Genome comparison using Gene Ontology (GO) with statistical testing

BACKGROUND: Automated comparison of complete sets of genes encoded in two genomes can provide insight on the genetic basis of differences in biological traits between species. Gene ontology (GO) is used as a common vocabulary to annotate genes for comparison. Current approaches calculate the fold of unweighted or weighted differences between two species at the high-level GO functional categories. However, to ensure the reliability of the differences detected, it is important to evaluate their statistical significance. It is also useful to search for differences at all levels of GO. RESULTS: We propose a statistical approach to find reliable differences between the complete sets of genes encoded in two genomes at all levels of GO. The genes are first assigned GO terms from BLAST searches against genes with known GO assignments, and for each GO term the abundance of genes in the two genomes is compared using a chi-squared test followed by false discovery rate (FDR) correction. We applied this method to find statistically significant differences between two cyanobacteria, Synechocystis sp. PCC6803 and Anabaena sp. PCC7120. We then studied how the set of identified differences vary when different BLAST cutoffs are used. We also studied how the results vary when only subsets of the genes were used in the comparison of human vs. mouse and that of Saccharomyces cerevisiae vs. Schizosaccharomyces pombe. CONCLUSION: There is a surprising lack of statistical approaches for comparing complete genomes at all levels of GO. With the rapid increase of the number of sequenced genomes, we hope that the approach we proposed and tested can make valuable contribution to comparative genomics

Research on Location Optimization of Waste Transfer Center in Harbin

This paper puts forward the background of the topic, expounds the research status of waste transfer center location at home and abroad, and summarizes and establishes a nonlinear mixed 0-1 planning type of multi transfer center location model in the relevant theory. The model gives the location constraints when the alternative point of the transfer center has been determined. Under the constraints, it mainly considers the total transportation cost of the waste passing through the transfer center, the treatment cost due to the classification, compression and packaging of waste, and the fixed investment cost of the construction of the waste transfer center, so as to minimize the total cost of these four parts. Based on Gaode map, on the basis of establishing the model, the investigation, statistics and analysis data are substituted to solve the optimal location result

Comparison of Dissolved Gases in Mineral and Vegetable Insulating Oils under Typical Electrical and Thermal Faults

Dissolved gas analysis (DGA) is attracting greater and greater interest from researchers as a fault diagnostic tool for power transformers filled with vegetable insulating oils. This paper presents experimental results of dissolved gases in insulating oils under typical electrical and thermal faults in transformers. The tests covered three types of insulating oils, including two types of vegetable oil, which are camellia insulating oil, Envirotemp FR3, and a type of mineral insulating oil, to simulate thermal faults in oils from 90 °C to 800 °C and electrical faults including breakdown and partial discharges in oils. The experimental results reveal that the content and proportion of dissolved gases in different types of insulating oils under the same fault condition are different, especially under thermal faults due to the obvious differences of their chemical compositions. Four different classic diagnosis methods were applied: ratio method, graphic method, and Duval’s triangle and Duval’s pentagon method. These confirmed that the diagnosis methods developed for mineral oil were not fully appropriate for diagnosis of electrical and thermal faults in vegetable insulating oils and needs some modification. Therefore, some modification aiming at different types of vegetable oils based on Duval Triangle 3 were proposed in this paper and obtained a good diagnostic result. Furthermore, gas formation mechanisms of different types of vegetable insulating oils under thermal stress are interpreted by means of unimolecular pyrolysis simulation and reaction enthalpies calculation

Molecular-level investigation of plasticization of polyethylene terephthalate (PET) in supercritical carbon dioxide via molecular dynamics simulation

The current study aims to use the molecular dynamics (MD) simulation method to discuss the glass transition behaviour and fractional free volume (FFV) of the pure polyethylene terephthalate (PET) and the plasticized PET induced by supercritical carbon dioxide (SC-CO2) sorption. The adsorption concentration reproduced through sorption relaxation cycles (SRC) was firstly estimated and in an order of magnitude with the known experimental results available in the reported literature. The FFV induced by SC-CO2 in PET polymer changes regularly, which is proportional to the capacity of SC-CO2 adsorption with the changes in temperature and pressure. The glass transition temperature (Tg) was further estimated to be almost identical to the known experimental values and shows a gradually decreasing tendency with the increase of pressure. Meanwhile, the plasticization of PET polymer studied by radial distribution functions showed that CO2 molecules occupying the sorption sites on the PET backbone promoted plasticization by increasing the fluidity of the PET backbone chain

Structural basis for the immunomodulatory function of cysteine protease inhibitor from human roundworm Ascaris lumbricoides.

Immunosuppression associated with infections of nematode parasites has been documented. Cysteine protease inhibitor (CPI) released by the nematode parasites is identified as one of the major modulators of host immune response. In this report, we demonstrated that the recombinant CPI protein of Ascaris lumbricoides (Al-CPI) strongly inhibited the activities of cathepsin L, C, S, and showed weaker effect to cathepsin B. Crystal structure of Al-CPI was determined to 2.1 Å resolution. Two segments of Al-CPI, loop 1 and loop 2, were proposed as the key structure motifs responsible for Al-CPI binding with proteases and its inhibitory activity. Mutations at loop 1 and loop 2 abrogated the protease inhibition activity to various extents. These results provide the molecular insight into the interaction between the nematode parasite and its host and will facilitate the development of anthelmintic agents or design of anti-autoimmune disease drugs

Inhibition of protective immunity against <i>Staphylococcus aureus</i> infection by MHC-restricted immunodominance is overcome by vaccination

Recurrent Staphylococcus aureus infections are common, despite robust immune responses. S. aureus infection elicited protective antibody and T cell responses in mice that expressed the Major Histocompatibility Complex (MHC) of the H-2d haplotype, but not H-2b, demonstrating that host genetics drives individual variability. Vaccination with a-toxin or leukotoxin E (LukE) elicited similar antibody and T cell responses in mice expressing H-2d or H-2b, but vaccine-elicited responses were inhibited by concomitant infection in H-2d–expressing mice. These findings suggested that competitive binding of microbial peptides to host MHC proteins determines the specificity of the immunodominant response, which was confirmed using LukE-derived peptide-MHC tetramers. A vaccine that elicited T cell and antibody responses protected mice that expressed H-2d or H-2b, demonstrating that vaccination can overcome MHC-restricted immunodominance. Together, these results define how host genetics determine whether immunity elicted by S. aureus is protective and provide a mechanistic roadmap for future vaccine design

Modulation of Hot Electrons via Interface Engineering of Au@ZnIn2_2S4_4/Mxene for Efficient Photoelectrochemical Seawater Splitting under Visible Light

AbstractHighly effective hot electron transfer is critical in plasmonic metal-semiconductor system to harness its plasmonic functions to enhance solar energy conversion. The efficient injection and utilization of hot electrons are achieved by fabrication of Au@ZnIn$_2$S$_4$/Ti$_3$C$_2$ (Au@ZIS/Ti$_3$C$_2$) system, in which a high-quality interface is constructed between plasmonic Au and ZIS ternary sulfide by cation exchange reaction (CER) to obtain core-shell Au@ZIS, which are further anchored on Ti$_3$C$_2$ surface to produce Au@ZIS/Ti$_3$C$_2$. Different from the conventional core-shell nanostructure by epitaxial growth, the superior interface formed by the direct connect of Au core and ZIS shell without any defects is achieved, which optimizes the electron transfer pathway and greatly promotes the extraction of hot electrons from Au to ZIS. Moreover, the electrons concentrated on ZIS can be further transferred to Ti$_3$C$_2$ due to its outstanding conductivity and electron mobility, leading to highly efficient separation and transfer of electrons through a two-step transfer process. Photoelectrochemical (PEC) H$_2$ evolution from seawater is used to evaluate the activities of prepared samples. Comparisons of the PEC results indicate that the integration of Au and ZIS into an optimized core-shell structure and its further modification by Ti$_3$C$_2$ result in a drastic improvement in PEC activity

Regulation of the Sae Two-Component System by Branched- Chain Fatty Acids in Staphylococcus aureus

Staphylococcus aureus is a ubiquitous Gram-positive bacterium and an opportunistic human pathogen. S. aureus pathogenesis relies on a complex network of regulatory factors that adjust gene expression. Two important factors in this network are CodY, a repressor protein responsive to nutrient availability, and the SaeRS two-component system (TCS), which responds to neutrophil-produced factors. Our previous work revealed that CodY regulates the secretion of many toxins indirectly via Sae through an unknown mechanism. We report that disruption of codY results in increased levels of phosphorylated SaeR (SaeR~P) and that codY mutant cell membranes contain a higher percentage of branched-chain fatty acids (BCFAs) than do wild-type membranes, prompting us to hypothesize that changes to membrane composition modulate the activity of the SaeS sensor kinase. Disrupting the lpdA gene encoding dihydrolipoyl dehydrogenase, which is critical for BCFA synthesis, significantly reduced the abundance of SaeR, phosphorylated SaeR, and BCFAs in the membrane, resulting in reduced toxin production and attenuated virulence. Lower SaeR levels could be explained in part by reduced stability. Sae activity in the lpdA mutant could be complemented genetically and chemically with exogenous short- or full-length BCFAs. Intriguingly, lack of lpdA also alters the activity of other TCSs, suggesting a specific BCFA requirement managing the basal activity of multiple TCSs. These results reveal a novel method of posttranscriptional virulence regulation via BCFA synthesis, potentially linking CodY activity to multiple virulence regulators in S. aureus