Predicting Carriers of Ongoing Selective Sweeps without Knowledge of the Favored Allele

Methods for detecting the genomic signatures of natural selection have been heavily studied, and they have been successful in identifying many selective sweeps. For most of these sweeps, the favored allele remains unknown, making it difficult to distinguish carriers of the sweep from non-carriers. In an ongoing selective sweep, carriers of the favored allele are likely to contain a future most recent common ancestor. Therefore, identifying them may prove useful in predicting the evolutionary trajectory—for example, in contexts involving drug-resistant pathogen strains or cancer subclones. The main contribution of this paper is the development and analysis of a new statistic, the Haplotype Allele Frequency (HAF) score. The HAF score, assigned to individual haplotypes in a sample, naturally captures many of the properties shared by haplotypes carrying a favored allele. We provide a theoretical framework for computing expected HAF scores under different evolutionary scenarios, and we validate the theoretical predictions with simulations. As an application of HAF score computations, we develop an algorithm (PreCIOSS: Predicting Carriers of Ongoing Selective Sweeps) to identify carriers of the favored allele in selective sweeps, and we demonstrate its power on simulations of both hard and soft sweeps, as well as on data from well-known sweeps in human populations.     

Effects of microbial volatile organic compounds on Ganoderma lucidum growth and ganoderic acids production in Co-v-cultures (volatile co-cultures)

Abstract

Co-v-culture (co-cultivations of physically separated microbes that only interact through the air) systems were designed to investigate the effects of microbial volatile organic compounds (mVOCs) from about 20 different microbes, on a medicinal fungus, Ganoderma lucidum. For more accuracy in co-cultivations, a novel synchronized cultivation approach was tested for culturing G. lucidum. The hyphal growth of G. lucidum and the content of its ganoderic acids (GAs) were measured. In almost all of the co-v-cultures, there was an inhibiting effect on hyphal growth and a promoting effect on GAs contents. In inducing GAs production, Bacillus cereus PTCC 1247 and Pseudomonas aeruginosa UTMC 1404 were the most effective ones, as, compared to control cultures, GAs content increased 2.8 fold. Comparing different co-v-cultivations demonstrated that the concentrations of mVOCs, oxygen, and carbon dioxide were the main players in co-v-cultures. No correlation was found between hyphal growth and GAs production. Strains of the same species imposed totally different effects on hyphal growth or GAs production. This study has investigated the effects of mVOCs on G. lucidum for the first time. Moreover, it suggests that co-v-cultivation may be a promising biotechnological approach to improve the production in G. lucidum.     

Homology Modeling and Molecular Docking Studies of Glutamate Dehydrogenase (GDH) from Cyanobacterium Synechocystis sp. PCC 6803

Glutamate dehydrogenase (GDH), which is present in most bacteria and eukaryotes’ mitochondria, plays an important role in amino acid metabolism. In g     

In silico design and in vitro expression of novel multiepitope DNA constructs based on HIV-1 proteins and Hsp70 T-cell epitopes

Objectives

Epitope-driven vaccines carrying highly conserved and immunodominant epitopes have emerged as promising approaches to overcome human immunodeficiency virus-1 (HIV-1) infection.

Methods

Two multiepitope DNA constructs encoding T cell epitopes from HIV-1 Gag, Pol, Env, Nef and Rev proteins alone and/or linked to the immunogenic epitopes derived from heat shock protein 70 (Hsp70) as an immunostimulatory agent were designed. In silico analyses were applied including MHC-I and MHC-II binding, MHC-I immunogenicity and antigen processing, population coverage, conservancy, allergenicity, toxicity and hemotoxicity. The peptide-MHC-I/MHC-II molecular docking and cytokine production analyses were carried out for predicted epitopes. The selected highly immunogenic T-cell epitopes were then used to design two multiepitope fusion constructs. Next, prediction of the physicochemical and structural properties, B cell epitopes, and constructs-toll-like receptors (TLRs) molecular docking were performed for each construct. Finally, the eukaryotic expression plasmids harboring totally 12 cytotoxic T Lymphocyte (CTL) and 10 helper T lymphocytes (HTL) epitopes from HIV-1 proteins (i.e., pEGFP-N1-gag-pol-env-nef-rev), and linked to 2 CTL and 2 HTL epitopes from Hsp70 (i.e., pEGFP-N1-hsp70-gag-pol-env-nef-rev) were generated and transfected into HEK-293 T cells for evaluating the percentage of multiepitope peptides expression using flow cytometry and western blotting.

Results

The designed DNA constructs could be successfully expressed in mammalian cells. The expression rates of Gag-Pol-Env-Nef-Rev-GFP and Hsp70-Gag-Pol-Env-Nef-Rev-GFP were about 56–60% as the bands of?~?63 and?~?72 kDa confirmed in western blotting, respectively.

Conclusion

The combined in silico/in vitro methods indicated two multiepitope constructs can be produced and used as probable effective immunogens for HIV-1 vaccine development.

     

Heat stress aggravates oxidative stress,apoptosis, and endoplasmic reticulum stress in the cerebellum of male C57 mice

Molecular Biology Reports - The current study was set to assess the effect of heat stress exposure on oxidative stress, apoptosis, and endoplasmic reticulum stress markers in the cerebellum of male...     

ABA and BAP improve the accumulation of carbohydrates and alter carbon allocation in potato plants at elevated CO2

Elevated CO₂ interactions with other factors affects the plant performance. Regarding the differences between cultivars in response to CO₂ concentrations, identifying the cultivars that better respond to such conditions would maximize their potential benefits. Increasing the ability of plants to benefit more from elevated CO₂ levels alleviates the adverse effects of photoassimilate accumulation on photosynthesis and increases the productivity of plants. Despite its agronomic importance, there is no information about the interactive effects of elevated CO₂ concentration and plant growth regulators (PGRs) on potato (Solanum tuberosum L.) plants. Hence, the physiological response and source-sink relationship of potato plants (cvs. Agria and Fontane) to combined application of CO₂ levels (400 vs. 800 µmol mol⁻¹) and plant growth regulators (PGR) [6-benzylaminopurine (BAP) + Abscisic acid (ABA)] were evaluated under a controlled environment. The results revealed a variation between the potato cultivars in response to a combination of PGRs and CO₂ levels. Cultivars were different in leaf chlorophyll content; Agria had higher chlorophyll a, b, and total chlorophyll content by 23, 43, and 23%, respectively, compared with Fontane. The net photosynthetic rate was doubled at the elevated compared with the ambient CO₂. In Agria, the ratio of leaf intercellular to ambient air CO₂ concentrations [C_i:C_a] was declined in elevated-CO₂-grown plants, which indicated the stomata would become more conservative at higher CO₂ levels. On the other hand, the increased C_i:C_a in Fontane showed a stomatal acclimation to higher CO₂ concentration. The higher leaf dark respiration of the elevated CO₂-grown and BAP + ABA-treated plants was associated with a higher leaf soluble carbohydrates and starch content. Elevated CO₂ and BAP + ABA shifted the dry matter partitioning to the belowground more than the above-media organs. The lower leaf soluble carbohydrate content and greater tuber yield in Fontane might indicate a more efficient photoassimilate translocation than Agria. The results highlighted positive synergic effects of the combined BAP + ABA and elevated CO₂ on tuber yield and productivity of the potato plants.     

Pathogen Presence in Wild Birds Inhabiting Landfills in Central Iran

EcoHealth - Wild birds are important in the transmission of many zoonotic pathogens such as salmonella and avian influenza virus (AIV). The current study investigated the presence of bacterial and...     

Increasing the quality of services and resource utilization in vehicular cloud computing using best host selection methods

One of the technology for increasing the safety and welfare of humans in roads is Vehicular Cloud Computing (VCC). This technology can utilize cloud computing advantages in the Vehicular Ad Hoc Network (VANET). VCC by utilizing modern equipment along with current vehicles, can play a significant role in the area of smart transportation systems. Given the potential of this technology, effective methods for managing existing resources and providing the expected service quality that is essential for such an environment are not yet available as it should. One of the most important barriers to providing such solutions seems to be resource constraints and very high dynamics in vehicles in VCC. In this article, based on virtualization and taking into account the environment with these features, we propose simple ways to manage resources better and improve the quality of service. We were able to achieve better results in simulation than previous methods by providing a flexible data structure to control the important data in the environment effectively. To illustrate the impact of the proposed methods, we compared them with some of the most important methods in this context, and we used SUMO 1.2.0 and MATLAB R2019a software to simulate them. Simulation results indicate that the proposed methods provide better results than previous methods in terms of resource efficiency, Quality of Service (QoS), and load balancing.