Inhibitory Effects of Hydrogen Sulfide on Oxidative Damage and Pericarp Browning in Harvested Litchi

Journal of Plant Growth Regulation - Postharvest pericarp browning (PB) drastically affects acceptability and marketability of litchi fruits. This study was aimed to assess the effect of vacuum...     

Biologic effects of microwave exposure. II. Studies on the mechanisms controlling susceptibility to microwave-induced increases in complement receptor-positive spleen cells

In attempting to evaluate the mechanisms responsible for susceptibility to the inductive increase in splenic complement receptor-positive (CR⁺) cells following exposure to 2450-MHz microwaves, it was found that sensitivity to microwave-induced CR⁺cell increases was under genetic control. In particular, evidence was accumulated suggesting that regulation was under the control of a gene or genes closely associated with but outside of the mouse major histocompatibility complex (H-2). All responsive strains of mice tested were of the H-2^k haplotype, while mice of the H-2^a, H-2^b, H-2^d and H-2i⁵ haplotypes were refractory to the microwave-induced increases in CR⁺ cells. By utilizing certain H-2^k strains of mice that were genetically unable to respond to endotoxin, we were able to show that these strains of mice responded to microwaves, but not to endotoxin, by increasing CR⁺ cells. Microwave-induced increases in CR⁺cells were not mimicked by the intraperitoneal injection of hydrocortisone. Athymic mice responded to microwave exposure, indicating that this event was not regulated by the T-cell population. Mice less than eight weeks old were found not to be susceptible to exposure to 2450-MHz microwaves. These studies indicate that microwaves do induce changes in the population of cells with specific cell-surface receptors, that susceptibility to these changes is under genetic control, and that it is unlikely that endotoxin, corticosteroids, or regulatory T cells play a significant role in the mechanisms regulating these increases.     

Improving SWATH-MS analysis by deep-learning

Data-independent acquisition (DIA) of tandem mass spectrometry spectra has emerged as a promising technology to improve coverage and quantification of proteins in complex mixtures. The success of DIA experiments is dependent on the quality of spectral libraries used for data base searching. Frequently, these libraries need to be generated by labor and time intensive data dependent acquisition (DDA) experiments. Recently, several algorithms have been published that allow the generation of theoretical libraries by an efficient prediction of retention time and intensity of the fragment ions. Sequential windowed acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS) is a DIA method that can be applied at an unprecedented speed, but the fragmentation spectra suffer from a lower quality than data acquired on Orbitrap instruments. To reliably generate theoretical libraries that can be used in SWATH experiments, we developed deep-learning for SWATH analysis (dpSWATH), to improve the sensitivity and specificity of data generated by Q-TOF mass spectrometers. The theoretical library built by dpSWATH allowed us to increase the identification rate of proteins compared to traditional or library-free methods. Based on our analysis we conclude that dpSWATH is a superior prediction framework for SWATH-MS measurements than other algorithms based on Orbitrap data.     

Label free high throughput screening for apoptosis inducing chemicals using time-lapse microscopy signal processing

Label free time-lapse microscopy has opened a new avenue to the study of time evolving events in living cells. When combined with automated image analysis it provides a powerful tool that enables automated large-scale spatiotemporal quantification at the cell population level. Very few attempts, however, have been reported regarding the design of image analysis algorithms dedicated to the detection of apoptotic cells in such time-lapse microscopy images. In particular, none of the reported attempts is based on sufficiently fast signal processing algorithms to enable large-scale detection of apoptosis within hours/days without access to high-end computers. Here we show that it is indeed possible to successfully detect chemically induced apoptosis by applying a two-dimensional linear matched filter tailored to the detection of objects with the typical features of an apoptotic cell in phase-contrast images. First a set of recorded computational detections of apoptosis was validated by comparison with apoptosis specific caspase activity readouts obtained via a fluorescence based assay. Then a large screen encompassing 2,866 drug like compounds was performed using the human colorectal carcinoma cell line HCT116. In addition to many well known inducers (positive controls) the screening resulted in the detection of two compounds here reported for the first time to induce apoptosis.     

The effect of α-mating factor secretion signal mutations on recombinant protein expression in Pichia pastoris

The methylotrophic yeast, Pichia pastoris, has been genetically engineered to produce many heterologous proteins for industrial and research purposes. In order to secrete proteins for easier purification from the extracellular medium, the coding sequence of recombinant proteins is initially fused to the Saccharomyces cerevisiae α-mating factor secretion signal leader. Extensive site-directed mutagenesis of the prepro-region of the α-mating factor secretion signal sequence was performed in order to determine the effects of various deletions and substitutions on expression. Though some mutations clearly dampened protein expression, deletion of amino acids 57–70, corresponding to the predicted 3rd alpha helix of α-mating factor secretion signal, increased secretion of reporter proteins horseradish peroxidase and lipase at least 50% in small-scale cultures. These findings raise the possibility that the secretory efficiency of the leader can be further enhanced in the future.     

Annual TSP and Trace Metal Distribution in the Urban Atmosphere of Islamabad in Comparison with Mega-Cities of the World

The objective of this work was to assess the current concentrations of total suspended particles (TSP) and trace metals in the urban atmosphere of Islamabad, Pakistan, where local industries, transportation, and urbanization are adversely affecting air quality. Air sampling was done using a high-volume sampler and the metals were estimated in TSP by Flame Atomic Absorption Spectrophotometry. An annual mean TSP of 151.9 μ g/m³ was determined for the period May 2003–April 2004, which exceeded the World Health Organization's (WHO's) primary and secondary standards of air quality. The TSP metal concentrations were compared with those reported in literature for other regions of the world and with air quality standards laid down by regulatory agencies. The levels of Na, Fe, Zn, Pb, Mn, Cr, Co, and Cd for the present study were higher than most of the levels reported for other typical industrial and urban areas of the world. The airborne Ni concentrations were higher than the WHO and the U.S. Environmental Protection Agency's standards. Cluster and Principal Component Analyses of the data were used to identify the sources of the metals and establish their mutual correlations in the local atmosphere.     

MITOL-dependent ubiquitylation negatively regulates the entry of PolγA into mitochondria

Mutations in mitochondrial replicative polymerase PolγA lead to progressive external ophthalmoplegia (PEO). While PolγA is the known central player in mitochondrial DNA (mtDNA) replication, it is unknown whether a regulatory process exists on the mitochondrial outer membrane which controlled its entry into the mitochondria. We now demonstrate that PolγA is ubiquitylated by mitochondrial E3 ligase, MITOL (or MARCH5, RNF153). Ubiquitylation in wild-type (WT) PolγA occurs at Lysine 1060 residue via K6 linkage. Ubiquitylation of PolγA negatively regulates its binding to Tom20 and thereby its mitochondrial entry. While screening different PEO patients for mitochondrial entry, we found that a subset of the PolγA mutants is hyperubiquitylated by MITOL and interact less with Tom20. These PolγA variants cannot enter into mitochondria, instead becomes enriched in the insoluble fraction and undergo enhanced degradation. Hence, mtDNA replication, as observed via BrdU incorporation into the mtDNA, was compromised in these PEO mutants. However, by manipulating their ubiquitylation status by 2 independent techniques, these PEO mutants were reactivated, which allowed the incorporation of BrdU into mtDNA. Thus, regulated entry of non-ubiquitylated PolγA may have beneficial consequences for certain PEO patients.

This study shows that mitochondrial entry of the replicative polymerase PolgA is regulated by ubiquitylation by the E3 ligase MITOL; however, by manipulating their ubiquitylation status, some progressive external ophthalmoplegia mutants whose PolgA is polyubiquitylated and cannot enter the mitochondrion can be reactivated and hence become functionally active.