Organelle Size Scaling of the Budding Yeast Vacuole Is Tuned by Membrane Trafficking Rates

Organelles serve as biochemical reactors in the cell, and often display characteristic scaling trends with cell size, suggesting mechanisms that coordinate their sizes. In this study, we measure the vacuole-cell size scaling trends in budding yeast using optical microscopy and a novel, to our knowledge, image analysis algorithm. Vacuole volume and surface area both show characteristic scaling trends with respect to cell size that are consistent among different strains. Rapamycin treatment was found to increase vacuole-cell size scaling trends for both volume and surface area. Unexpectedly, these increases did not depend on macroautophagy, as similar increases in vacuole size were observed in the autophagy deficient mutants atg1Δ and atg5Δ. Rather, rapamycin appears to act on vacuole size by inhibiting retrograde membrane trafficking, as the atg18Δ mutant, which is defective in retrograde trafficking, shows similar vacuole size scaling to rapamycin-treated cells and is itself insensitive to rapamycin treatment. Disruption of anterograde membrane trafficking in the apl5Δ mutant leads to complementary changes in vacuole size scaling. These quantitative results lead to a simple model for vacuole size scaling based on proportionality between cell growth rates and vacuole growth rates.     

Mitochondrial involvement in cell death of non-mammalian eukaryotes

Although mitochondria are essential organelles for long-term survival of eukaryotic cells, recent discoveries in biochemistry and genetics have advanced our understanding of the requirements for mitochondria in cell death. Much of what we understand about cell death is based on the identification of conserved cell death genes in Drosophila melanogaster and Caenorhabditis elegans. However, the role of mitochondria in cell death in these models has been much less clear. Considering the active role that mitochondria play in apoptosis in mammalian cells, the mitochondrial contribution to cell death in non-mammalian systems has been an area of active investigation. In this article, we review the current research on this topic in three non-mammalian models, C. elegans, Drosophila, and Saccharomyces cerevisiae. In addition, we discuss how non-mammalian models have provided important insight into the mechanisms of human disease as they relate to the mitochondrial pathway of cell death. The unique perspective derived from each of these model systems provides a more complete understanding of mitochondria in programmed cell death. This article is part of a Special Issue entitled Mitochondria: the deadly organelle.     

Organelle Size Scaling of the Budding Yeast Vacuole Is Tuned by Membrane Trafficking Rates

Organelles serve as biochemical reactors in the cell, and often display characteristic scaling trends with cell size, suggesting mechanisms that coordinate their sizes. In this study, we measure the vacuole-cell size scaling trends in budding yeast using optical microscopy and a novel, to our knowledge, image analysis algorithm. Vacuole volume and surface area both show characteristic scaling trends with respect to cell size that are consistent among different strains. Rapamycin treatment was found to increase vacuole-cell size scaling trends for both volume and surface area. Unexpectedly, these increases did not depend on macroautophagy, as similar increases in vacuole size were observed in the autophagy deficient mutants atg1Δ and atg5Δ. Rather, rapamycin appears to act on vacuole size by inhibiting retrograde membrane trafficking, as the atg18Δ mutant, which is defective in retrograde trafficking, shows similar vacuole size scaling to rapamycin-treated cells and is itself insensitive to rapamycin treatment. Disruption of anterograde membrane trafficking in the apl5Δ mutant leads to complementary changes in vacuole size scaling. These quantitative results lead to a simple model for vacuole size scaling based on proportionality between cell growth rates and vacuole growth rates.     

Characterization of crystals of a cytochrome oxidase (nitrite reductase) from Pseudomonas aeruginosa by x-ray diffraction and electron microscopy

Cytochrome oxidase from Pseudomonas aeruginosa has been crystallized from 2 m-ammonium sulfate. The crystals occur principally as thin diamond-shaped plates of space group P2₁2₁2 with unit cell dimensions of 92 Å × 115 Å × 76 Å. Determination of the density of glutaraldehyde-fixed, water-equilibrated crystals (1.167 g/cm³), coupled with the unit cell volume (804,000 ų), indicates that there is one subunit (~63,000 Mr) per asymmetric unit. X-ray diffraction data which were limited to 12 Å resolution due to small crystal size were obtained for the hk0 and 0kl zones using precession photography. Amplitude and phase data for the hk0, 0kl, and h0l zones were obtained from computer-based Fourier analysis of appropriate micrographs recorded from negatively stained microplates and thin sections of larger crystals using minimal beam electron microscopy. For crystals embedded in the presence of tannic acid it was possible to achieve 20 Å resolution which is comparable to the resolution achieved with negative staining of thin crystalline arrays. In addition, unstained electron diffraction on glutaraldehyde-fixed, glucose-stabilized plates was recorded to a resolution of 9 Å. The three-dimensional packing of the cytochrome oxidase dimer in the unit cell has been deduced from computer reconstructed images of the three principal projections along the crystallographic axes. The cytochrome oxidase dimer is located in the unit cell with the dimer axis coincident with a crystallographic 2-fold axis; thus within the resolution of the present data in projection (9 Å) the two subunits are identical, in agreement with biochemical evidence. The crystals have been prepared with the enzyme in the fully oxidized state and upon reduction a progressive cracking of the crystals is observed, possibly due to a conformational change dependent on the oxidation state of the heme iron.     

Inhibition by ultraviolet light of pole cell formation in Smittia sp (Chironomidae,Diptera): Action spectrum and photoreversibility

The formation of pole cells (primordial germ cells) in Smittia sp can be inhibited by ultraviolet (uv) irradiation without causing significant mortality. Until 70 min after egg deposition, pole cells are suppressed by low uv doses applied to the posterior pole region. Microbeam irradiation of a target area including the oosome inhibits pole cell formation; this is not observed after irradiation of other target areas. The action spectrum for uv inhibition of pole cells shows a distinct peak at 260 nm; its shape suggests that a nucleic acid or nucleic acid-protein complex acts as an effective target. Independent evidence for the involvement of a nucleic acid moiety is derived from the fact that uv inhibition of pole cell formation is photoreversible. The results are discussed in the context of pole cell determination by localized cytoplasmic components.     

Comparison of Two Mathematical Models of Cellularity Calculation

OBJECT: Nowadays, there is increasing evidence that functional magnetic resonance imaging (MRI) modalities, namely, diffusion-weighted imaging (DWI) and dynamic-contrast enhanced MRI (DCE MRI), can characterize tumor architecture like cellularity and vascularity. Previously, two formulas based on a logistic tumor growth model were proposed to predict tumor cellularity with DWI and DCE. The purpose of this study was to proof these formulas. METHODS: 16 patients with head and neck squamous cell carcinomas were included into the study. There were 2 women and 14 men with a mean age of 57.0 ± 7.5 years. In every case, tumor cellularity was calculated using the proposed formulas by Atuegwu et al. In every case, also tumor cell count was estimated on histopathological specimens as an average cell count per 2 to 5 high-power fields. RESULTS: There was no significant correlation between the calculated cellularity and histopathologically estimated cell count by using the formula based on apparent diffusion coefficient (ADC) values. A moderate positive correlation (r=0.515, P=.041) could be identified by using the formula including ADC and V_e values. CONCLUSIONS: The formula including ADC and V_e values is more sensitive to predict tumor cellularity than the formula including ADC values only.     

Distribution of heavy metals and arsenic in soils and indigenous plants near an iron ore mine in northwest Iran

Heavy metal contaminations in the environment of mining area have become a global problem. The vicinity of an iron ore mine was investigated to estimate the concentrations of As, Pb, Cd, Mn, Ni, Zn, and Cr in the soil and the feasibility of using native plants for phytoremediation. For this, concentrations of elements in soil samples collected and were analyzed by inductivity coupled plasma optical emission spectrometry. The concentrations of heavy metals and arsenic in the roots and aerial parts of Dactylis glomerata L. and Scleranthus orientalis Rössler were analyzed by inductively coupled plasma mass spectrometer too. As concentrations in the samples surpassed the soil toxicity threshold. Cd concentration in soil samples was considerably high next to mine pit. Neither species was identified as a hyperaccumulator, but both species could be considered as excluder plants for As.     

Comparative analysis of embryonic cell lineage between Caenorhabditis briggsae and Caenorhabditis elegans

Comparative genomic analysis of important signaling pathways in Caenorhabditis briggsae and Caenorhabditis elegans reveals both conserved features and also differences. To build a framework to address the significance of these features we determined the C. briggsae embryonic cell lineage, using the tools StarryNite and AceTree. We traced both cell divisions and cell positions for all cells through all but the last round of cell division and for selected cells through the final round. We found the lineage to be remarkably similar to that of C. elegans. Not only did the founder cells give rise to similar numbers of progeny, the relative cell division timing and positions were largely maintained. These lineage similarities appear to give rise to similar cell fates as judged both by the positions of lineally equivalent cells and by the patterns of cell deaths in both species. However, some reproducible differences were seen, e.g., the P4 cell cycle length is more than 40% longer in C. briggsae than that in C. elegans (p < 0.01). The extensive conservation of embryonic development between such divergent species suggests that substantial evolutionary distance between these two species has not altered these early developmental cellular events, although the developmental defects of transpecies hybrids suggest that the details of the underlying molecular pathways have diverged sufficiently so as to not be interchangeable.     

Forest situation analysis and future forecasting of famous Upper Tanawal forests ecosystems on western banks of lesser Himalaya

The current work was carried out in Upper Tanawal which lies in the mid of Western part of lesser Himalaya. The area lies between 34°0.34.40′ N to 34°0.48.88′ N latitude and 72°0.84.27′ E to 73°0.10.50′ E longitude. Upper Tanawal is rich in biodiversity. No work regarding forest and forest situation is done previously in this area. (Farooq, et al., 2017). The area was once housing notable and thick forest strands famous for their habitat uniqueness to harbor number of pheasant and other wildlife species. Due to security reasons and worse situation of law and order compromising government writ the area remained scientifically as well departmentally neglected resulting rapid and vigorous ruthless deforestation. The area was extensively visited and sampled using Quadrate method for phytosociological data collection. Phytosociological attributes like density, cover, and frequency were also Calculated and recorded for all tree species of the area in each quadrat. Altitude, slope angle, atmospheric humidity and temperature were also considered as environmental variables for each sampling site. Results reflect that Upper Tanawal hosts 52 different tree species of 39 genera belonging to 25 tree families.The important forests of Upper Tanawal are under high anthropogenic and environmental disturbances. Some of them may easily be managed because of the presence of large number of seedling; however, some areas need serious attention. It was observed that Pinus roxburghii and Pinus wallichiana are the potential tree species for reforestation and afforestation in the area. This study will be the baseline for new researchers in the study area.     

Trichinella spiralis: Differential effect of host bile on the in vitro invasion of infective larvae into epithelial cells

The differential effect of fox and pig bile and its corresponding low molecular weight fraction (LMW) was investigated on the in vitro invasion of MDCK-AA7 epithelial cell monolayers by Trichinella spiralis muscle larvae. Seven invasion experiments were performed and a total of 274 cell monolayers were examined. Fox and pig raw bile at 1:10 and 1:20 dilution and their LMW fractions at 1:10 dilution activated T. spiralis larvae to invade the cell monolayers. In addition, fox raw bile caused significantly larger cell damage than pig raw bile at both dilutions. The area of cell damage was larger at 1:10 than at 1:20 dilution for both fox and pig raw bile (p < 0.05). On the other hand, there was no significant difference between the areas of cell damage caused by the LMW fractions of fox and pig bile. It is concluded that differences between host bile actions may account for differences in host susceptibility to T. spiralis.     

Migration inhibitory factor (MIF) and proliferative responses by human lymphocyte subpopulations separated by sheep erythrocyte rosette formation.

Human peripheral blood lymphocytes were separated by a combination of rosette formation with sheep erythrocytes and differential density centrifugation into subpopulations of rosette positive (T-enriched) cells and rosette negative (T depleted) cells. These were then tested in vitro for the production of macrophage migration inhibitory factor (MIF) and for incorporation of ³H-thymidine in response to specific antigens. Both T enriched and T depleted cell populations produced MIF but only T enriched cells exhibited significant antigen-induced ³H-thymidine incorporation. These findings using a T cell surface marker as the basis for cell separation, a technique which should not alter the B cell surface, confirm an earlier report in which human cells were separated on the basis of surface immunoglobulin, a B cell marker.     

Synthesis, in vitro and in silico evaluation of novel trans-stilbene analogues as potential COX-2 inhibitors

25 new trans-stilbene and trans-stilbazole derivatives were investigated using in vitro and in silico techniques. The selectivity and potency of the compounds were assessed using commercial ELISA test. The obtained results were incorporated into 2D QSAR assay. The most promising compound 4-nitro-3′,4′,5′-trihydroxy-trans-stilbene (N1) was synthetized and its potency and selectivity were confirmed. N1 was classified as preferential COX-2 inhibitor. Its ability to inhibit COX-2 in MCF-7 cell line was established and its cytotoxicity by MTT test was assessed. The compound was more cytotoxic than celecoxib within studied concentration range. Finally, the investigated trans-stilbene was docked into COX-1 and COX-2 active sites using “CDOCKER” protocol.     

Interactions between eosinophils and antibodies: In vivo protective role against rat schistosomiasis

An original protocol of cell transfer from Schistosoma mansoni-infected rats to normal recipient rats is used to investigate the protective role of phagocytic cell populations, described as effector cells in vitro, against a challenge infection with S. mansoni. Nonadherent, eosinophil-enriched and -adherent, macrophage-rich cell preparations, injected via intradermal and subcutaneous routes at the precise site of exposure to cercariae, were able to significantly protect the recipient rats. The time-course study of this protective effect according to the time after infection of donor rats revealed that eosinophils were the major cell population involved in the early phase of infection (4 to 5 weeks), whereas macrophages could also be incriminated thereafter. A rosette assay using anti-immunoglobulin-coated erythrocytes indicated a sequence of the various antibody isotypes under study (IgG₁, IgG_2a, IgE) on the eosinophil surface, during the course of infection. As previously shown in vitro, cytophilic antibodies seemed to participate in the protective effect of eosinophils, since eosinophil-enriched cells from normal rats, sensitized in vitro with immune complexes present in infected rat serum, could also confer significant protection. These observations establish therefore the relevance between our previous in vitro studies and rat resistance to a challenge infection with S. mansoni, underlining the major role played by the interaction between antibodies and phagocytic cells (eosinophils and macrophages).     

Actin Heterogeneity in primary embryonic culture cells from Drosophila melanogaster.

We have investigated actin heterogeneity in differentiating primary embryonic cell cultures from Drosophila melanogaster. Proteins labeled with [³⁵S]methionine have been separated using O'Farrell two-dimensional gel electrophoresis. Cultures of heterogeneous cell types synthesize at least three major forms of actin, each differing slightly in isoelectric point. We have used a cell separation technique based on differential cell adhesion in the presence of ethylene glycol-bis(β-aminoethyl ether) N,N′-tetraacetate to prepare cultures either highly enriched for, or highly depleted of, myogenic cells. Postfusion myogenic cells synthesize predominantly the most acidic actin form (actin I), while nonmyogenic cells synthesize almost exclusively the two more basic forms (actins II and III). Synthesis of actins at earlier intervals in myogenic cell differentiation in vitro has also been examined. Immediately prior to the onset of myoblast fusion, the synthesis of actin I represents approximately 40% of total actin synthesis. As myogenic cell differentiation progresses this actin form is synthesized at an increasing rate, relative to actins II and III. Drosophila appears to be quite similar to vertebrates with regard to the number of actin species synthesized, as well as to cell and developmental specificity of actin synthesis.     

High-Throughput Screening of Myxoid Liposarcoma Cell Lines: Survivin Is Essential for Tumor Growth

Myxoid liposarcoma (MLS) is a soft tissue sarcoma characterized by a recurrent t(12;16) translocation. Although tumors are initially radio- and chemosensitive, the management of inoperable or metastatic MLS can be challenging. Therefore, our aim was to identify novel targets for systemic therapy. We performed an in vitro high-throughput drug screen using three MLS cell lines (402091, 1765092, DL-221), which were treated with 273 different drugs at four different concentrations. Cell lines and tissue microarrays were used for validation. As expected, all cell lines revealed a strong growth inhibition to conventional chemotherapeutic agents, such as anthracyclines and taxanes. A good response was observed to compounds interfering with Src and the mTOR pathway, which are known to be affected in these tumors. Moreover, BIRC5 was important for MLS survival because a strong inhibitory effect was seen at low concentration using the survivin inhibitor YM155, and siRNA for BIRC5 decreased cell viability. Immunohistochemistry revealed abundant expression of survivin restricted to the nucleus in all 32 tested primary tumor specimens. Inhibition of survivin in 402-91 and 1765-92 by YM155 increased the percentage S-phase but did not induce apoptosis, which warrants further investigation before application in the treatment of metastatic MLS. Thus, using a 273-compound drug screen, we confirmed previously identified targets (mTOR, Src) in MLS and demonstrate survivin as essential for MLS survival.     

Effect of optical panel thickness for nutrient removal and cultivation of microalgae in the photobioreactor

The aim of this study was to quantitatively evaluate the effect of the illumination area and the thickness of the optical panel (OP) on the biomass growth of Chlorella vulgaris (C. vulgaris) algae with simultaneous removal of nutrients. For this purpose, three different thicknesses of OPs were used and designated as follows: 4 mm v-cut OP (Run 1), 6 mm v-cut OP (Run 2) and 8 mm v-cut OP (Run 3). The results indicated that the Run 2 and Run 3 samples possessed higher chlorophyll content, as calculated per cell and per unit area of the cell volume, and a shorter doubling time compared to the Run 1 samples. The growth of the biomass using Run 2 and Run 3 was approximately 11.18 %, and this growth was higher than that of Run 1. Furthermore, higher nutrient removal was observed with Run 2 than Run 1. The nutrient removal, biomass growth and specific growth rate for the Run 2 and Run 3 fractions were found to be almost identical. However, in terms of economic consideration, Run 2 with simultaneous nutrient removal was more effective than Run 1 and Run 3 in cultivating the microalgae C. vulgaris.     

2,4,5-Tris(alkoxyaryl)imidazoline derivatives as potent scaffold for novel p53-MDM2 interaction inhibitors: Design,synthesis, and biological evaluation

Imidazoline-based small molecule inhibitors of p53-MDM2 interaction intended for the treatment of p53 wild-type tumors are the promising structures for design of anticancer drugs. Based on fragment approach we have investigated a key role of substituents in cis-imidazoline core for biological activity of nutlin family compounds. Although the necessity of the substituents in the phenyl rings of cis-imidazoline has been shown, there are no studies in which the replacements of a halogen by other substituents have been investigated. A series of simple cis-imidazoline derivatives containing halogen, hydroxy and alkoxy-substituents were synthesized. The biological activity of the compounds was studied using assays of cytotoxicity (MTT) and p53 level. It was found that the hydroxyl-derivatives were not cytotoxic whereas the alkoxy analogues were the same or more active as halogen-substituted compounds in cell viability test. The synthesized alkoxy derivatives induced an increase of p53 level and did not promote necrotic cell death in the concentration up to 40 µM.     

Flow cytometric determination of zoospore DNA content and population DNA distribution in cultured Pfiesteria spp. (Pyrrhophyta)

The relative cellular DNA content from 23 different clonal cultures of Pfiesteria spp. zoospores was determined using a DNA fluorochrome and flow cytometry. Significant differences between Pfiesteria piscicida and P. shumwayae were detected, both in mean zoospore DNA content and population cell cycle DNA distribution. Intraspecific differences in DNA content were found between clonal zoospore cultures established from different geographical regions. Long-term cultures (years) of P. piscicida were available for testing, and a negative correlation was observed between zoospore DNA content and time in culture. Zoospore cell cycle-related DNA distributions were also markedly different between the two species in these clonal cultures. In most cultures tested, P. piscicida zoospores exhibited bimodal DNA flow histograms with G1-S-G2+M distributions, typical of eukaryotic asynchronously cycling cells. In contrast, cultures of P. shumwayae zoospores exhibited one DNA peak distribution, indicative of synchronized cells. The data are consistent with the hypothesis that P. shumwayae zoospores are interphasic cells, and mitosis in zoospore cultures of this species predominantly occurs as benthic or adherent non-motile division cysts. Light microscopy observations of the nuclear condition of electrostatically sorted zoospores of each Pfiesteria species also support this hypothesis. If highly conserved, this disparity in modes of vegetative reproduction would ramify the population dynamics of the two Pfiesteria species.     

Optimization of Pre-transplantation Conditions to Enhance the Efficacy of Mesenchymal Stem Cells

Mesenchymal stem cells (MSCs) are considered a potential tool for cell based regenerative therapy due to their immunomodulatory property, differentiation potentials, trophic activity as well as large donor pool. Poor engraftment and short term survival of transplanted MSCs are recognized as major limitations which were linked to early cellular ageing, loss of chemokine markers during ex vivo expansion, and hyper-immunogenicity to xeno-contaminated MSCs. These problems can be minimized by ex vivo expansion of MSCs in hypoxic culture condition using well defined or xeno-free media i.e., media supplemented with growth factors, human serum or platelet lysate. In addition to ex vivo expansion in hypoxic culture condition using well defined media, this review article describes the potentials of transient adaptation of expanded MSCs in autologous serum supplemented medium prior to transplantation for long term regenerative benefits. Such transient adaptation in autologous serum supplemented medium may help to increase chemokine receptor expression and tissue specific differentiation of ex vivo expanded MSCs, thus would provide long term regenerative benefits.     

Relationships among Cell Size, Membrane Permeability, and Preservative Resistance in Yeast Species

The rate of uptake of propanoic acid and the cell dimensions were measured for 23 yeasts differing in their resistance to weak-acid-type preservatives. Relationships between reciprocal uptake rate, reciprocal permeability, cell volume, cell area, volume/area, and the MICs of benzoic acid and propanoic acid for the yeasts were tested by correlation analysis on pairs of parameters. The MIC of methylparaben, which is not a weak-acid-type preservative, was included. The most significant relationships found were between both reciprocal uptake rate and reciprocal permeability and the MICs of propanoic and benzoic acids Cell volume, area, and volume/area were each individually correlated with propanoic and benzoic acid MICs, but less strongly. In multiple regression analyses, inclusion of terms for volume, area, or volume/area did not markedly increase the significance. The MIC of methylparaben was unrelated to the uptake and permeability parameters, but did show a correlation with cell volume/area. Schizosaccharomyces pombe was anomalous in having very low permeability. Exclusion of these outlying data revealed particularly strong relationships (P < 0.001) between both reciprocal uptake rate and reciprocal permeability and the benzoic acid MIC. MICs for Zygosaccharomyces bailii isolates were substantially higher than for the other species, and therefore Z. baillii isolates had a large influence on the regressions. However, the relationships observed remained significant even after removal of the Z. bailii data. In showing a correlation between the rate at which propanoic acid enters yeast cells and the ability of the cells to tolerate this and other weak-acid-type preservatives, but not methylparaben, the results suggest that the resistance mechanism, in which preservative is continuously removed from the cell, is a common and major determinant of the preservative tolerance of yeast species.