Understanding the Effect of Secondary Structures and Aggregation on Human Protein Folding Class Evolution

Using several model organisms it has been shown earlier that protein designability is related to contact density or fraction of buried residues and influence protein evolutionary rates dramatically. Here, using Homo sapiens as a model organism, we have analyzed two main folding classes (all-α and all-β) to examine the factors affecting their evolutionary rates. Since, secondary structures are the most fundamental components of the protein folding classes, we explored the effect of protein secondary structure composition on evolution. Our results show that sheet and helix fractions exhibit positive and negative correlations, respectively, with the rate of protein evolution. On dividing the secondary structure components according to solvent accessibility, linear regression model identified two factors namely buried sheet fraction and relative aggregation propensity. Both these factors together can explain about 13.4% variability in the rate of human protein evolution, while buried sheet residues can alone account to 9.9% variability.     

粤港两地田间发现夜蛾黑卵蜂与螟黄赤眼蜂寄生草地贪夜蛾

草地贪夜蛾是新入侵我国的重大危险性害虫,了解野外条件下天敌的发生情况对于挖掘和利用本地天敌资源开展生物防治有重要意义。2019年4月至7月,定期在广州及香港地区的玉米田中开展草地贪夜蛾发生情况调查时,发现野外两种卵寄生蜂寄生草地贪夜蛾。通过分子生物学方法鉴定为夜蛾黑卵蜂和螟黄赤眼蜂,并分别建立实验种群,为人工扩繁及田间应用打下基础,为利用本地天敌开展草地贪夜蛾生物防治提供重要参考。     

High IFN－α expression is associated with the induction of experimental autoimmune uveitis （EAU） in Fischer 344 rat

INTRODUCTIONThe CD4 T cells can be subdivided intoTh1 and Th2 subsets based on their secreted cy-tokine profile. Th1 cells characteristical1y secreteInterferonry (IFN--ry), whereas Th2 cells maiuly pro--duce IL--4[1]. IL-12 po1arizes the differentiation ofnaitre, CD4 T cells towards Th1 pathWay, in con-trast IL--4 directs T cell differentiation towards Th2pathWay The broken balance between Th1 and Th2immune responses and predominant Th1 responseare crucial factors in initiation…     

Polyaniline grafted polyacylonitrile conductive composite fibers for reversible immobilization of enzymes: Stability and catalytic properties of invertase

Polyacylonitrile fibers (PAN) surfaces were modified with chemical polymerization of conductive polyaniline (PANI) in the presence of potassium dichromate as an oxidizing agent. The effect of aniline concentration on the grafting efficiency and on the electrical surface resistance of PAN/PANI composite fibers was investigated. The surface resistance of the conductive composite fibers in this work was found to be between 8.0 and 0.5 kΩ/cm. As the amount of grafted PANI increased on the PAN fibers the electrical resistance of composite fibers decreased. The PAN/PANI composite fibers were characterized by SEM and FTIR studies. Composite PAN/PANI fibers were used for reversible immobilization of invertase. The immobilization efficiency and the activity of the immobilized invertase (from 1.0 mg/mL invertase solution at pH 5.5) were increased with increasing PANI contents of the composite fibers. The maximum amount of immobilized enzyme onto composite fibers containing 2.0% PANI was about 76.6 mg/g. The optimum pH for the free enzyme was observed at 5.0. On the other hand, immobilized invertase yielded a broad optimum pH profile between pH 5.0 and 7.0. Immobilized invertase exhibited 83% of its original activity even after two months storage at 4 °C while the free enzyme showed only 7% of its initial activity.     

Genome-Wide Association Mapping for Yield and Other Agronomic Traits in an Elite Breeding Population of Tropical Rice (Oryza sativa)

Genome-wide association mapping studies (GWAS) are frequently used to detect QTL in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome. Generally, diversity panels genotyped with high density SNP panels are utilized in order to assay a wide range of alleles and haplotypes and to monitor recombination breakpoints across the genome. By contrast, GWAS have not generally been performed in breeding populations. In this study we performed association mapping for 19 agronomic traits including yield and yield components in a breeding population of elite irrigated tropical rice breeding lines so that the results would be more directly applicable to breeding than those from a diversity panel. The population was genotyped with 71,710 SNPs using genotyping-by-sequencing (GBS), and GWAS performed with the explicit goal of expediting selection in the breeding program. Using this breeding panel we identified 52 QTL for 11 agronomic traits, including large effect QTLs for flowering time and grain length/grain width/grain-length-breadth ratio. We also identified haplotypes that can be used to select plants in our population for short stature (plant height), early flowering time, and high yield, and thus demonstrate the utility of association mapping in breeding populations for informing breeding decisions. We conclude by exploring how the newly identified significant SNPs and insights into the genetic architecture of these quantitative traits can be leveraged to build genomic-assisted selection models.     

Comparing Glaucoma Progression on 24-2 and 10-2 Visual Field Examinations

PurposeTo compare the rate of mean deviation (MD) change on 24-2 versus 10-2 VFs in treated glaucomatous eyes with 5 or more examinations.MethodsIn a retrospective study, 24-2 and 10-2 VFs of 131 glaucoma patients (167 eyes) who had undergone at least 5 VFs examinations during their follow-up were analyzed. All these patients had VF defects both on 24-2 and 10-2 VFs. Rates of MD change were calculated using best linear unbiased predictions (BLUP).ResultsMedian age, MD on 24-2 VF at baseline, number of VFs performed during follow-up and follow-up duration were 55 years, -16.9 dB, 9 and 9 years respectively. Median rate of MD change was significantly greater (p<0.001) on 10-2 VF (-0.26 dB/year; interquartile range [IQR]: -0.47, -0.11) compared to 24-2 VFs (-0.19 dB/year; IQR: -0.41, -0.03). Comparing the rates of MD change in eyes with different severities of VF loss (early [MD better than -6 dB], moderate [-6 dB to -12 dB], advanced [-12 to -20 dB] and severe [MD worse than -20 dB]) at baseline (based on the MD on 24-2 VF), median rate of MD change was comparable between 10-2 and 24-2 VFs in mild (-0.45 dB/year vs. -0.40 dB/year, P = 0.42) and moderate (-0.32 dB/year vs. -0.40 dB/year, P = 0.26) VF loss categories, while the same were significantly greater on 10-2 VFs in advanced (-0.28 dB/year vs. -0.21 dB/year, P = 0.04) and severe (-0.18 dB/year vs. -0.06 dB/year, P<0.001) VF loss categories.ConclusionsIn patients with VF defects both on 24-2 and 10-2 VFs, evaluating the rate of MD change on 10-2 VFs may help in better estimation of glaucoma progression, especially so in eyes with advanced glaucoma at baseline.     

Differential type I IFN-inducing abilities of wild-type versus vaccine strains of measles virus

Laboratory adapted and vaccine strains of measles virus (MV) induced type I IFN in infected cells. The wild-type strains in contrast induced it to a far lesser extent. We have investigated the mechanism for this differential type I IFN induction in monocyte-derived dendritic cells infected with representative MV strains. Laboratory adapted strains Nagahata and Edmonston infected monocyte-derived dendritic cells and activated IRF-3 followed by IFN-beta production, while wild-type MS failed to activate IRF-3. The viral IRF-3 activation is induced within 2 h, an early response occurring before protein synthesis. Receptor usage of CD46 or CD150 and nucleocapsid (N) protein variations barely affected the strain-to-strain difference in IFN-inducing abilities. Strikingly, most of the IFN-inducing strains possessed defective interference (DI) RNAs of varying sizes. In addition, an artificially produced DI RNA consisting of stem (the leader and trailer of MV) and loop (the GFP sequence) exhibited potential IFN-inducing ability. In this case, however, cytoplasmic introduction was needed for DI RNA to induce type I IFN in target cells. By gene-silencing analysis, DI RNA activated the RIG-I/MDA5-mitochondria antiviral signaling pathway, but not the TLR3-TICAM-1 pathway. DI RNA-containing strains induced IFN-beta mRNA within 2 h while the same recombinant strains with no DI RNA required >12 h postinfection to attain similar levels of IFN-beta mRNA. Thus, the stem-loop structure, rather than full genome replication or specific internal sequences of the MV genome, is required for an early phase of type I IFN induction by MV in host cells.     

Effect of germicidal UVC light on fungi isolated from grapes and raisins

AIMS: To examine how UVC affects the different genera of fungi commonly isolated from grapes, with the aim of understanding changes in mycobiota during grape ripening and possible applications for preventing grape decay during storage. METHODS AND RESULTS: Spores of Aspergillus carbonarius, Aspergillus niger, Cladosporium herbarum, Penicillium janthinellum and Alternaria alternata (between 100-250 spores/plate agar) were UVC irradiated for 0 (control), 10, 20, 30, 60, 300 and 600 s. Plates were incubated at 25 degrees C and colonies were counted daily up to 7 days. Alternaria alternata and Aspergillus carbonarius were the most resistant fungi. Conidial germination in these species was reduced by approx. 25% after 10 s of exposure, compared with greater than 70% reduction for the remaining species tested. Penicillium janthinellum spores were the most susceptible at this wavelength. UVC exposures of 300 s prevented growth of all isolates studied, except for Alternaria alternata. CONCLUSIONS: UVC irradiation plays a major role in selecting for particular fungi that dominate the mycobiota of drying grapes. SIGNIFICANCE AND IMPACT OF THE STUDY: The UVC irradiation of harvested grapes could prevent germination of contaminant fungi during storage or further dehydration.     

Signaling molecules involved in the transition of growth to development of Dictyostelium discoideum

The social amoeba Dictyostelium discoideum, a powerful paradigm provides clear insights into the regulation of growth and development. In addition to possessing complex individual cellular functions like a unicellular eukaryote, D. discoideum cells face the challenge of multicellular development. D. discoideum undergoes a relatively simple differentiation process mainly by cAMP mediated pathway. Despite this relative simplicity, the regulatory signaling pathways are as complex as those seen in metazoan development. However, the introduction of restriction-enzyme-mediated integration (REMI) technique to produce developmental gene knockouts has provided novel insights into the discovery of signaling molecules and their role in D. discoideum development. Cell cycle phase is an important aspect for differentiation of D. discoideum, as cells must reach a specific stage to enter into developmental phase and specific cell cycle regulators are involved in arresting growth phase genes and inducing the developmental genes. In this review, we present an overview of the signaling molecules involved in the regulation of growth to differentiation transition (GDT), molecular mechanism of early developmental events leading to generation of cAMP signal and components of cAMP relay system that operate in this paradigm.