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Abstract Background Orthologs (genes that have diverged after a speciation event) tend to have similar function, and so their prediction has become an important component of comparative genomics and genome annotation. The gold standard phylogenetic analysis approach of comparing available organismal phylogeny to gene phylogeny is not easily automated for genome-wide analysis; therefore, ortholog prediction for large genome-scale datasets is typically performed using a reciprocal-best-BLAST-hits (RBH) approach. One problem with RBH is that it will incorrectly predict a paralog as an ortholog when incomplete genome sequences or gene loss is involved. In addition, there is an increasing interest in identifying orthologs most likely to have retained similar function. Results To address these issues, we present here a high-throughput computational method named Ortholuge that further evaluates previously predicted orthologs (including those predicted using an RBH-based approach) – identifying which orthologs most closely reflect species divergence and may more likely have similar function. Ortholuge analyzes phylogenetic distance ratios involving two comparison species and an outgroup species, noting cases where relative gene divergence is atypical. It also identifies some cases of gene duplication after species divergence. Through simulations of incomplete genome data/gene loss, we show that the vast majority of genes falsely predicted as orthologs by an RBH-based method can be identified. Ortholuge was then used to estimate the number of false-positives (predominantly paralogs) in selected RBH-predicted ortholog datasets, identifying approximately 10% paralogs in a eukaryotic data set (mouse-rat comparison) and 5% in a bacterial data set (Pseudomonas putida – Pseudomonas syringae species comparison). Higher quality (more precise) datasets of orthologs, which we term "ssd-orthologs" (supporting-species-divergence-orthologs), were also constructed. These datasets, as well as Ortholuge software that may be used to characterize other species' datasets, are available at http://www.pathogenomics.ca/ortholuge/ (software under GNU General Public License). Conclusion The Ortholuge method reported here appears to significantly improve the specificity (precision) of high-throughput ortholog prediction for both bacterial and eukaryotic species. This method, and its associated software, will aid those performing various comparative genomics-based analyses, such as the prediction of conserved regulatory elements upstream of orthologous genes.

This paper investigates delivery of encapsulated drug from poly lactic-co-glycolic micro-/nano-particles. Experimental data collected from about 50 papers are analyzed by machine learning algorithms including linear regression, principal component analysis, Gaussian process regression, and artificial neural networks. The focus is to understand the effect of drug solubility, drug molecular weight, particle size, and pH-value of the release matrix/environment on drug release profiles. The results obtained from machine learning is then used as guidelines for designing new in vitro experiments to examine dependence of drug release profiles on those four factors. It is interesting to see that indeed the results of the new in vitro experiments are in basic agreement with the results obtained from machine learning., (© 2025. The Author(s).)

Exometabolomics is an approach to assess how microorganisms alter, or react to their environments through the depletion and production of metabolites. It allows the examination of how soil microbes transform the small molecule metabolites within their environment, which can be used to study resource competition and cross-feeding. This approach is most powerful when used with defined media that enable tracking of all metabolites. However, microbial growth media have traditionally been developed for the isolation and growth of microorganisms but not metabolite utilization profiling through Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS). Here, we describe the construction of a defined medium, the Northen Lab Defined Medium (NLDM), that not only supports the growth of diverse soil bacteria but also is defined and therefore suited for exometabolomic experiments. Metabolites included in NLDM were selected based on their presence in R2A medium and soil, elemental stoichiometry requirements, as well as knowledge of metabolite usage by different bacteria. We found that NLDM supported the growth of 108 of the 110 phylogenetically diverse (spanning 36 different families) soil bacterial isolates tested and all of its metabolites were trackable through LC-MS/MS analysis. These results demonstrate the viability and utility of the constructed NLDM medium for growing and characterizing diverse microbial isolates and communities., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 de Raad, Li, Kuehl, Andeer, Kosina, Hendrickson, Saichek, Golini, Han, Wang, Bowen, Deutschbauer, Arkin, Chakraborty and Northen.)

Endophytic nitrogen-fixing (diazotrophic) bacteria are essential members of the microbiome of switchgrass ( Panicum virgatum ), considered to be an important commodity crop in bioenergy production. While endophytic diazotrophs are known to provide fixed atmospheric nitrogen to their host plant, there are many other plant growth-promoting (PGP) capabilities of these organisms to be demonstrated. The diversity of PGP traits across different taxa of switchgrass-colonizing endophytes is understudied, yet critical for understanding endophytic function and improving cultivation methods of important commodity crops. Here, we present the isolation and characterization of three diazotrophic endophytes: Azospirillum agricola R1C, Klebsiella variicola F10Cl, and Raoultella terrigena R1Gly. Strains R1C and F10Cl were isolated from switchgrass and strain R1Gly, while isolated from tobacco, is demonstrated herein to colonize switchgrass. Each strain exhibited highly diverse genomic and phenotypic PGP capabilities. Strain F10Cl and R1Gly demonstrated the highest functional similarity, suggesting that, while endophyte community structure may vary widely based on host species, differences in functional diversity are not a clearly delineated. The results of this study advance our understanding of diazotrophic endophyte diversity, which will allow us to design robust strategies to improve cultivation methods of many economically important commodity crops., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Gushgari-Doyle, Schicklberger, Li, Walker and Chakraborty.)

Zinc (Zn 2+ ) is stored in the nucleus, endoplasmic reticulum (ER), Golgi apparatus, mitochondria, lysosomes, and zinc-binding proteins. The acidity of the microenvironment affects the binding between zinc and proteins in which zinc become free or loosely bound. In this study, when cells were treated with an acidic medium, we started seeing free zinc 'hot spots' or zincosomes where we found bright zinc fluorescence. The rising free zinc quickly across whole cells with both intensity and distribution were pH-dependent. Interestingly, the nucleus was more sensitive to acidic treatment as the increase of nuclear zinc was faster and higher than the increase of cytosolic zinc. In addition, we re-cultured strong acid-challenged cells in a normal medium. Comparing to the control, these cells exhibited multiple zinc 'hot spots' beside the nucleus, suggesting that free zinc became more extensively distributed. To investigate further the function of zinc in cell shaping and morphological changes, we categorized strong acid-challenged cells into different shapes and found that the proportion of each cell shape had changed after the acid challenge. These acid-induced changes of the cell shape percentage were partially reversed by the reduction of zinc, suggesting that zinc participated in directing the cell shapes and morphologies during cell growth. Our findings reveal that acidic pH affects the dynamics of cellular zinc by making zinc more accessible to cellular compartments and zinc-binding proteins, which provided new insights into understanding the cellular behavior and the function of zinc in it., Competing Interests: None., (IJPPP Copyright © 2021.)

Zinc (Zn 2+ ) is important in cellular processes. In the cell, free zinc is tightly regulated and found in minuscule amounts. However, in an unhealthy cellular environment, such as hypoxia, zinc increases in the cell and zinc overload may occur. Studies have shown that zinc overload causes cellular and mitochondrial stress. Mitochondrial stress affects mitochondrial morphology. In normal cells, mitochondrial morphology resembles a long, tubular shape. In unhealthy cells, mitochondrial morphology resembles fragmented, circular shape. To address whether zinc overload contributes directly to the abnormal changes of mitochondrial morphology, we imaged and analyzed mitochondria that were treated with the application of exogenous zinc. In the first part of the study, exogenous zinc was applied to HeLa cells at 1 µM, 10 µM, 50 µM, 100 µM, or 200 µM zinc chloride along with 10 µM pyrithione. Mitochondrial morphology was analyzed with Mito-Morphology micro in ImageJ. Mitochondrial morphology changed from a healthy tubular shape to an unhealthy circular shape and fragmentation. Mitochondrial morphology changes were observed in a dose-dependent fashion. The second part of the study involved applying the metal ion chelator TPEN after applying 50 µM zinc chloride along with 10 µM pyrithione. TPEN reduced zinc-induced abnormal mitochondrial morphology after zinc treatment. This present study supports that zinc overload may cause morphology changes induced by mitochondrial stress that may lead to cell death., Competing Interests: None., (IJPPP Copyright © 2021.)

Biomaterials to facilitate the restoration of cardiac tissue is of emerging importance. While there are many aspects to consider in the design of biomaterials, mechanical properties can be of particular importance in this dynamically remodeling tissue. This review focuses on one specific processing method, electrospinning, that is employed to generate materials with a fibrous microstructure that can be combined with material properties to achieve the desired mechanical behavior. Current methods used to fabricate mechanically relevant micro-/nanofibrous scaffolds, in vivo studies using these scaffolds as therapeutics, and common techniques to characterize the mechanical properties of the scaffolds are covered. We also discuss the discrepancies in the reported elastic modulus for physiological and pathological myocardium in the literature, as well as the emerging area of in vitro mechanobiology studies to investigate the mechanical regulation in cardiac tissue engineering. Lastly, future perspectives and recommendations are offered in order to enhance the understanding of cardiac mechanobiology and foster therapeutic development in myocardial regenerative medicine.

Cardiovascular disorder occurs when a local blood clot obstructs an artery or a vein to its surround organs, causing related tissues to lose function and die. It is one of the leading causes of mortality and a major cause of disability. The effect of thrombolysis induced by injecting intravenous thrombolytic agents is critical for reducing tissue damages. Streptokinase (SK) is a widely used thrombolytic agent in the treatment of thromboembolism in the blood vessels. A high unit of streptokinase is used in thrombolytic therapies for thrombotic disorders and could improve tissue reperfusion. It is a potent plasminogen activator. However, safety concerns for the usage of a high unit of streptokinase have been raised for the hemorrhagic transformation. In the present study, we studied how zinc would affect streptokinase-induced thrombolysis in vitro , and proposed a strategy to improve streptokinase's effectiveness in promoting thrombolysis. The mice whole blood was used to form the blood clot in vitro by incubating with calcium at 37°C for 30 minutes. Streptokinase was used for inducing thrombolysis measured with the spectrophotometer. Zinc and its chelator, Ca-EDTA, were applied with streptokinase, respectively. Results showed that the co-application zinc inhibited the thrombolytic effect of streptokinase in a dose-dependent manner. Zinc chelator, Ca-EDTA, significantly increased the effect of streptokinase-induced thrombolysis. Our results suggest that zinc chelation improved the efficiency of streptokinase in thrombolysis. The results may have a significant clinical implication by potentially reducing the adverse effect of streptokinase application., Competing Interests: None.

Polydiacetylenes (PDAs) are conjugative polymers that demonstrate color changes as a response to an external stimulus. In this study, 10,12-pentacosadiynoic acid (PCDA) was mixed with a supporting polymer including poly(ethylene oxide) (PEO) and polyurethane (PU), and the mixture solution was electrospun to construct fiber composites. The electrospun fibers were then photopolymerized using UV irradiation to produce PEO-PDA and PU-PDA nanofiber mats with a fiber diameter ranging from 130 nm to 2.5 μm. The morphologies of both PEO-PDA and PU-PDA nanofibers were dependent on electrospinning parameters such as the ratio of PCDA to PEO or PCDA to PU and the total polymer concentrations. Scanning electron microscopy images showed beaded fibers of PEO-PDA and PU-PDA at 2 and 18 w/v % concentrations, respectively. Smooth fibers were found when the solvent concentration was increased to 3.75 w/v % in PEO-PDA and 25 w/v % in PU-PDA fibers. Both PEO-PDA and PU-PDA nanofiber composites demonstrated excellent colorimetric responses to the presence of Escherichia coli ATCC25922 bacterial cells and the changes in pH as external stimuli. The nanofibers underwent a rapid colorimetric response when exposed directly to E. coli ATCC25922 grown on Luria-Bertani agar. The comparison between the PEO-PDA and PU-PDA suggested that the combination of PEO and PDA is favorable because it provides a sensitive response to the presence of E. coli . The results were compared with samples of a PDA polymer in the absence of a matrix polymer. The colorimetric response was similar when the PDA polymer and the PDA nanofiber composites were exposed to pH changes, and the color change was found to occur at pH 10 and enhanced at pH 11-13. The PDA-containing nanofiber composites showed stronger colorimetric responses than those of the PDA polymer only, suggesting their potential as biosensors and chemosensors., Competing Interests: The authors declare no competing financial interest.

Both zinc (Zn 2+ ) and reactive oxygen species (ROS) have been shown to accumulate during hypoxic-ischemic stress and play important roles in pathological processes. To understand the cross talk between the two of them, here we studied Zn 2+ and ROS accumulation by employing fluorescent probes in HeLa cells to further the understanding of the cause and effect relationship of these two important cellular signaling systems during chemical-ischemia, stimulated by oxygen and glucose deprivation (OGD). We observed two Zn 2+ rises that were divided into four phases in the course of 30 min of OGD. The first Zn 2+ rise was a transient, which was followed by a latent phase during which Zn 2+ levels recovered; however, levels remained above a basal level in most cells. The final phase was the second Zn 2+ rise, which reached a sustained plateau called Zn 2+ overload. Zn 2+ rises were not observed when Zn 2+ was removed by TPEN (a Zn 2+ chelator) or thapsigargin (depleting Zn 2+ from intracellular stores) treatment, indicating that Zn 2+ was from intracellular storage. Damaging mitochondria with FCCP significantly reduced the second Zn 2+ rise, indicating that the mitochondrial Zn 2+ accumulation contributes to Zn 2+ overload. We also detected two OGD-induced ROS rises. Two Zn 2+ rises preceded two ROS rises. Removal of Zn 2+ reduced or delayed OGD- and FCCP-induced ROS generation, indicating that Zn 2+ contributes to mitochondrial ROS generation. There was a Zn 2+ -induced increase in the functional component of NADPH oxidase, p47 phox , thus suggesting that NADPH oxidase may mediate Zn 2+ -induced ROS accumulation. We suggest a new mechanism of cross talk between Zn 2+ and mitochondrial ROS through positive feedback processes that eventually causes excessive free Zn 2+ and ROS accumulations during the course of ischemic stress., (Copyright © 2017 the American Physiological Society.)

Zinc (Zn(2+)) is required for numerous cellular functions. As such, the homeostasis and distribution of intracellular zinc can influence cellular metabolism and signaling. However, the exact distribution of free zinc within live cells remains elusive. Previously we showed the release of zinc from thapsigargin/IP3-sensitive endoplasmic reticulum (ER) storage in cortical neurons. In the present study, we investigated if other cellular organelles also contain free chelatable zinc and function as organelle storage for zinc. To identify free zinc within the organelles, live cells were co-stained with Zinpyr-1, a zinc fluorescent dye, and organelle-specific fluorescent dyes (MitoFluor Red 589: mitochondria; ER Tracker Red: endoplasmic reticulum; BODIPY TR ceramide: Golgi apparatus; Syto Red 64: nucleus). We examined organelles that represent potential storing sites for intracellular zinc. We showed that zinc fluorescence staining was co-localized with MitoFluor Red 589, ER Tracker Red, and BODIPY TR ceramide respectively, suggesting the presence of free zinc in mitochondria, endoplasmic reticulum, and the Golgi apparatus. On the other hand, cytosol and nucleus had nearly no detectable zinc fluorescence. It is known that nucleus contains high amount of zinc binding proteins that have high zinc binding affinity. The absence of zinc fluorescence suggests that there is little free zinc in these two regions. It also indicates that the zinc fluorescence detected in mitochondria, ER and Golgi apparatus represents free chelatable zinc. Taken together, our results support that these organelles are potential zinc storing organelles during cellular zinc homeostasis.

Mitochondrial reactive oxygen species (ROS) are known to accumulate during chemical hypoxia, causing adverse effects on cell function and survival. Recent studies show important role zinc accumulation plays in dysfunction associated with hypoxia. It is well known that ROS accumulation also plays a major role in cellular damage by hypoxia. In this study, fluorescent imaging and pharmacological methods were used in live HeLa cells to determine role of zinc in initial ROS accumulation in mitochondria during chemical hypoxia (oxygen glucose depravation with 4 mM sodium dithionite). Accumulation of both was observed as a very rapid phenomenon with initial rapid zinc increase (zinc wave) within 60 seconds of hypoxia onset and ROS increase within 4.5 minutes. Zinc chelation with TPEN removed the initial zinc wave which in turn abolished ROS accumulation. Influx of exogenous zinc induced rapid ROS accumulation. Inhibition of NADPH oxidase with apocynin, a NADPH oxidase inhibitor, showed significant and prolonged reduction in zinc induced ROS accumulation. We proposed a novel mechanism of intracellular zinc increase that activates NADPH oxidase which in turn triggers mitochondrial ROS production.

Polydiacetylene (PDA) is an attractive conjugated material for use in biosensors due to its unique characteristic of undergoing a blue-to-red color change in response to external stimuli. 10,12-Pentacosadiynoic acid (PCDA) and poly (ethylene oxide) (PEO) were used in this study to develop fiber composites via an electrospinning method at various mass ratios of PEO to PCDA, solution concentrations, and injection speeds. The PEO-PDA fibers in blue phase were obtained via photo-polymerization upon UV-light irritation. High mass ratios of PEO to PCDA, low polymer concentrations of spinning solution, and low injection speeds promoted fine fibers with small diameters and smooth surfaces. The colorimetric transition of the fibers was investigated when the fibers were heated at temperatures ranging from 25 °C to 120 °C. A color switch from blue to red in the fibers was observed when the fibers were heated at temperatures greater than 60 °C. The color transition was more sensitive in the fibers made with a low mass ratio of PEO to PCDA due to high fraction of PDA in the fibers. The large diameter fibers also promoted the color switch due to high reflectance area in the fibers. All of the fibers were analyzed using Fourier transform infrared spectroscopy (FT-IR) and differential scanning calorimetry (DSC) and compared before and after the color change occurred. The colorimetric transitional mechanism is proposed to occur due to conformational changes in the PDA macromolecules.

Understanding nanoparticle-surface adhesion is necessary to develop inert tracers for subsurface applications. Here we show that nanoparticles with neutral surface charge may make the best subsurface tracers, and that it may be possible to used SiO2 nanoparticle retention to measure the fraction of solid surface that has positive charge. We show that silica nanoparticles dispersed in NaCl electrolyte solutions are increasingly retained in calcium carbonate (calcite) sand-packed columns as the solution ionic strength increases, but are not retained if they are injected in pure water or Na2SO4 electrolyte solutions. The particles retained in the NaCl experiments are released when the column is flushed with pure water or Na2SO4 solution. AFM measurements on calcite immersed in NaCl solutions show the initial repulsion of a silica colloidal probe as the surface is approached is reduced as the solution ionic strength increases, and that at high ionic strengths it disappears entirely and only attraction remains. These AFM measurements and their interpretation with Derjaguin-Landau-Verwey-Overbeek (DLVO) theory shows the calcite surface charge is always negative for Na2SO4 solutions, but changes from negative to positive in a patchy fashion as the ionic strength of the NaCl solution increases. Since mixed-charge (patchy) surfaces may be common in the subsurface, nanoparticles with near-zero charge may make the best tracers., (Copyright © 2014 Elsevier Inc. All rights reserved.)

Diminished or inappropriate secretion of insulin is associated with type II diabetes. The cellular/molecular mechanism coupled with the regulation of insulin secretion is still under intense investigation. Divalent ion zinc (Zn(2+)) is co-packaged and co-secreted with insulin and is intimately involved in the process of insulin biosynthesis and the maturation of insulin secretory granules. The study reported here investigated glucose-stimulated zinc secretion (GSZS) and the effect of zinc on glucose-stimulated insulin secretion (GSIS) in the HIT-T15 pancreatic β-cell line. Zinc secretion was measured using a newly developed fluorescent zinc imaging approach, and the insulin secretion was measured using an enzyme-linked immunosorbent assay. There was apparent granular-like zinc staining in β-cells. The application of glucose induced detectable zinc secretion or GSZS. Like GSIS, GSZS was dependent on the glucose concentration (5-20 mm) and the presence of extracellular calcium. The application of a zinc chelator enhanced GSZS. When brief paired-pulse glucose stimulations, which involve the initial glucose stimulation followed by a second round of glucose stimulation, were applied, zinc secretion or GSZS that followed the first pulse was inhibited. This inhibition was reversed by zinc chelation, suggesting a feedback mechanism on GSZS by zinc secreted from β-cells. Finally, the application of zinc (50 μm) strongly inhibited GSIS as measured by enzyme-linked immunosorbent assay. The present study suggests that insulin secretion is regulated by co-secreted zinc that may act as an autocrine inhibitory modulator.

Zinc (Zn(2+)) appears to be intimately involved in insulin metabolism since insulin secretion is correlated with zinc secretion in response to glucose stimulation, but little is known about the regulation of zinc homeostasis in pancreatic beta-cells. This study set out to identify the intracellular zinc transient by imaging free cytosolic zinc in HIT-T15 beta-cells with fluorescent zinc indicators. We observed that membrane depolarization by KCl (30-60 mM) was able to induce a rapid increase in cytosolic concentration of zinc. Multiple zinc transients of similar magnitude were elicited during repeated stimulations. The amplitude of zinc responses was not affected by the removal of extracellular calcium or zinc. However, the half-time of the rising slope was significantly slower after removing extracellular zinc with zinc chelator CaEDTA, suggesting that extracellular zinc affect the initial rising phase of zinc response. Glucose (10 mM) induced substantial and progressive increases in intracellular zinc concentration in a similar way as KCl, with variation in the onset and the duration of zinc mobilization. It is known that the depolarization of beta-cell membrane is coupled with the secretion of insulin. Rising intracellular zinc concentration may act as a critical signaling factor in insulin metabolism of pancreatic beta-cells.

Acute cerebral ischemia is one of the leading causes of mortality and chronic disability. Animal models provide an essential tool for understanding the complex cellular and molecular pathophysiology of hypoxic-ischemia and for testing novel neuroprotective drugs in the pre-clinical setting. In this study we tested zebrafish as a novel model for hypoxic-ischemic brain damage. We built an air-proof chamber where water inside had a low oxygen concentration (0.6-0.8 mg/L) proximate to complete hypoxia. Each zebrafish was placed individually in the hypoxia chamber and was subjected to hypoxia treatment until it became motionless, lying on its side on the bottom of the chamber (time to hypoxia = 679.52 ± 90 seconds, mean ± SD, n =23), followed by transferring into a recovery beaker. Overall, 60.87% of subjects did not recover from hypoxia while 39% survived. The size and distribution of brain injury were determined by triphenyltetrazolium chloride (TTC) staining. Bilateral, moderate to complete TTC decoloration or demarcation of the infarct after 10 minutes of hypoxic treatment was clearly visible in the optic tectum of the optic lobe. The size of the infarct expanded to the deep structure of the optic lobe with longer hypoxic treatments. The zebrafish that survived hypoxia experienced initial twitching followed by unbalanced erratic movements until they regained coordinated, balanced swimming ability. These data indicate that zebrafish are susceptible to hypoxic attack and suggest that the model we present in this study can be used as an alternative model to evaluate hypoxia-induced brain damage.

Ultraviolet (UV) radiation is known to cause oxidative stress, inflammation, DNA damage and apoptotic cell death; however, many details of these malign mechanism have yet to be elucidated. In this study, the exposure of adult human epidermal keratinocytes (HEKa) with UVB (>100 mJ/cm(2)) resulted in the significant increase of intracellular zinc that was released from its storage and was detected by fluorescent zinc indicators. Toxicity testing revealed that UVB-induced zinc release in HEKa is associated with HEKa cell death. Cells that showed elevated intracellular zinc fluorescence upon UVB exposure were also stained by propidium iodide (PI), a traditional viability indicator whose fluorescent signal is as a result of its intercalating with DNA fragments and is unaffected by zinc concentration, showing significant colocalization [Pearson's correlation coefficients r=0.956 (n=6)]. The cytotoxicity of zinc was also determined by an MTT assay after applying the exogenous zinc (ZnCl2) along with its ionophore pyrithione (20 microM) into HEKa culture medium. A significant reduction in cell viability as a function of both zinc concentration and exposure time was observed. The treatments of 1, 10 and 100 microM ZnCl2 with pyrithione demonstrated 2.3, 60 and 84% cell deaths, respectively (control 0.5%) after 30 min. ZnCl2 (100 microM) was also found to induce complete HEKa death after 1 h. Thus, the present study demonstrates that UVB irradiation-induced increased zinc is detrimental to HEKa viability, and zinc may be a necessary step in UVB-induced cell death signaling pathways.

Background: Changes in ionic concentration have a fundamental effect on numerous physiological processes. For example, IP3-gated thapsigargin sensitive intracellular calcium (Ca2+) storage provides a source of the ion for many cellular signaling events. Less is known about the dynamics of other intracellular ions. The present study investigated the intracellular source of zinc (Zn2+) that has been reported to play a role in cell signaling., Results: In primary cultured cortical cells (neurons) labeled with intracellular fluorescent Zn2+ indicators, we showed that intracellular regions of Zn2+ staining co-localized with the endoplasmic reticulum (ER). The latter was identified with ER-tracker Red, a marker for ER. The colocalization was abolished upon exposure to the Zn2+ chelator TPEN, indicating that the local Zn2+ fluorescence represented free Zn2+ localized to the ER in the basal condition. Blockade of the ER Ca2+ pump by thapsigargin produced a steady increase of intracellular Zn2+. Furthermore, we determined that the thapsigargin-induced Zn2+ increase was not dependent on extracellular Ca2+ or extracellular Zn2+, suggesting that it was of intracellular origin. The applications of caged IP3 or IP3-3Kinase inhibitor (to increase available IP3) produced a significant increase in intracellular Zn2+., Conclusions: Taken together, these results suggest that Zn2+ is sequestered into thapsigargin/IP3-sensitive stores and is released upon agonist stimulation.

Much of our current evidence concerning of the role of calcium (Ca2+) as a second messenger comes from its interaction with fluorescent probes; however, many Ca2+ probes also have a higher affinity for another divalent cation: zinc (Zn2+). In this study, using a selective Zn2+ probe (Newport Green), we investigated the accumulation of intracellular Zn2+ transients in acute rat hippocampal slices during ischemia, simulated by oxygen and glucose deprivation (OGD). Subsequent reperfusion with glucose-containing oxygenated medium resulted in an additional increase in intracellular Zn2+. Such observations compelled us to investigate the contribution of Zn2+ to the alleged intracellular Ca2+ overload occurring in ischemia and reperfusion. Using confocal fluorescent microscopy of Calcium Green-1, a widely used Ca2+ indicator, we detected increases in fluorescence intensity during OGD and reperfusion. However, application of a Zn2+ chelator, at the peak of the fluorescence elevation (interpreted as Ca2+ overload), resulted in a significant drop in intensity, suggesting that rising Zn2+ is the primary source of the increasing Calcium Green-1 fluorescence. Finally, staining with the cell viability indicator propidium iodide revealed that Zn2+ is responsible for the ischemic neuronal cell death, because Zn2+ chelation prevented cells from sustaining ischemic damage. Current cellular models of ischemic injury center on Ca2+-mediated excitotoxicity. Our results indicate that Zn2+ elevation contributes to conventionally recognized Ca2+ overload and also suggest that the role of Ca2+ in neurotoxicity described previously using Ca2+ probes may need to be re-examined to determine whether effect previously attributed to Ca2+ could, in part, be attributable to Zn2+.

The mitogen-activated protein kinase (MAPK) (also called extracellular signal-regulated kinase [ERK]) pathway has been implicated in malignant transformation and in the regulation of cellular growth and proliferation of several tumor types, but its expression and function in Hodgkin disease (HD) are unknown. We report here that the active phosphorylated form of MAPK/ERK is aberrantly expressed in cultured and primary HD cells. Inhibition of the upstream MAPK kinase (also called MEK) by the small molecule UO126 inhibited the phosphorylation of ERK and demonstrated a dose- and time-dependent antiproliferative activity in HD cell lines. UO126 modulated the levels of several intracellular proteins including B-cell lymphoma protein 2 (Bcl-2), myeloid cell leukemia-1 (Mcl-1) and caspase 8 homolog FLICE-inhibitory protein (cFLIP), and induced G2M cell-cycle arrest or apoptosis. Furthermore, UO126 potentiated the activity of apoliprotein 2/tumor necrosis factor-related apoptosis-inducing ligand (APO2L/TRAIL) and chemotherapy-induced cell death. Activation of CD30, CD40, and receptor activator of nuclear kappabeta (RANK) receptors in HD cells by their respective ligands increased ERK phosphorylation above the basal level and promoted HD cell survival. UO126 inhibited basal and ligand-induced ERK phosphorylation, and inhibited ligand-induced cell survival of HD cell lines. These findings provide a proof-of-principle that inhibition of the MEK/ERK pathway may have therapeutic value in HD.