Approaches to studying cellular signaling: a primer for morphologists

Minimizing Shear Stress in Cell Signaling Studies

Cellular signal transduction comprises a complex series of biochemical reactions by which extracellular signals such as growth factors, hormones, cytokines, and neurotransmitters are translated into specific intracellular responses. Signal transduction is mediated by protein kinase phosphorylation cascades that culminate in the regulation of numerous cellular responses, including division, differentiation, migration, and survival. Importantly, signal relay pathways are dysregulated in human diseases, making the study of signal transduction important for both uncovering basic biology and understanding pathophysiology. Established laboratory cell culture models are useful for studying signal transduction mechanisms, but differences in sample handling procedures can introduce unwanted variability in experimental outcomes and conclusions. One such potential source of experimental variability is the introduction of fluid shear stress upon handling of tissue culture cells. Fluid shear stress triggers a wide range of cellular responses in adherent cell culture, including stimulating the production of cyclic AMP, potentiating the activation of extracellular signal-regulated kinases 1 and 2 (ERK1/2), and ultimately inducing changes in the gene expression of growth and remodeling factors. Further, mechanical stress on cells is physiologically relevant to the development of many pathologies. Here, we describe a detailed protocol for cell lysis and protein extraction that minimizes shear stress induced by classical cell harvest protocols. We also highlight the impact of fluid shear stress by using immunoblotting to assess ERK pathway activation as a readout for this protocol. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Gentle cell lysis and protein extraction Basic Protocol 2: Immunoblotting for cell signaling readouts by SDS-PAGE.

Insights into the neurobiology of suicidality: explicating the role of glutamatergic systems through the lens of ketamine

Suicidality is a prevalent mental health condition, and managing suicidal patients is one of the most challenging tasks for health care professionals due to the lack of rapid-acting, effective psychopharmacological treatment options. According to the literature, suicide has neurobiological underpinnings that are not fully understood, and current treatments for suicidal tendencies have considerable limitations. To treat suicidality and prevent suicide, new treatments are required; to achieve this, the neurobiological processes underlying suicidal behavior must be thoroughly investigated. Although multiple neurotransmitter systems, particularly serotonergic systems, have been studied in the past, less has been reported in relation to disruptions in glutamatergic neurotransmission, neuronal plasticity, and neurogenesis that result from stress-related abnormalities of the hypothalamic-pituitary-adrenal system. Informed by the literature, which reports robust antisuicidal and antidepressive properties of subanaesthetic doses of ketamine, this review aims to provide an examination of the neurobiology of suicidality (and relevant mood disorders) with implications of pertinent animal, clinical, and postmortem studies. We discuss dysfunctions in the glutamatergic system, which may play a role in the neuropathology of suicidality and the role of ketamine in restoring synaptic connectivity at the molecular levels.

Structure and Computational Electrophysiology of Ac-LS3, a Synthetic Ion Channel

Computer simulations are reported on Ac-LS3, a synthetic ion channel, containing 21 residues with a Leu-Ser-Ser-Leu-Leu-Ser-Leu heptad repeat, which forms ions channels upon application of voltage. A hexameric, coiled-coil bundle initially positioned perpendicular to the membrane settled into a stable, tilted structure after 1.5 μs, most likely to improve contacts between the non-polar exterior of the channel and the hydrophobic core of the membrane. Once tilted, the bundle remained in this state during subsequent simulations of nearly 10 μs at voltages ranging from 200 to -100 mV. In contrast, attempts to identify a stable pentameric structure failed, thus supporting the hypothesis that the channel is a hexamer. Results at 100 mV were used to reconstruct the free energy profiles for K⁺ and Cl^- in the channel. This was done by way of several methods in which results of molecular dynamics (MD) simulations were combined with the electrodiffusion model. Two of them developed recently do not require knowledge of the diffusivity. Instead, they utilize one-sided density profiles and committor probabilities. The consistency between different methods is very good, supporting the utility of the newly developed methods for reconstructing free energies of ions in channels. The flux of K⁺, which accounts for most of the current through the channel, calculated directly from MD matches well the total measured current. However, the current of Cl^- is somewhat overestimated, possibly due to a slightly unbalanced force field involving chloride. The current-voltage dependence was also reconstructed by way of a recently developed, efficient method that requires simulations only at a single voltage, yielding good agreement with the experiment. Taken together, the results demonstrate that computational electrophysiology has become a reliable tool for studying how channels mediate ion transport through membranes.

The effect of electron dose on positive polymethyl methacrylate resist for nanolithography of gold bowtie nanoantennas

Plasmonic structures, such as bowtie nanoantennas, may be used in Surface Enhanced Raman Spectroscopy (SERS). Nanoantennas can be employed to amplify the biomolecular and chemical reactions, which is useful for biomedical applications. The electric field created by nanoantennas are optimized when the resonant wavelength of the probed laser light closely matches the resonant wavelength of the plasmonic structure. In this work, we fabricated several bowtie nanoantennas with varying geometric spacing for use with a 532 nm wavelength laser line in Raman Spectroscopy. The fabrication utilized nanolithography by electron beam lithography on a Raith Voyager, development, deposition, and metal lift-off. This study explored a specific bowtie nanoantenna geometry of 270 nm equilateral sides triangle pairs with 3 varying gap sizes, 50 nm, 20 nm, and 10 nm, and the effect of varying electron beam doses on the final structure of the nanoantenna. The results presented here, will show that the working dose factor range is 6.5-10.3 (650-10,300 μC/cm²) for 120 nm thick polymethyl methacrylate (PMMA), and with a 44.78% increase in dose, the footprint area increases between 5.9% and 10.7%.

Nanotechnology to the Rescue: Treatment Perspective for the Immune Dysregulation Observed in COVID-19

The study of the use of nanotechnology for drug delivery has been extensive. Nanomedical approaches for therapeutics; drug delivery in particular is superior to conventional methods in that it allows for controlled targeted delivery and release, higher stability, extended circulation time, minimal side-effects, and improved pharmacokinetic clearance (of the drug) form the body, to name a few. The magnitude of COVID-19, the current ongoing pandemic has been severe; it has caused widespread the loss of human life. In individuals with severe COVID-19, immune dysregulation and a rampant state of hyperinflammation is observed. This kind of an immunopathological response is detrimental and results in rapid disease progression, development of secondary infections, sepsis and can be fatal. Several studies have pin-pointed the reason for this immune dysregulation; deviations in the signaling pathways involved in the mediation and control of immune responses. In severe COVID-19 patients, many signaling cascades including JAK/STAT, NF-κB, MAPK/ERK, TGF beta, VEGF, and Notch signaling were found to be either upregulated or inactivated. Targeting these aberrant signaling pathways in conjunction with antiviral therapy will effectuate mitigation of the hyperinflammation, hypercytokinemia, and promote faster recovery. The science of the use of nanocarriers as delivery agents to modulate these signaling pathways is not new; it has already been explored for other inflammatory diseases and in particular, cancer therapy. Numerous studies have evaluated the efficacy and potential of nanomedical approaches to modulate these signaling pathways and have been met with positive results. A treatment regime, that includes nanotherapeutics and antiviral therapies will prove effective and holds great promise for the successful treatment of COVID-19. In this article, we review different nanomedical approaches already studied for targeting aberrant signaling pathways, the host immune response to SARS-CoV-2, immunopathology and the dysregulated signaling pathways observed in severe COVID-19 and the current treatment methods in use for targeting signaling cascades in COVID-19. We then conclude by suggesting that the use of nanomedical drug delivery systems for targeting signaling pathways can be extended to effectively target the aberrant signaling pathways in COVID-19 for best treatment results.

Perspectives of future water sources in Qatar by phytoremediation: biodiversity at ponds and modern approach

Anthropogenic and industrial wastewater (IWW) could be an additional future source of water to support the needs of the people of the State of Qatar. New lagoons have been built using modern technologies to optimize water use and waste recycling, as well as increasing the green spaces around the country. To achieve successful development of these new lagoons, lessons should be learned from the old ponds by examining their biodiversity, ecology, and the roles played by aquatic plants and algae to remediate wastewaters at these ponds. The perspectives of using IWW (from oil and gas activities), that is currently pumped deep into the ground are presented. Instead of causing great damage to groundwater, IWW can be stored in artificial ponds prepared for ridding it of all impurities and pollutants of various types, organic and inorganic, thereby making it serviceable for various human uses. Phycoremediation, bioremediation, and phytoremediation methods adopted by algae, bacteria and aquatic native plants are discussed, and special attention should be paid to those that proved successful in removing heavy metals and degrading organic compounds. At least three native plants namely: Amaranthus viridis, Phragmites australis, and Typha domingensis should be paid special attention, since these plants are efficient in remediation of arsenic and mercury; elements found abundantly in wastewater of gas activities. Some promising modern and innovative experiences and biotechnologies to develop efficient transgenic plants and microorganisms in removing and degrading pollutants are discussed, as an important strategy to keep the ecosystem clean and safe. Novelty statementIndustrial wastewater (IWW) could be an alternative source of water at the Arabian Gulf region. Currently, IWW is pumped deep into the ground causing a great damage to groundwater; little information about this issue has been reported. Such IWW can be stored in artificial ponds designed for ridding them of all impurities of various types; various remediation methods can be used. Modern biotechnology to develop transgenic plants and microorganisms to enhance these remediation methods can be adopted.

Second harmonic generation imaging reveals asymmetry in the rotational helicity of collagen lamellae in chicken corneas

High tensile strength and optical clarity are unique properties of the cornea. These features are dictated by the three-dimensional architecture of corneal lamellae. Therefore, understanding the microscopic details of the cornea's structural organization may contribute to the development of artificial cornea for the treatment of corneal diseases. In this study, the combination of forward second harmonic generation (SHG) microcopy and fast Fourier-transform based image analysis was used to characterize the depth-dependent superstructure of chicken corneal stroma. Our results show that from the surface, adjacent lamellae of anterior chicken cornea lamella rotate in a counterclockwise direction, and the same rotational helicity is observed in left and right corneas. Furthermore, the overall average rotational pitch of lamellae is 0.92 ± 0.11 degree/µm which persists for 176 ± 14 µm in the anterior stroma. As depth further increased, the rate of lamellar rotation decreases. Upon reaching posterior stroma, lamellar orientation remains constant. Throughout the stroma, collagen lamellae in chicken rotate a total of 169 ± 21 degrees. The lack of lamellar rotation in posterior stroma suggests that packing efficiency cannot be used to explain the helicity of depth-dependent rotation of anterior stroma. In addition, although the right cornea has a higher rotational pitch (0.95 ± 11 vs 0.90 ± 10 degrees/µm) and thinner anterior stroma (173 ± 13 vs 179 ± 14 µm) than the left cornea, the two effects cancel each other out and result in similar total angular rotation of anterior stroma (161 ± 23 and 165 degrees ± 21). Finally, our observation of a total angular rotation of 169 ± 21 degrees shows that within experimental error, chicken cornea lamellae rotate around 180 degrees or half of a complete turn. Additional studies are needed to arrive at an explanation of chicken superstructure in three dimensions.

ROCK inhibitor (Y27632) increases apoptosis and disrupts the actin cortical mat in embryonic avian corneal epithelium

The embryonic chicken corneal epithelium is a unique tissue that has been used as an in vitro epithelial sheet organ culture model for over 30 years (Hay and Revel [1969] Fine structure of the developing Avian cornea. Basel, Switzerland: S. Karger A.G.). This tissue was used to establish that epithelial cells could produce extracellular matrix (ECM) proteins such as collagen and proteoglycans (Dodson and Hay [1971] Exp Cell Res 65:215-220; Meier and Hay [1973] Dev Biol 35:318-331; Linsenmayer et al. [1977] Proc Natl Acad Sci U S A 74:39-43; Hendrix et al. [1982] Invest Ophthalmol Vis Sci 22:359-375). This historic model was also used to establish that ECM proteins could stimulate actin reorganization and increase collagen synthesis (Sugrue and Hay [1981] J Cell Biol 91:45-54; Sugrue and Hay [1982] Dev Biol 92:97-106; Sugrue and Hay [1986] J Cell Biol 102:1907-1916). Our laboratory has used the model to establish the signal transduction pathways involved in ECM-stimulated actin reorganization (Svoboda et al. [1999] Anat Rec 254:348-359; Chu et al. [2000] Invest Ophthalmol Vis Sci 41:3374-3382; Reenstra et al. [2002] Invest Ophthalmol Vis Sci 43:3181-3189). The goal of the current study was to investigate the role of ECM in epithelial cell survival and the role of Rho-associated kinase (p160 ROCK, ROCK-1, ROCK-2, referred to as ROCK), in ECM and lysophosphatidic acid (LPA) -mediated actin reorganization. Whole sheets of avian embryonic corneal epithelium were cultured in the presence of the ROCK inhibitor, Y27632 at 0, 0.03, 0.3, 3, or 10 microM before stimulating the cells with either collagen (COL) or LPA. Apoptosis was assessed by Caspase-3 activity assays and visualized with annexin V binding. The ROCK inhibitor blocked actin cortical mat reformation and disrupted the basal cell lateral membranes in a dose-dependent manner and increased the apoptosis marker annexin V. In addition, an in vitro caspase-3 activity assay was used to determine that caspase-3 activity was higher in epithelia treated with 10 microM Y-27632 than in those isolated without the basal lamina or epithelia stimulated with fibronectin, COL, or LPA. In conclusion, ECM molecules decreased apoptosis markers and inhibiting the ROCK pathway blocked ECM stimulated actin cortical mat reformation and increased apoptosis in embryonic corneal epithelial cells.

ECM-stimulated signaling and actin reorganization in embryonic corneal epithelia are Rho dependent

PURPOSE

The goal of this study was to investigate the role of the small guanosine triphosphatase (GTPase), Rho, in the corneal epithelial response to extracellular matrix (ECM) molecules. The avian corneal epithelial model was used to establish that Rho is required for actin reorganization and tyrosine phosphorylation of integrin-mediated signal pathway proteins.

METHODS

Whole embryonic corneal epithelia were isolated without the basal lamina and either transfected with Rho-specific antisense oligonucleotides or treated with Clostridium botulinum C3 exoenzyme and then stimulated with fibronectin (FN) or collagen (COL). The epithelia were evaluated for actin reorganization and protein production including Rho protein levels and tyrosine phosphorylation with Western blot analysis.

RESULTS

After an overnight transient transfection with antisense oligonucleotides, Rho protein levels were decreased more than 80%, and tyrosine phosphorylation of all integrin-mediated signal transduction proteins was decreased compared with control epithelia. Intracellular Rho distribution did not change in the presence of antisense oligonucleotides; however, the amount of immunolabeled Rho decreased. Disrupting the signaling cascade with Rho antisense also blocked FN- and COL-stimulated actin cortical mat reformation. C. botulinum C3 exoenzyme, a pharmacologic agent that specifically causes adenosine diphosphate (ADP) ribosylation and inactivation of Rho, also blocked actin reorganization and tyrosine phosphorylation. In contrast, decreasing Raf protein levels did not change FN-mediated actin reorganization or tyrosine phosphorylation.

CONCLUSIONS

Decreasing Rho protein or blocking its function inhibited ECM-stimulated actin reorganization and signal transduction, as measured by tyrosine phosphorylation.