GTP-dependent regulation of heterochromatin fluctuations at subtelomeric regions in Saccharomyces cerevisiae

In eukaryotes, single cells in a population display different transcriptional profiles. One of the factors regulating this heterogeneity is the chromatin state in each cell. However, the mechanisms of epigenetic chromatin regulation of specific chromosomal regions remain unclear. Therefore, we used single-cell tracking system to analyze IMD2. IMD2 is located at the subtelomeric region of budding yeast, and its expression is epigenetically regulated by heterochromatin fluctuations. Treatment with mycophenolic acid, an inhibitor of de novo GTP biosynthesis, triggered a decrease in GTP, which caused heterochromatin fluctuations at the IMD2 locus. Interestingly, within individually tracked cells, IMD2 expression state underwent repeated switches even though IMD2 is positioned within the heterochromatin region. We also found that 30% of the cells in a population always expressed IMD2. Furthermore, the addition of nicotinamide, a histone deacetylase inhibitor, or guanine, the GTP biosynthesis factor in salvage pathway of GTP biosynthesis, regulated heterogeneity, resulting in IMD2 expression being uniformly induced or suppressed in the population. These results suggest that gene expression heterogeneity in the IMD2 region is regulated by changes in chromatin structure triggered by slight decreases in GTP.

HIF-1 inhibition reverses opacity in a rat model of galactose-induced cataract

Cataract is an eye disease, in which the lens becomes opaque, causing vision loss and blindness. The detailed mechanism of cataract development has not been characterized, and effective drug therapies remain unavailable. Here, we investigated the effects of Hypoxia-inducible factor 1 (HIF-1) inhibitors using an ex vivo model, in which rat lenses were cultured in galactose-containing medium to induce opacity formation. We found that treatment with the HIF-1 inhibitors 2-Methoxyestradiol (2ME2), YC-1, and Bavachinin decreased lens opacity. Microarray analysis on 2ME2-treated samples, in which opacity was decreased, identified genes upregulated by galactose and downregulated by inhibitor treatment. Subsequent STRING analysis on genes that showed expression change by RT-qPCR identified two clusters. First cluster related to the cytoskeleton and epithelial-mesenchymal transition (EMT). Second cluster related to the oxidative stress, and apoptosis. ACTA2, a known marker for EMT, and TXNIP, a suppressor of cell proliferation and activator of apoptosis, were present in each cluster. Thus, suppression of EMT and apoptosis, as well as activation of cell proliferation, appear to underlie the decrease in lens opacity.

IMD2, which is located near the boundary of heterochromatin regions, is regulated by the use of multiple HAT-related factors

In Saccharomyces cerevisiae, boundaries formed by DNA sequence-dependent or -independent histone modifications stop the spread of the heterochromatin region formed via the Sir complex. However, it is unclear whether the histone modifiers that control DNA sequence-independent boundaries function in a chromosome-specific or -nonspecific manner. In this study, we evaluated the effects of the SAGA complex, a histone acetyltransferase (HAT) complex, and its relationship with other histone-modifying enzymes to clarify the mechanism underlying boundary regulation of the IMD2 gene on the right subtelomere of chromosome VIII. We found that Spt8, a component of the SAGA complex, is important for boundary formation in this region and that the inclusion of Spt8 in the SAGA complex is more important than its interaction with TATA-binding protein and TFIIS. In addition to SAGA, various HAT-related factors, such as NuA4 and Rtt109, also functioned in this region. In particular, the SAGA complex induced weak IMD2 expression throughout the cell, whereas NuA4 induced strong expression. These results indicate that multiple HATs contribute to the regulation of boundary formation and IMD2 expression on the right subtelomeres of chromosome VIII and that IMD2 expression is determined by the balance between these factors.

RNA synthesis in liposomes with negatively charged lipids after fusion via freezing-thawing

The freezing-thawing (F/T) method for fusing giant unilamellar vesicles (GUVs) can provide substrates, enzymes and membrane material simultaneously and repetitively, and is useful for constructing a recursive model of an artificial cell. However, enzymatic efficiency after F/T is reduced due to rupture of the GUVs and leakage of the inner solution during F/T. Previously, liposomes composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and a negatively charged lipid, such as 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG), showed lower rupture and leakage rates during F/T. In this study, we investigated the effect of POPG on the supply of components required for T7 RNA polymerase reactions via F/T by flow cytometry analysis. We found that the addition of POPG to liposome preparations reduced the efficiency of RNA synthesis. In addition, DNA was concentrated during F/T and RNA synthesis occurred after F/T in liposomes composed of POPC and POPG. Our results provide new insights for more efficient supply of substrates and enzymes by the F/T method, thereby increasing the utility of the F/T method for the construction of recursive bioreactors.

A novel tracking and analysis system for time-lapse cellular imaging of Schizosaccharomyces pombe

The significance of employing the parent-progeny relationship tracking technique in single-cell analysis has grown with the passage of time. In this study, fundamental image processing techniques were amalgamated to develop software capable of inferring cell cycle alterations in fission yeasts exhibiting equipartition during division. These methods, exclusively relying on bright-field images as input, could track parent-progeny relationships after cellular division through the assessment of temporal morphological transformation of these cells. In the application of this technique, the software was employed for calculate the intracellular fluorescent dots during every stage of the cell cycle, leveraging the yeast strain GFP-fused Swi6, which is present in cells and binds to chromatin. The results obtained with this software were consistent with those of previous studies. This software facilitated the single-cell level tracking of parent-progeny relationships in cells exhibiting equipartition during division and enabled the monitoring of spatial fluctuations in cell cycle-dependent proteins. This method, expediting the analysis of extensive datasets, may also empower large-scale screening experiments that would be unfeasible to conduct manually.

Glutamate is effective in decreasing opacity formed in galactose-induced cataract model

Although cataract is the leading cause of blindness worldwide, the detailed pathogenesis of cataract remains unclear, and clinically useful drug treatments are still lacking. In this study, we examined the effects of glutamate using an ex vivo model in which rat lens is cultured in a galactose-containing medium to induce opacity formation. After inducing lens opacity formation in galactose medium, glutamate was added, and the opacity decreased when the culture was continued. Next, microarray analysis was performed using samples in which the opacity was reduced by glutamate, and genes whose expression increased with galactose culture and decreased with the addition of glutamate were extracted. Subsequently, STRING analysis was performed on a group of genes that showed variation as a result of quantitative measurement of gene expression by RT-qPCR. The results suggest that apoptosis, oxidative stress, endoplasmic reticulum (ER) stress, cell proliferation, epithelial-mesenchymal transition (EMT), cytoskeleton, and histones are involved in the formation and reduction of opacity. Therefore, glutamate may reduce opacity by inhibiting oxidative stress and its downstream functions, and by regulating the cytoskeleton and cell proliferation.

Gene profiles and mutations in the development of cataracts in the ICR rat model of hereditary cataracts

Cataracts are opacifications of the lens that cause loss of visual acuity and ultimately of eyesight. Age-related cataract develops in most elderly people, but the mechanisms of cataract onset are incompletely understood. The Ihara Cataract Rat (ICR) is an animal model of hereditary cataracts showing cortical opacity that commonly develops prematurely. We identified putative mechanisms of cataract onset in the ICR rat model by measuring gene expression changes before and after cortical cataract development and conducting point mutation analysis. Genes differentially expressed between 4-week-old animals without cortical cataracts and 8-10-week-old animals with cortical cataracts were selected from microarray analysis. Three connections were identified by STRING analysis: (i) Epithelial-Mesenchymal Transition (EMT), including Col1a2, and Pik3r1. (ii) Lens homeostasis, including Aqp5, and Cpm. (iii) Lipid metabolism, including Scd1, Srebf1, and Pnpla3. Subsequently, mutation points were selected by comparing ICR rats with 12 different rats that do not develop cataracts. The apolipoprotein Apoc3 was mutated in ICR rats. Analyses of gene expression changes and point and mutations suggested that abnormalities in EMT or lipid metabolism could contribute to cataract development in ICR rats.

Chronic Antioxidant Capacity Loss in Anterior Chamber Environment After Iridectomy

Purpose

To compare the ascorbic acid concentration and total antioxidant capacity in the aqueous humor of pigmented Rex rabbits after sham operation (control), iridectomy, and trabeculectomy.

Methods

Pigmented Rex rabbits were divided into control, iridectomy, and trabeculectomy groups and followed up for 12 months after surgery. Ascorbic acid concentration and total antioxidant capacity in the aqueous humor, intraocular pressure, and the occurrence of cataracts were examined in each group.

Results

The ascorbic acid concentration and total antioxidant capacity after iridectomy and trabeculectomy were significantly lower at one week and at one, six, and 12 months after operation than those in the control group (P ≤ 0.03). Ascorbic acid concentration was positively and significantly correlated with total antioxidant capacity in the aqueous humor (P < 0.01). Compared to the control and the iridectomy groups, intraocular pressure in the trabeculectomy group was significantly lower at one week and at one and six months after surgery (one week: P < 0.01 and P < 0.01, respectively; one month: P < 0.01 and P = 0.03, respectively; six months: P = 0.03). Histological findings in the iridectomy and trabeculectomy groups included the appearance of vacuoles in the lens at six and 12 months after surgery.

Conclusions

Iridectomy causes a sustained decrease in ascorbic acid concentration, followed by a long-term decrease in the total antioxidant capacity within the aqueous humor.

Translational Relevance

The animal model possibly predicts the vulnerability focusing on the antioxidant level in the anterior chamber environment after trabeculectomy and iridectomy per se in clinical settings.

Spt3 and Spt8 Are Involved in the Formation of a Silencing Boundary by Interacting with TATA-Binding Protein

In Saccharomyces cerevisiae, a heterochromatin-like chromatin structure called the silencing region is present at the telomere as a complex of Sir2, Sir3, and Sir4. Although spreading of the silencing region is blocked by histone acetylase-mediated boundary formation, the details of the factors and mechanisms involved in the spread and formation of the boundary at each telomere are unknown. Here, we show that Spt3 and Spt8 block the spread of the silencing regions. Spt3 and Spt8 are members of the Spt-Ada-Gcn5-acetyltransferase (SAGA) complex, which has histone acetyltransferase activity. We performed microarray analysis of the transcriptome of spt3Δ and spt8Δ strains and RT-qPCR analysis of the transcript levels of genes from the subtelomeric region in mutants in which the interaction of Spt3 with TATA-binding protein (TBP) is altered. The results not only indicated that both Spt3 and Spt8 are involved in TBP-mediated boundary formation on the right arm of chromosome III, but also that boundary formation in this region is DNA sequence independent. Although both Spt3 and Spt8 interact with TBP, Spt3 had a greater effect on genome-wide transcription. Mutant analysis showed that the interaction between Spt3 and TBP plays an important role in the boundary formation.

Effects of Charged Lipids on Giant Unilamellar Vesicle Fusion and Inner Content Mixing via Freeze-Thawing

Fusion between giant unilamellar vesicles (GUVs) can incorporate and mix components of biochemical reactions. Recently, GUV fusion induced by freeze-thawing (F/T) was employed to construct artificial cells that can easily and repeatedly fuse GUVs with efficient content mixing. However, GUVs were ruptured during F/T, and the inner contents leaked. Herein, we investigated the effects of charged lipids on GUV fusion via F/T. The presence of 10 %-50 % (w/w%) negatively charged lipids in GUV membranes, mainly composed of the neutral charged lipid 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), improved resistance to GUV rupture and decreased inner content leakage. Furthermore, we found that the presence of positively charged lipids in GUV membranes elevated GUV rupture compared with F/T between GUVs containing POPC alone. Modified GUVs may better incorporate nutrients and lipid membranes with less damage following GUV fusion via F/T, providing an improved artificial model.

Histone acetyltransferase inhibition reverses opacity in rat galactose-induced cataract

Cataract, a disease that causes opacity of the lens, is the leading cause of blindness worldwide. Cataracts secondary to diabetes are common, even in young patients, so they are of significant clinical importance. Here, we used an ex vivo model of galactose-induced cataracts in the rat lens to investigate the therapeutic effects of histone acetyltransferase (HAT) inhibitors. Among the tested HAT inhibitors, TH1834 was the only one that could reverse most of the opacity once it had formed in the lens. Combination treatment with C646/CPTH2 and CBP30/CPTH2 also had therapeutic effects. In lens cross-sections, vacuoles were present in the tissue of the cortical equatorial region of untreated cataract samples. In treated cataract samples, lens tissue regenerated to fill the vacuoles. To identify the genes regulated by HAT inhibitors, qRT-PCR was performed on treated and untreated cataract samples to determine candidate genes. Expression of Acta1 and Stmn4, both of which are involved in the cytoskeleton, were altered significantly in C646+CPTH2 samples. Expression of Emd, a nuclear membrane protein, and Prtfdc1, which is involved in cancer cell proliferation, were altered significantly in CBP30+CPTH2 samples. Acta1, Acta2, Arrdc3, Hebp2, Hist2h2ab, Pmf1, Ppdpf, Rbm3, RGD1561694, Slc16a6, Slfn13, Tagln, Tgfb1i1, and Tuba1c in TH1834 samples were significantly altered. These genes were primarily related to regulation of cell proliferation, the cytoskeleton, and cell differentiation. Expression levels increased with the onset of cataracts and was suppressed in samples treated with HAT inhibitors.

Atm inhibition decreases lens opacity in a rat model of galactose-induced cataract

Cataract causes vision loss and blindness due to formation of opacities of the lens. The regulatory mechanisms of cataract formation and progression remain unclear, and no effective drug treatments are clinically available. In the present study, we tested the effect of ataxia telangiectasia mutated (Atm) inhibitors using an ex vivo model in which rat lenses were cultured in galactose-containing medium to induce opacity formation. After lens opacities were induced by galactose, the lenses were further incubated with the Atm inhibitors AZD0156 or KU55933, which decreased lens opacity. Subsequently, we used microarray analysis to investigate the underlying molecular mechanisms of action, and extracted genes that were upregulated by galactose-induced opacity, but not by inhibitor treatment. Quantitative measurement of mRNA levels and subsequent STRING analysis revealed that a functional network consisting primarily of actin family and actin-binding proteins was upregulated by galactose treatment and downregulated by both Atm inhibitors. In particular, Acta2 is a known marker of epithelial-mesenchymal transition (EMT) in epithelial cells, and other genes connected in this functional network (Actn1, Tagln, Thbs1, and Angptl4) also suggested involvement of EMT. Abnormal differentiation of lens epithelial cells via EMT could contribute to formation of opacities; therefore, suppression of these genes by Atm inhibition is a potential therapeutic target for reducing opacities and alleviating cataract-related visual impairment.

Effects of Sugars on Giant Unilamellar Vesicle Preparation, Fusion, PCR in Liposomes, and Pore Formation

The water-in-oil emulsion transfer method was developed for preparing giant unilamellar vesicles (GUVs) and is useful for studying cellular functions under conditions that mimic cellular environments. A shortcoming of this method for encapsulating biochemical reactions is that it requires high sugar concentrations to enable the density effect to transverse the oil-water interface. In this study, we investigated the effects of sugars on GUV preparation and several biochemical reactions. We found that changing the sugar in the inner solution from sucrose to maltose or trehalose improved GUV formation. The fusion ratio of the freeze-thaw method was better in the traditional glucose-sucrose condition compared with the other examined conditions. For the inner biochemical reaction, we performed PCR in liposomes. The presence of maltose in the inner solution improved the stability of GUVs against damage caused by thermal cycles. Finally, fructose in the outer solution reduced leakage of the inner solution via pores on the membranes of GUVs. Our findings provide new insight for optimizing sugar conditions for preparing GUVs and inner GUV reactions. This could increase the utilization of GUVs as artificial cell compartment models.

Synthesis, physico-mechanical and microstructural characterization of Al6063/SiC/PKSA hybrid reinforced composites

The utilization of agro-residues ash as complementary reinforcing materials continues to gain prominence for metal matrix composite (MMCs) development. A rarely investigated but largely available ash among these agro-residues is the palm kernel shell ash (PKSA). Thus, the present study investigates the influence of PKSA particulates hybridized with SiC on the physico-mechanical properties and microstructure of Al6063 metal composites. The composites are synthesized using the double stir-casting technique with SiC held constant at 2 wt.%, while the PKSA contents are varied from 0 to 8 wt.%. The phases present and morphology of the composites are investigated using X-ray diffractometer (XRD) and scanning electron microscopy (SEM), respectively. The density, porosity, hardness, tensile and fracture toughness tests are carried out on the hybrid composites. X-ray diffractometer revealed that for Al 6063, only Al cubic crystal system was identifiable within the matrix. However, for the reinforced composites, major phases identified are Al, Fe₃Si, SiC, MgO, and SiO₂. The SEM images show that the particulates reinforcements (SiC and PKSA) were uniformly dispersed in the matrix. The percentage porosity for the composites ranged from 2.06 to 2.39%. In addition, hardness, yield strength and ultimate tensile strength of the composites are about 10.3%, 18.5% and 10.4%, respectively better than for Al 6063. However, the percent elongation and fracture toughness are lower for the hybrid composites than for Al 6063 and SiC reinforced composite with values decreasing with increase in ash content. Hence, the MMCs produced will be applicable for light-weight engineering applications.

Regulation of HP1 protein by phosphorylation during transcriptional repression and cell cycle

HP1 (Heterochromatin Protein 1), a key factor for the formation of heterochromatin, binds to the methylated lysine 9 of histone H3 (H3K9me), and represses transcription. While the H3K9me mark and HP1 binding are thought to be faithfully propagated to daughter cells, the heterochromatin structure could be dynamically regulated during cell cycle. As evidenced by the well-known phenomenon called Position Effect Variegation (PEV), heterochromatin structure is dynamically and stochastically altered during developmental processes, and thus the expression of genes within or in the vicinity of heterochromatin could be affected by mutations in factors regulating DNA replication as well as by other epigenetic factors. Recent reports show that HP1 also plays an important role in the maintenance and transmission of chromosomes. Like many other factors ensuring faithful chromosome segregation, HP1 family proteins are subjected to posttranslational modifications, most notably phosphorylation, in a cell-cycle dependent manner. Recent studies identified a conserved phosphorylation site that profoundly affects the functions of HP1 during mitotic phase. In this commentary, we discuss dynamic regulation of HP1 protein by phosphorylation during transcriptional repression and cell cycle.

Exchange of Proteins in Liposomes through Streptolysin O Pores

Liposomes, which are vesicles surrounded by lipid membranes, can be used as biochemical reactors by encapsulating various reactions. Accordingly, they are useful for studying cellular functions under controlled conditions that mimic the environment within a cell. However, one of the shortcomings of liposomes as biochemical reactors is the difficulty of introducing or removing proteins due to the impermeability of the membrane. In this study, we established a method for exchanging proteins in liposomes by forming reversible pores in the membrane. We used the toxic protein streptolysin O (SLO); this forms pores in membranes made of phospholipids containing cholesterol that can be closed by the addition of calcium ions. After optimizing the experimental procedure and lipid composition, we observed the exchange of fluorescent proteins (transferrin Alexa Fluor 488 and 647) in 9.9 % of liposomes. We also introduced T7 RNA polymerase, a 98-kDa enzyme, and observed RNA synthesis in ∼8 % of liposomes. Our findings establish a new method for controlling the internal protein composition of liposomes, thereby increasing their utility as bioreactors.

Gene expression profile analysis of the rabbit retinal vein occlusion model

The rabbit retinal vein occlusion (RVO) model is an experimental system that mimics retinal ischemic diseases in humans. The rabbit RVO model is widely used to assess the therapeutic efficacy of various experimental surgical procedures. In the present study, we measured temporal retinal expression of Vegfa, which is known as an ischemic response gene, in rabbit RVO. This analysis revealed that the retinal Vegfa transcriptional response began 7 days after generation of RVO, rather than immediately after induction of ischemia. Next, in order to analyze ischemia-induced changes in gene expression profiles, we performed microarray analysis of day 7 RVO retina versus control retina. The angiogenic regulators Dcn and Mmp1 and pro-inflammatory factors Mmp12 and Cxcl13 were significantly upregulated in RVO retinas. Further, we suggest that epigenetic regulation via the REST/cofactor-complex could contribute to RVO pathology. Among human homologous genes in rabbits, genes associated with hypoxia, angiogenesis, and inflammation were significantly upregulated in RVO retinas. Components of the Tumor necrosis factor-alpha (TNFα) and Nuclear factor-kappa B (NF-κB) pathways, which play regulatory roles in angiogenesis and inflammation, were significantly upregulated in RVO, and the expression levels of downstream factors, such as the transcription factor AP-1 and chemokines, were increased. Further, connectivity map analyses suggested that inhibitors of the NF-κB pathway are potential therapeutic agents for retinal ischemic disease. The present study revealed new insights into the pathology of retinal ischemia using the rabbit RVO model, which accurately recapitulates human disease.

A novel tracking and analysis system for time-lapse cell imaging of Saccharomyces cerevisiae

Recent studies have revealed that tracking single cells using time-lapse fluorescence microscopy is an optimal tool for spatiotemporal evaluation of proteins of interest. Using this approach with Saccharomyces cerevisiae as a model organism, we previously found that heterochromatin regions involved in epigenetic regulation differ between individual cells. Determining the regularity of this phenomenon requires measurement of spatiotemporal epigenetic-dependent changes in protein levels across more than one generation. In past studies, we conducted these analyses manually to obtain a dendrogram, but this required more than 15 h, even for a single set of microscopic cell images. Thus, in this study, we developed a software-based analysis system to analyze time-lapse cellular images of S. cerevisiae, which allowed automatic generation of a dendrogram from a given set of time-lapse cell images. This approach is divided into two phases: a cell extraction and tracking phase, and an analysis phase. The cell extraction and tracking phase generates a set of necessary information for each cell, such as geometrical properties and the daughter-mother relationships, using image processing-based analysis techniques. Then, based on this information, the analysis phase allows generation of the final dendrogram by analyzing the fluorescent characteristics of each cell. The system is equipped with manual error correction to correct for the inevitable errors that occur in these analyses. The time required to obtain the final dendrograms was drastically reduced from 15 h in manual analysis to 0.8 h using this novel system.

Performance of Methyl-5-Benzoyl-2-Benzimidazole Carbamate (Mebendazole) as Corrosion Inhibitor for Mild Steel in Dilute Sulphuric Acid

The inhibitive effect of mebendazole (MBZ) on the corrosion of low-carbon steel in H2SO4 was investigated by gravimetric and electrochemical techniques as well as examination of specimens in the scanning electron microscope with attached energy dispersive X-ray spectrometer (EDS). From gravimetric analysis, the highest inhibition efficiency of about 96.6% was obtained for 1.0 g of inhibitor in H2SO4 solution at 24 h, while with longer exposure times of between 72 to 120 h, the efficiencies averaged between 92 and 95%. Tafel extrapolations from the polarization curves showed that 1.0 g MBZ gave a maximum inhibition efficiency of approximately 99% for the investigation conducted at 30°C, whereas 1.5 g of MBZ gave a maximum inhibition efficiency of about 85% at 60°C. Inhibition efficiency increased with increasing concentrations of MBZ and decreased at elevated temperatures. The inhibitive action was attributed to physical adsorption of MBZ species on the mild steel surface which followed the Langmuir adsorption isotherm. MBZ performed as a mixed-type inhibitor on mild steel in dilute H2SO4.

The microenvironment surrounding FAD mediates its conversion to 8-formyl-FAD in Aspergillus oryzae RIB40 formate oxidase

Aspergillus oryzae RIB40 formate oxidase has Arg87 and Arg554 near the formyl group and O(4) atom of 8-formyl-flavin adenine dinucleotide (FAD), respectively, with Asp396 neighbouring Arg554. Herein, we probed the roles of these three residues in modification of FAD to 8-formyl-FAD. Replacement of Arg87 or Arg554 with Lys or Ala decreased and abolished the modification, respectively. Replacement of Asp396 with Ala or Asn lowered the modification rate. The observation of unusual effects of maintaining pH 7.0 on the modification in R87K, R554K and D396 variants indicates initial and subsequent processes with different pH dependencies. Comparison of the initial process at pH 4.5 and 7.0 suggests that the microenvironment around Arg87 and the protonation state of Asp396 affect the initial process in the native enzyme. Comparison of the crystal structures of native and R554 variants showed that the replacements had minimal effect on catalytic site structure. The positively charged Arg87 might contribute to the formation of an anionic quinone-methide tautomer intermediate, while the positively charged Arg554, in collaboration with the negatively charged Asp396, might stabilize this intermediate and form a hydrogen bonding network with the N(5)/O(4) region, thereby facilitating efficient FAD modification.