged with toluene diisocyanate (TDI). Our findings revealed an increase in mast cells and DCs within the DRG under ACD condition. Additionally, when DRG neurons were cultured with mast cells, a higher proportion of neurons exhibited responses to non-histaminergic pruritogens compared to neurons cultured alone. This suggests that mast cells may contribute to heightened sensitivity to non-histaminergic pruritogens. Furthermore, we conducted transcriptomic analysis of DCs within the DRG using RNA sequencing, followed by pathway enrichment analysis. Our analysis revealed that sorted DCs are implicated in immune responses, inflammation, and itch, with notable upregulation of Cathepsin S (Ctss) and sphingosine-1-phosphate (S1P) phosphatase 2 (Sgpp2). Subsequent functional experiments targeting CTSS in co-culture studies validated suppressed response to pruritogen and agonists of TRPA1 and TRPV1, indicating a potential role in peripheral sensitization. Additionally, the co-culture study indicated that the neuroimmune interaction between DCs and DRG neurons might involve S1P metabolism and S1P receptor signaling. In conclusion, targeting DCs and exploring the non-histaminergic functions of mast cells within the DRG, holds promise as novel targets for treating pruritus.

Microtubule-driven cell shape changes and actomyosin flow synergize to position the centrosome

The regulation of centrosome position is critical to the alignment of intracellular structures with extracellular cues. The exact nature and spatial distribution of the mechanical forces that balance at the centrosome are unknown. Here, we used laser-based nanoablations in adherent cells and found that forces along microtubules were damped by their anchoring to the actin network, rendering them ineffective in moving the microtubule aster. In contrast, the actomyosin contractile network was responsible for the generation of a centripetal flow that robustly drives the centrosome toward the geometrical center of the cell, even in the absence of microtubules. Unexpectedly, we discovered that the remodeling of cell shape around the centrosome was instrumental in aster centering. The radial array of microtubules and cytoplasmic dyneins appeared to direct this reorganization. This revised view of the respective roles of actin and microtubules in centrosome positioning offers a new perspective for understanding the establishment of cell polarity.

Harnessing nanotechnology in HIV therapy: Exploring molecular pathogenesis and treatment strategies with special reference to chemotherapy and immunotherapy

Human immunodeficiency virus (HIV) continues to be a global threat, contributing substantially to social and economic burdens worldwide. Synthetic ARV drugs are classified into six different classes viz NRTIs, NNRTIs, PIs, IIs, INSTIs, and FIs. Highly active anti-retroviral therapy (HAART) which is a combination of two or more ARV drugs from different classes is gaining immense popularity in the HIV therapy regimen due to its better therapeutic outcome. However, despite its successful endeavor in significant viral suppression, synthetic drugs are associated with numerous adverse effects. To mitigate this issue, scientists are exploring ARV agents derived from various natural sources like plants, and marine organisms that can exhibit potent anti-HIV activity with minimal side effects. Nevertheless, both synthetically and naturally derived ARV agents have failed to exhibit eradication of HIV from latent reservoirs. Henceforth, researchers are shifting their attention towards formulating a drug-encapsulated nano-delivery system to ensure a significant amount of drug delivery into these reservoirs. Additionally, the discovery of a novel HIV vaccine that can induce robust immune responses against multiple HIV strains and facilitate complete removal of the virus before the establishment of a latent reservoir is the need of an hour. Briefly, we discussed various synthetic and natural chemotherapeutic agents along with their specificity and limitations, different drug-delivery devices for ART, immunotherapy, vaccines, and lastly, challenges and strategies associated with vaccine development.

Moderate electric field-stimulated brown rice germination: Insights into membrane permeability modulation and antioxidant system activation

This study investigated the effects of moderate electric fields (MEF) on the germination of brown rice (BR) and the underlying mechanisms, focusing on membrane permeability and the antioxidant system. The results revealed a significant increase in germination rate, from 62 % to 84 %, at the 12th hour after exposure to a 100-V MEF. This enhancement was attributed to an increase in cell membrane permeability, a crucial factor in MEF-induced germination. The MEF may induce the formation of reversible electrical pores, thereby increasing cell membrane permeability. Concurrently, MEF treatment triggered the production of reactive oxygen species (ROS), leading to oxidative stress, which has sustained membrane permeability during germination. Furthermore, MEF was found to enhance the antioxidant system, aiding in the elimination of excessive ROS and ensuring normal metabolic activities. These findings underscore the role of MEF in modulating BR germination and highlight its potential for practical applications in agricultural seed technology.

mRNA vaccines for prostate cancer: A novel promising immunotherapy

The treatment of advanced prostate cancer (PCa) primarily based on androgen deprivation therapy (ADT); however, patients inevitably progress to the castration-resistant prostate cancer (CRPC) stage. Despite the recent advancements in CRPC treatment with novel endocrine drugs that further inhibit androgen receptor signaling, resistance ultimately develops, underscoring the urgent need for new effective therapeutic strategies. Therapeutic cancer vaccines, a form of immunotherapy, exert anti-cancer effects by activating the host's immune system. Over the past few decades, various conventional therapeutic PCa vaccines based on cells, microbes, proteins, peptides, or DNA have been developed and tested in patients with advanced PCa. These attempts have largely failed to improve survival, with the sole exception of sipuleucel-T, which extended the median overall survival of asymptomatic or minimally symptomatic metastatic CRPC (mCRPC) patients by four months. The rapid development and high efficacy of mRNA vaccines during the COVID-19 pandemic have garnered worldwide attention. Compared to conventional vaccines, mRNA vaccines offer several unique advantages, including high production efficiency, low cost, high safety, strong immune response induction, and high adaptability and precision. These attributes make mRNA vaccines a promising frontier in the treatment of advanced PCa.

Phytochemical intervention in BCRP-driven cancer drug resistance: A comprehensive review

Drug resistance (DR) remains a significant challenge in cancer treatment, accounting for over 90 % of cancer-related deaths. Multidrug resistance (MDR) complicates chemotherapy by enabling cancer cells to evade therapeutic agents. This review focuses on the role of ATP-binding cassette (ABC) transporters, particularly the breast cancer resistance protein (BCRP), in mediating drug resistance. BCRP functions as a drug efflux pump, actively transporting chemotherapeutic agents out of cancer cells, thereby reducing their efficacy. The regulation of BCRP is influenced by various signaling pathways, including PI3K/AKT, MAPK/ERK, NF-κB, and Wnt/β-catenin, all of which collectively enhance its expression and contribute to the MDR phenotype. Recent studies have highlighted the potential of phytochemical-based strategies to reverse drug resistance by inhibiting these transporters. Compounds such as tetrandrine and resveratrol have shown promise in sensitizing drug-resistant cancer cells. Understanding the complex interplay between BCRP regulation and these signaling pathways is essential for the development of effective therapeutic strategies to counteract cancer. Targeting multiple pathways or employing combination therapies may offer new avenues to overcome MDR and improve treatment outcomes for cancer patients.

A review of denoising methods in single-particle cryo-EM

Cryo-EM has become a vital technique for resolving macromolecular structures at near-atomic resolution, enabling the visualization of proteins and large molecular complexes. However, the images are often accompanied by extremely low SNR, which poses significant challenges for subsequent processes such as particle picking and 3D reconstruction. Effective denoising methods can substantially improve SNR, making downstream analyzes more accurate and reliable. Thus, image denoising is an essential step in cryo-EM data processing. This paper comprehensively reviews recent advances in image denoising methods for single-particle analysis, covering approaches from traditional filtering methods to the latest deep learning-based strategies. By analyzing and comparing mainstream denoising methods, this review aims to advance the field of single-particle cryo-EM denoising, facilitate the acquisition of higher-quality images, and offer valuable insights for researchers new to the field.

Interaction of native and aggregated albumin with DMPC bilayers

The study of protein-lipid interaction offers interesting insights into the mutual alterations determined in the formation of the supramolecular complex. It gains even more interest, not only in basic research but also in biomedical and biomaterial applications, when protein aggregation and fibril formation are involved. In this study, the reciprocal influence of human serum albumin (HSA), in both the native and the thermally aggregated state, and dimyristoylphosphatidylcholine (DMPC) bilayers is investigated by combining UV-Vis scattering, attenuated total reflection Fourier transform infrared (ATR-FTIR), and spin-label electron paramagnetic resonance (EPR) spectroscopies. Temperature-dependent optical density at fixed wavelength reveals the pre- and the main phase transitions in DMPC bilayers as well as the onset of protein aggregation at Tagg ≈ 70 °C. In native protein/lipid complexes, the protein adsorption on the membrane surfaces suppresses the pre-transition and downshifts the temperature of the main phase transitions of DMPC, whereas the presence of DMPC increases Tagg without affecting the thermal profile. Kinetics experiments reveal that lipid bilayers reduce the thermally-induced aggregation of the protein. ATR-FTIR data indicate that albumin weakens the hydrogen bonding network at the carbonyl groups of the membrane. Conversely, lipid bilayers in any physical state do not alter the structural features of both native and aggregated HSA. In protein/lipid complexes, spin-label EPR of the lipid component reveals that the proteins reduce the packing density of the first chain segments and stabilize the fluid state, the effect being more evident for the native protein.

Viscoelastic mechanics of living cells

In cell mechanotransduction, cells respond to external forces or to perceive mechanical properties of their supporting substrates by remodeling themselves. This ability is endowed by modulating cells' viscoelastic properties, which dominates over various complex cellular processes. The viscoelasticity of living cells, a concept adapted from rheology, exhibits substantially spatial and temporal variability. This review aims not only to discuss the rheological properties of cells but also to clarify the complexity of cellular rheology, emphasizing its dependence on both the size scales and time scales of the measurements. Like typical viscoelastic materials, the storage and loss moduli of cells often exhibit robust power-law rheological characteristics with respect to loading frequency. This intrinsic feature is consistent across cell types and is attributed to internal structures, such as cytoskeleton, cortex, cytoplasm and nucleus, all of which contribute to the complexity of cellular rheology. Moreover, the rheological properties of cells are dynamic and play a crucial role in various cellular and tissue functions. In this review, we focus on elucidating time- and size-dependent aspects of cell rheology, the origins of intrinsic rheological properties and how these properties adapt to cellular functions, with the goal of interpretation of rheology into the language of cell biology.

The relevance of RNA-DNA interactions as regulators of physiological functions

RNA-DNA interactions are fundamental to cellular physiology, playing critical roles in genome integrity, gene expression, and stress responses. This review highlights the diverse structures of RNA-DNA hybrids, including R-loops, RNA-DNA triplexes, and RNA-DNA hybrid G-quadruplexes (hG4s) and their relevance in physiology. R-loops are formed during transcription and replication, which regulate gene expression and chromatin dynamics but can also threaten genome stability. RNA-DNA triplexes, often formed by long noncoding RNAs (lncRNAs) such as FENDRR and MEG3, recruit chromatin modifiers like Polycomb repressive complex 2 to modulate gene expression, influencing organogenesis and cell specification. hG4s, formed by guanine-rich sequences in RNA and DNA, regulate transcription termination and telomere stability. Through this, hG4s can affect gene suppression and replication regulation. RNA-DNA hybrids are tightly regulated by helicases, RNase H enzymes, and topoisomerases, with altered regulation linked to genomic instability and disease. This review discusses the complexity of RNA-DNA interactions and their recently identified contributions to cellular physiology.

The role of RNA binding proteins in cancer biology: A focus on FMRP

RNA-binding proteins (RBPs) act as crucial regulators of gene expression within cells, exerting precise control over processes such as RNA splicing, transport, localization, stability, and translation through their specific binding to RNA molecules. The diversity and complexity of RBPs are particularly significant in cancer biology, as they directly impact a multitude of RNA metabolic events closely associated with tumor initiation and progression. The fragile X mental retardation protein (FMRP), as a member of the RBP family, is central to the neurodevelopmental disorder fragile X syndrome and increasingly recognized in the modulation of cancer biology through its influence on RNA metabolism. The protein's versatility, stemming from its diverse RNA-binding domains, enables it to govern a wide array of transcript processing events. Modifications in FMRP's expression or localization have been associated with the regulation of mRNAs linked to various processes pertinent to cancer, including tumor proliferation, metastasis, epithelial-mesenchymal transition, cellular senescence, chemotherapy/radiotherapy resistance, and immunotherapy evasion. In this review, we emphasize recent findings and analyses that suggest contrasting functions of this protein family in tumorigenesis. Our knowledge of the proteins that are regulated by FMRP is rapidly growing, and this has led to the identification of multiple targets for therapeutic intervention of cancer, some of which have already moved into clinical trials or clinical practice.

Synthetic Forms Most Beautiful: Engineering Insights into Self-Organization

Reflecting on the diversity of the natural world, Darwin famously observed that "from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved." However, the examples that we are able to observe in nature are a consequence of chance, constrained by selection, drift, and epistasis. Here we explore how the efforts of synthetic biology to build new living systems can expand our understanding of the fundamental design principles that allow life to self-organize biological form, from cellular to organismal levels. We suggest that the ability to impose a length or timescale onto a biological activity is an essential strategy for self-organization in evolved systems and a key design target that is now being realized synthetically at all scales. By learning to integrate these strategies together, we are poised to expand on evolution's success and realize a space of synthetic forms not only beautiful but with diverse applications and transformative potential.

A pH-Centric Model of Nucleolar Activity and Regulation

The nucleolus is essential for the efficient and accurate production of ribosomal subunits, which are crucial for assembling ribosomes-the cellular machinery responsible for protein synthesis. Emerging insights into its liquid-like nature have shed new light on the role of its unique biophysical properties in the activity and regulation of this organelle. In this perspective, we examine recent insights into nucleolar biophysical homeostasis, with a focus on its regulation as an acidic biomolecular condensate. We review current evidence on how nucleolar composition and biochemical activities could generate and maintain a proton gradient. Additionally, we propose an integrative model explaining how nucleolar acidity contributes to homeostasis at a molecular level, providing a unified framework for its role in health and disease.

A novel method of droplet generation based on the self-propelling of water phase and its potential application in multiplexing continuous flow PCR

Despite the benefits of microfluidic continuous flow PCR (CF-PCR) such as simplified thermal management and expedited heat transfer, challenge remains in processing multiple targets by CF-PCR, particularly regarding spatial multiplexing. The segregation of the target sample into droplets as isolated reactors is an effective method for achieving spatial multiplexing. Nevertheless, conventional techniques for droplet generation necessitate the management of both oil and water phases, thereby augmenting the complexity of channel design and device operation, particularly when parallel channels were needed for manipulating multiple targets. This study presented an innovative technique for droplet formation employing the self-propelling of the aqueous phase through the principles of Laplace pressure and utilizing a time order of fluid loading instead of simultaneous management of fluids. As a result, only a singular type of fluid was necessary for manipulation at one time, thereby streamlining chip design, device configuration, and operations. Spatial multiplexing droplets were generated by multiple microstructures with both functions of the segmentation of the sample target solution and droplet generation. In this study, four types of droplets generated from restoring the preloaded specific primers by target solution with PCR mix completed CF-PCR amplification via the serpentine channel in 10 min. Utilizing the idea of self-propelling of the aqueous phase, this study demonstrated an alternative method for droplet generation and significant promise for a simple way to achieve spatial multiplexing in CF-PCR when detecting multiple targets.

Biotechnological production and emerging applications of betalains: A review

Betalains are food-grade hydrophilic pigments with antioxidant and biological activities, predominantly found in plants. Betanin is a red-violet betalain synthesized from tyrosine through L-DOPA formation, its subsequent aromatic ring-opening, spontaneous cyclization to betalamic acid, and then pH-dependent condensation with i) cyclo-DOPA-5-O-glucoside or ii) cyclo-DOPA followed by 5-O-glucosylation. This short pathway in plants for betanin biosynthesis has been heterologously expressed in other organisms (e.g. non-betalainic plants, yeasts, and fungi) using CYP76AD1, DOD1, and cDOPA5GT or B5GT, corresponding to the enzymatic steps mentioned above. For the red-violet color formation through heterologous expression of the pathway genes in non-betalainic plants, a simplified reporter gene called RUBY has been developed recently. Without any systems engineering, expression of RUBY in non-betalainic plants resulted in accumulation of up to 203 mg betalains/100 g fresh weight of peanut leaves. In yeasts, Saccharomyces cerevisiae and Yarrowia lipolytica, and fungus Fusarium venenatum, betanin production has been achieved through overexpression of the pathway genes, with productivity reaching up to 0.62 mg/L/h, 26 mg/L/h, and 26.4 mg/L/h from d-glucose as carbon source, respectively, after considerable systems engineering and gene copy number augmentation. This review critically analyzes recent biotechnological production of betalains to highlight the advancements and strategies for improvement in the technology. Also, emerging applications of betalain biosynthetic gene products or betalains as biosensors, fluorescent probes, meat analog colors, and others are discussed to strengthen the need for systems engineering and process optimization for large-scale industrial production of these pigments.

Deciphering the complex roles of leucine-rich repeat receptor kinases (LRR-RKs) in plant signal transduction

Leucine-rich repeat receptor kinases (LRR-RKs) are essential receptor protein kinases in plants that are the key to signal perception and responses and central to regulating plant growth, development, and defense. Despite extensive research on the LRR-RK family, gaps persist in our understanding of their ligand recognition and activation mechanisms, interactions with co-receptor, signal transduction pathways, and biochemical and molecular regulation. Researchers have made significant advances in understanding the critical roles of LRR-RKs in plant growth and development, signal transduction, and stress responses. Here, we first summarized the gene expression levels of LRR-RKs in plants. We then reviewed the conservation and evolutionary relationships of these genes across different species. We also investigated the molecular mechanisms underlying the variations in LRR-RK signaling under different environmental conditions. Finally, we provide a comprehensive summary of how abiotic and biotic stresses modulate LRR-RK signaling pathways in plants.

The transcription factor IID subunit Taf13 is dispensable for TATA binding protein promoter recruitment and RNA polymerase II transcription

The multiprotein complex TFIID, comprising the TATA binding protein (TBP) and 13 TBP-associated factors (TAFs), is an essential component of the RNA polymerase II (Pol II) preinitiation complex (PIC). Cryo-electron microscopy studies suggested a critical role of the TAF11-TAF13 heterodimer in TBP promoter deposition upstream of the transcription start site. To investigate this hypothesis, we inactivated the gene encoding Taf13 in mice and embryonic stem cells (ESCs). Taf13-null embryos implant and survive until E6.5, but fail to undergo gastrulation, while Taf13-null ESCs are viable, but fail to form embryoid bodies and differentiate. Taf13 loss had little effect on TFIID integrity and led to only a mild reduction of TBP promoter recruitment, but led to altered PIC formation and globally reduced Pol II recruitment. Thus, the Taf11-Taf13 heterodimer is not essential for TBP/TFIID recruitment, revealing plasticity in the pathways of PIC formation.

Direct Arp2/3-vinculin binding is required for pseudopod extension, but only on compliant substrates and in 3D

A critical step in cell morphogenesis is the extension of actin-dense pseudopods, controlled by actin-binding proteins (ABPs). While this process is well-understood on glass coverslips, it is less so in compliant three-dimensional environments. Here, we knocked out a series of ABPs in osteosarcoma cells and evaluated their effect on pseudopod extension on glass surfaces (2D) and in collagen gels (3D). Cells lacking the longest Arp3 gene variant, or with attenuated Arp2/3 activity, had the strongest reduction in pseudopod formation between 2D and 3D. This was largely due to reduced activity of the hybrid Arp2/3-vinculin complex, which was dispensable on glass. Our data suggests that concurrent formation of actin branches and nascent adhesions, supported by Arp2/3-vinculin interactions, is essential to form mechanically stable links between fibrous extracellular matrix and actin in 3D. This highlights how experiments on stiff, planar substrates may conceal actin architectural features that are essential for morphogenesis in 3D.

Cost-effective strategies for CAR-T cell therapy manufacturing

CAR-T cell therapy has revolutionized cancer treatment, with approvals for conditions like acute B-leukemia, large B cell lymphoma (LBCL), follicular lymphoma (FL), mantle cell lymphoma (MCL), and multiple myeloma. However, its high costs limit accessibility. Key factors driving these costs include the need for personalized, autologous treatments, transportation to specialized facilities, reliance on viral vectors requiring advanced laboratories, and lengthy cell expansion processes. To address these challenges, alternative strategies aim to simplify and reduce production complexity. Non-viral vectors, such as Sleeping Beauty, piggyBac, and CRISPR, delivered via nanoparticles or electroporation, present promising solutions. These methods could streamline manufacturing, eliminate the need for viral vectors, and reduce associated costs. Furthermore, shortening cell expansion periods and optimizing protocols could significantly accelerate production. An emerging approach involves using genetically edited T cells from healthy donors to create universal CAR-T products capable of treating multiple patients. Finally, decentralized point-of-care (POC) manufacturing of CAR-T cells minimize logistical expenses, eliminating the need for complex infrastructure, and enabling localized production closer to patients. This innovative strategy holds potential for broadening access and reducing costs, representing a step toward democratizing CAR-T therapy. Combined, these advances could make this groundbreaking treatment more feasible for healthcare systems worldwide.

Ginsenoside Rb3 represses CPZ-induced demyelination and neuroinflammation by inhibiting TRAF6 K63 ubiquitination

Multiple sclerosis is a chronic inflammatory and neurodegenerative disorder of the central nervous system. Despite ongoing research, effective treatments remain limited, especially during progressive phase. Saponins extracted from the stem and leaf of Panax notoginseng (PNSL) demonstrate a superior anti-inflammatory effect by inhibiting NO production in LPS-induced BV2 cells. Ginsenoside Rb3, the primary active and most abundant component in PNSL, has been demonstrated to mitigate inflammation-induced damage. However, whether Rb3 mitigates demyelination by inhibiting neuroinflammation had not been previously reported. In this study, biochemical and histological assays revealed that ginsenoside Rb3 effectively mitigated Cuprizone-induced demyelination and attenuated aberrant microglial activation and reactive astrogliosis within the demyelinated areas. Mechanistic investigations demonstrated that Rb3 suppresses glial cell activation and consequently mitigates inflammatory responses by inhibiting the secretion of TNF-α, IL-6, and IL-1β. TNF receptor-associated factor 6 (TRAF6) is activated by K63-linked polyubiquitination, which leads to downstream activation of the inhibitor of nuclear factor-κB kinase (IKK) complex and mitogen-activated protein kinases (MAPKs). Furthermore, Rb3 was found to inhibit the activation of nuclear factor-κB (NF-κB) and MAPKs, as evidenced by the dephosphorylation of NF-κB p65 and the MAPKs p38 and JNK. Further investigation revealed that Rb3 binds to TRAF6 at residues 69 and 88, thereby inhibiting its K63-linked polyubiquitination. Conversely, the TRAF6 mutation at E69Q or R88N abolished the inhibition effects of Rb3 on K63-linked ubiquitination of TRAF6 and subsequent downstream signaling activation. Meta-analysis showed that Rb3 exerts its anti-inflammatory effects primarily by inhibiting the NF-κB pathway. Collectively, it is concluded that Rb3 alleviates demyelination and inhibits inflammation through bound to TRAF6 to prevent its K63-linked ubiquitination and subsequent activation of NF-κB. In this study, we have for the first time elucidated that dual mechanism by which Rb3 inhibits both NF-κB and MAPK pathways to exert its anti-inflammatory effects. This study demonstrates that Rb3 shows promising preclinical therapeutic potential. Additionally, TRAF6 represents a potential therapeutic target for MS treatment.

A specific negatively charged sequence confers intramolecular regulation on Munc13-1 function in synaptic exocytosis

Munc13 family proteins are crucial for the secretion of neurotransmitters and hormones necessary for cell communication. They share a conserved C-terminal region that includes C2 and the MUN domains, which facilitate membrane interactions and the assembly of soluble N-ethylmaleimide sensitive factor attachment protein receptor (SNARE) complexes. Neuronal isoforms of Munc13 possess a variable N-terminal region that is essential for neurotransmitter release and short-term plasticity, although the precise functions of this region remain not fully understood. Here, we identified a negatively charged sequence within the N terminus of Munc13-1, termed polyE, which is specific to Munc13-1 among all Munc13 isoforms and potentially derived from a common ancestor of homeotherms. We found that polyE binds significantly to the MUN domain through charge-charge interactions, inhibiting MUN activity in promoting SNARE complex assembly. Disrupting the polyE-MUN interaction by introducing pseudophosphorylated mutations in the MUN domain alleviates this inhibition, thereby enhancing neurotransmitter release. Strikingly, Ca2+ ions exhibit significant binding to polyE. We found that 40 μM of Ca2+ adequately competes with the polyE-MUN interaction to reduce polyE inhibition. This concentration is comparable to presynaptic local [Ca2+]i triggered by a single action potential. Taken together, these results indicate an autoinhibition conformation of Munc13-1 mediated by the polyE-MUN interaction. In addition, the relief of this autoinhibition conformation of Munc13-1 by presynaptic Ca2+ influx and/or posttranslational modifications in the MUN domain may underlie Munc13-1 function in neurotransmitter release and short-term plasticity.

Acetaldehyde dehydrogenase 2 attenuates lipopolysaccharide -induced endothelial barrier damage by inhibiting mitochondrial fission in sepsis-associated encephalopathy

Sepsis-associated encephalopathy (SAE) is a common neurological complication of sepsis, and acetaldehyde dehydrogenase 2 (ALDH2) has been identified as a protective factor for endothelial cells against oxidative stress. In this study, we aimed to investigate the therapeutic potential of ALDH2 and its impact on mitochondrial dynamics using both mouse and brain microvascular endothelial cells (BMECs) injury models induced by lipopolysaccharide (LPS). Our findings demonstrated that ALDH2 attenuated LPS-induced brain endothelial barrier damage, as evidenced by reduced brain water content and Evans blue dye in mice, decreased transepithelial electrical resistance (TEER), and increased fluorescein isothiocyanate-dextran (FITC-Dextran) leakage in bEnd.3 cells. Furthermore, ALDH2 reduced the levels of reactive oxygen species (ROS) and malondialdehyde (MDA), while enhancing the activities of superoxide dismutase (SOD) and catalase (CAT). ALDH2 also decreased 4-HNE content and restored mitochondrial membrane potential and ATP production, promoting a balanced mitochondrial fission and fusion. Notably, our use of the mitochondrial fission inhibitor Mdivi-1 confirmed that ALDH2 alleviated mitochondrial damage by inhibiting dynamin-related protein 1 (Drp1). Consequently, our findings suggest that the effects of ALDH2 on LPS-induced blood-brain barrier (BBB) damage and oxidative stress may alleviate SAE by inhibiting Drp1 to maintain mitochondrial homeostasis.

Advancing biosensing through super-resolution fluorescence microscopy

Advancement of super-resolution fluorescence microscopy (SRM) has recently allowed applications to the biosensing by offering significant advantages over conventional methods. Its nanoscale spatial resolution and single-molecule sensitivity allow visualization and quantification of biomolecular targets without the need of signal amplification steps typically required in traditional biosensing methods. Moreover, recent innovations in probe design and imaging protocols have expanded SRM capabilities to enable dynamic biosensing in living cells, revealing molecular processes in their native cellular contexts. In this review, we discuss these applications of various SRM techniques to biosensing by highlighting their unique capabilities in providing spatial distribution information and high molecular sensitivity. We address several challenges that must be overcome for the broader application of SRM-based biosensing. Finally, we discuss perspectives on future directions for advancing this field towards practical applications.

Investigation of Chemical Properties within Chaperonins in Stabilizing Substrate Protein Conformations Using Biomolecular Environment-Mimicking Model

Molecular chaperonins, such as GroEL/ES, are considered to assist in protein folding through both the confinement effect and chemical interactions provided by chaperonins themselves. Although the confinement effect on protein folding has been extensively investigated, the role of the chemical properties within chaperonins remains underexplored. To address this, we propose a Chaperonin Environment-Mimicking Model (CEMM) based on the effective radii and components of the GroEL/ES structure. Using enhanced molecular dynamics simulations, we compared the ability of CEMM with non-polar, polar uniform models and dilute environment to stabilize the experimental conformations of model substrate proteins. Consequently, the CEMM most effectively stabilized each experimental protein conformation, highlighting the importance of chemical properties within chaperonins in assisting protein folding. Furthermore, the analyses of the substrate proteins within each model suggest that the chemical diversity within chaperonins contributes to their ability to assist in protein folding.

An overview on in-vivo generation of CAR-T cells using CRISPR-loaded functionalized nanocarriers for treating B-cell lineage acute lymphoblastic leukemia

Chimeric antigen receptor T (CAR-T) cell therapy has become a milestone in the management of B cell lineage acute lymphoblastic leukemia. Yet, the traditional method-dependent on ex vivo manipulation, amplification, and reinfusion of autologous T cells-is high-cost, low-scalability, and severely immune-related toxicity. Here, we report a new nano-immunoengineering platform that allows in vivo production of chimeric antigen receptor T cells through the use of functionalized nanoparticles carrying clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) gene editing elements. These nanoparticles are engineered to specifically target blood circulating T lymphocytes and deliver CRISPR/Cas9 complexes that have the ability to integrate chimeric antigen receptor constructs into the TRAC locus and knock out immune checkpoint genes like programmed cell death protein 1 (PD-1) simultaneously. Targeted delivery, endosomal escape, and efficient genome editing with minimal off-target effects are ensured through gold-based and DNA nanostructure-based carriers. Preclinical models show effective in vivo programming of functional chimeric antigen receptor T cells with vigorous antitumor efficacy, improved persistence, and decreased cytokine release syndrome. This method is a revolutionary breakthrough in cancer immunotherapy that provides a scalable, economical, and clinically flexible replacement for conventional chimeric antigen receptor T cell production.

'Intelligent' proteins

We present an idea of protein molecules that challenges the traditional view of proteins as simple molecular machines and suggests instead that they exhibit a basic form of "intelligence". The idea stems from suggestions coming from Integrated Information Theory (IIT), network theory, and allostery to explore how proteins process information, adapt to their environment, and even show memory-like behaviors. We define protein intelligence using IIT and focus on how proteins integrate information (in terms of the parameter Φ coming from IIT) and balance their core (stable, ordered regions) and periphery (flexible, disordered regions). This balance allows proteins to remain stable while adapting to changes and operating in a critical state where order and disorder coexist. We summarize recent findings on conformational memory, allosteric regulation, protein intrinsic disorder, liquid-liquid phase separation, and critical transitions, and compare protein behavior to other complex systems like ecosystems and neural networks. While our perspective offers a unified framework to understand proteins, it also raises questions about applying intelligence concepts to molecular systems. We discuss how this understanding could advance protein engineering, drug design, and synthetic biology, while at the same time acknowledging the challenges of creating adaptive, "intelligent" proteins. This concept bridges the gap between mechanistic and systems-level views of proteins and offers a comprehensive understanding of their dynamic and adaptive nature. We have tried to redefine the traditionally metaphorical concept of "intelligence" in biochemistry as a measurable property while simultaneously establishing the material foundation of protein intelligence through the identification of fundamental elements such as memory and learning in molecular systems.

Evolution of the cytoskeleton: Emerging clues from the diversification and specialisation of archaeal cytoskeletal proteins

Recent research in archaeal cell biology has revealed a remarkable diversity of cytoskeletal proteins related to those found in bacteria and eukaryotes, such as the tubulin, actin, and ESCRT protein superfamilies, and archaea-specific proteins that self-assemble and have been implicated in cytoskeletal roles. Here, we outline an emerging view that the archaeal cytoskeleton has several conceptual ties to the sophisticated eukaryotic cytoskeleton. We highlight that duplication and specialisation of protein function is common among archaeal cytoskeletal systems, and that some paralogues show coordinated, opposing functions in the regulation of cell morphogenesis and structural homeostasis. Furthermore, the presence of homologues of eukaryotic cytoskeletal regulators in Asgard archaea, the closest known relatives of eukaryotes, underscores further linkages between eukaryotic and increasingly sophisticated archaeal cytoskeletal systems.