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Detecting non-neutral heterogeneity across a region of DNA sequence in the ratio of polymorphism to divergence 总被引:11,自引:4,他引:7
Natural selection, in the form of balancing selection or selective sweeps,
can result in a decoupling of the amounts of molecular polymorphism and
divergence. Thus natural selection can cause some areas of DNA sequence to
have greater silent polymorphism, relative to divergence between species,
than other areas. It would be useful to have a statistical test for
heterogeneity in the polymorphism to divergence ratio across a region of
DNA sequence, one that could identify heterogeneity greater than that
expected from the neutral processes of mutation, drift, and recombination.
The only currently available test requires that a region be arbitrarily
divided into sections that are compared with each other, and the
subjectivity of this division could be problematic. Here a test is proposed
in which runs of polymorphic and fixed sites are counted, where a "run" is
a set of one or more sites of one type preceded and followed by the other
type. The number of runs is smaller than otherwise expected if
polymorphisms are clumped together. By simulating neutral evolution and
comparing the observed number of runs to the simulations, a statistical
test is possible which does not require any a priori decisions about
subdivision.
相似文献
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Haq Abdul Shaik Archana Mishra Hany M. Hussein Oxana Skoková Habuštová František Sehnal 《Journal of Applied Entomology》2020,144(6):481-490
Entomopathogenic nematodes and parasitoid larvae of some wasps play important roles in the natural control of the pest insects. However, it has not been excluded that competition between nematodes and wasps may in some cases reduce their efficacy in the pest control. Using caterpillars of Spodoptera littoralis, we examined interactions between the nematode Steinernema carpocapsae and the venom of the parasitoid Habrobracon hebetor. The survival of S. littoralis caterpillars was reduced in a dose-dependent manner when 5 to 500 nematodes or 0.005–0.1 venom units were applied to single caterpillars. High doses of either nematodes or the venom caused death within 1–3 days in all treated hosts. The low doses of nematodes killed caterpillars within a week, in some cases when they attempted to pupate. Caterpillars receiving low venom doses were characterized by extended survival time terminated with death due to starvation. Combined treatment of nematodes and the venom were mutually synergistic and elicited severe lethal effects. The nematodes were fully resistant to the venom and can feed and grow on the symbiotic bacteria in vitro. The venom impairs food processing and causes death of caterpillars due to starvation. Disruption of the hormonal regulation of metamorphosis by ecdysteroids and juvenile hormone could be responsible for defective moults block at different stages of the moulting process, regionally restricted moulting, moults to “intermediates” combining regions of newly secreted larval and pupal cuticles. 相似文献
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Mohammed Rafi Shaik Rabbani Syed Syed Farooq Adil Mufsir Kuniyil Mujeeb Khan Mohammed S. Alqahtani Jilani P. Shaik Mohammed Rafiq H. Siddiqui Abdulrahman Al-Warthan Mohammed A.F. Sharaf Abdelatty Abdelgawad Emad Mahrous Awwad 《Saudi Journal of Biological Sciences》2021,28(2):1196-1202
Due to their inexpensive and eco-friendly nature, and existence of manganese in various oxidation states and their natural abundance have attained significant attention for the formation of Mn3O4 nanoparticles (Mn3O4 NPs). Herein, we report the preparation of Mn3O4 nanoparticles using manganese nitrate as a precursor material by utilization of a precipitation technique. The as-prepared Mn3O4 nanoparticles (Mn3O4 NPs) were characterized by using X-ray powder diffraction (XRD), UV–Visible spectroscopy (UV–Vis), High-Resolution Transmission electron microscopy (HRTEM), Field emission scanning electron microscopy (FESEM), Thermal gravimetric analysis (TGA) and Fourier-transform infrared spectroscopy (FT-IR). The antimicrobial properties of the as-synthesized Mn3O4 nanoparticles were investigated against numerous bacterial and fungal strains including S. aureus, E. coli, B. subtilis, P. aeruginosa, A. flavus and C. albicans. The Mn3O4 NPs inhibited the growth of S. aureus with a minimum inhibitory concentration (MIC) of 40 μg/ml and C. albicans with a MIC of 15 μg/ml. Furthermore, the Mn3O4 NPs anti-cancer activity was examined using MTT essay against A549 lung and MCF-7 breast cancer cell lines. The Mn3O4 NPs revealed significant activity against the examined cancer cell lines A549 and MCF-7. The IC50 values of Mn3O4 NPs with A549 cell line was found at concentration of 98 µg/mL and MCF-7 cell line was found at concentration of 25 µg/mL. 相似文献
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V. Ramana Gopavajhula K. Viswanatha Chaitanya P. Akbar Ali Khan Jilani P. Shaik P. Narasimha Reddy Mohammad Alanazi 《Genetics and molecular biology》2013,36(2):225-236
Superoxide dismutase (SOD, EC 1.15.1.1) is an important metal-containing antioxidant enzyme that provides the first line of defense against toxic superoxide radicals by catalyzing their dismutation to oxygen and hydrogen peroxide. SOD is classified into four metalloprotein isoforms, namely, Cu/Zn SOD, Mn SOD, Ni SOD and Fe SOD. The structural models of soybean SOD isoforms have not yet been solved. In this study, we describe structural models for soybean Cu/Zn SOD, Mn SOD and Fe SOD and provide insights into the molecular function of this metal-binding enzyme in improving tolerance to oxidative stress in plants. 相似文献
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Sandeep Kumar Mulukala Narasimha Shravan Kumar Gunda Mahmood Shaik 《Journal of molecular modeling》2013,19(4):1891-1900
The cytoplasm of a eukaryotic cell consists of a wide variety of membrane bound cell organelles and continuous flow of proteins amongst these organelles is a major challenge and must be stringently maintained in order to continue the correct biochemical functioning inside a cell. The transportation of various proteins amongst these organelles is facilitated by a vast Tubulo-vesicular network mediated by carrier proteins. The Rabs belong to small G proteins super family involved in the regulation and vesicle transport in between the organelles by shuttling between the active GTP and inactive GDP bound states. In this paper we put forth the homology modeling and docking studies of Rab6A proteins (Mus musculus, Gallus gallus and Caenorhabditis elegans) with GTP, GMP-PNP and GDP molecules and a comparative study between these proteins is done to identify key residues out of which serine of the phosphate binding loop (P – loop) and aspartic acid showed prominent interactions with the GTP, GDP and GMP-PNP nucleotides and cogitate that aspartic acid might also help in the stabilization of the switch I region of the Rab proteins besides serine. 相似文献
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Janine JH Oosterhof G Jolanda Elving Ietse Stokroos Arie van nieuw Amerongen Henny C van der Mei Henk J Busscher 《Biofouling》2013,29(6):347-353
The integrity of biofilms on voice prostheses used to rehabilitate speech in laryngectomized patients causes unwanted increases in airflow resistance, impeding speech. Biofilm integrity is ensured by extracellular polymeric substances (EPS). This study aimed to determine whether synthetic salivary peptides or mucolytics, including N-acetylcysteine and ascorbic acid, influence the integrity of voice prosthetic biofilms. Biofilms were grown on voice prostheses in an artificial throat model and exposed to synthetic salivary peptides, mucolytics and two different antiseptics (chlorhexidine and Triclosan). Synthetic salivary peptides did not reduce the air flow resistance of voice prostheses after biofilm formation. Although both chlorhexidine and Triclosan reduced microbial numbers on the prostheses, only the Triclosan-containing positive control reduced the air flow resistance. Unlike ascorbic acid, the mucolytic N-acetylcysteine removed most EPS from the biofilms and induced a decrease in air flow resistance. 相似文献