CoaSim: A flexible environment for simulating genetic data under coalescent models

Background  

Coalescent simulations are playing a large role in interpreting large scale intra-specific sequence or polymorphism surveys and for planning and evaluating association studies. Coalescent simulations of data sets under different models can be compared to the actual data to test the importance of different evolutionary factors and thus get insight into these.     

Anticandidal cytotoxicity,antitumor activities,and purified cell wall modulation by novel Schiff base ligand and its metal (II) complexes against some pathogenic yeasts

The preparation of metal (II) complexes [CoCl₂·6H₂O, Ni(CH₃COO)₂·4H₂O, Cu(CH₃COO)₂·2H₂O, and Zn (CH3COO)₂ ·2H₂O] with 2[N-(cinnamlidene) amino]-5-nitro phenol as a novel ligands and their biological evaluation against candida species was studied. The inhibitory effects of the tested metal complexes were tested against six pathogenic yeasts (Candida albicans, C. fructus, C. glabrata, C. oleophila, C. parapsilosis, and C. tropicalis). The effect of the most efficient metal complex (Zn(II) complex) was more pronounced at 1.25 μg/ml, while Ni(II) complex was exhibited the least suppressive effect. Co(II) and Zn(II) complexes act as potential antitumor agents, while Zn(II) complex has shown promising cytotoxic activity with slow candidal respiration rate. Addition of Zn(II) complex leading to suppression of cell wall components in all candidal cells accompanied with leaking out of amino acids. Purification of the cell wall mannoprotein of C. glabrata treated with Zn(II) complex was established, resulting one pure fissured protein peak. Cell wall protein modulation was showed by appearance of two new protein bands with molecular weights of 72 and 39 KDa in C. glabrata cells treated with Zn(II) complex compared with one pure protein band 55.6 KDa in the non treated yeast cell.     

Novel inhibition of some pathogenic fungal and bacterial species by new synthetic phytochemical coumarin derivatives

novel antifungal and antibacterial activities of new synthesized phytochemical coumarin compounds [H2L1, HL2 and H2L3] and their copper (II) complexes [L1Cu], [L2Cu(OAc)] and [(L3)Cu2(H2O)4(OAc)2] were evaluated against nine pathogenic fungal species (Alternaria alternata, Aspergillus flavus, Botrytis cinerea, Cladosporium herbarum, Fusarium moniliforme, Helminthosporium tetramera, Penicillium expansum, Rhizopus stolonifer andVerticillium albo-atrum) and eight pathogenic bacterial species, from which four Gram-positive bacteria (Bacillus subtilis, Micrococcus luteus, Staphylococcus citrus andStreptococcus pneumoniae) and four Gram-negative bacteria (Enterobacter aerogenes, Escherichia coli, Pseudomonas aeruginosa andSalmonella typhi). The phytochemical copper (II) complex [L2Cu(OAc)] was the most effective derivative, where it reaches to 90 and 100% inhibition in the most sensitive pathogens (B. subtilis and A. flavus), respectively accompanied with a significant reduction in pectinolytic and cellulytic enzyme activities in all tested pathogenic species. Addition of [L2Cu(OAc)] complex leading to leakage of sugars and electrolytes from the most sensitive microbial cells accompanied with collapsed hyphae ofA. Flavus and membrane blobbing ofB. Subtilis. The production of mycotoxins decreased with the extension exposure to [L2Cu(OAc)] complex reaching to a minimum values for the mycelium originating from the inoculum exposed to the minimum inhibitory concentration (2%). Both aflatoxin (AFB1) and citrinin were the most sensitive toxins.     

Bottlenecks drive temporal and spatial genetic changes in alpine caddisfly metapopulations

Background

Extinction and re-colonisation of local populations is common in ephemeral habitats such as temporary streams. In most cases, such population turnover leads to reduced genetic diversity within populations and increased genetic differentiation among populations due to stochastic founder events, genetic drift, and bottlenecks associated with re-colonisation. Here, we examined the spatio-temporal genetic structure of 8 alpine caddisfly populations inhabiting permanent and temporary streams from four valleys in two regions of the Swiss Alps in years before and after a major stream drying event, the European heat wave in summer 2003.

Results

We found that population turnover after 2003 led to a loss of allelic richness and gene diversity but not to significant changes in observed heterozygosity. Within all valleys, permanent and temporary streams in any given year were not differentiated, suggesting considerable gene flow and admixture between streams with differing hydroperiods. Large changes in allele frequencies after 2003 resulted in a substantial increase in genetic differentiation among valleys within one to two years (1-2 generations) driven primarily by drift and immigration. Signatures of genetic bottlenecks were detected in all 8 populations after 2003 using the M-ratio method, but in no populations when using a heterozygosity excess method, indicating differential sensitivity of bottleneck detection methods.

Conclusions

We conclude that genetic differentiation among A. uncatus populations changed markedly both temporally and spatially in response to the extreme climate event in 2003. Our results highlight the magnitude of temporal population genetic changes in response to extreme events. More specifically, our results show that extreme events can cause rapid genetic divergence in metapopulations. Further studies are needed to determine if recovery from this perturbation through gradual mixing of diverged populations by migration and gene flow leads to the pre-climate event state, or whether the observed changes represent a new genetic equilibrium.     

In vitro organogenesis and plant regeneration of Thymus serpyllum L.: an important aromatic medicinal plant

An efficient in vitro propagation system has been developed for the rapid micropropagation of Thymus serpyllum L. (Banajwain), an aromatic medicinal herb from nodal explant on MS medium. Phenolic leaching and high rate of contamination was the most significant problem in establishing in vitro culture of Thymus serpyllum which was overcome by preparing explants in an antioxidant ascorbic acid (1000 ppm) at 6°C for 45 min and addition of the same antioxidant (50 mgl⁻¹) to the MS medium. The frequency of shoot production was influenced by different cytokinins (Kn, BAP, and Kn + BAP) and 95.56% shoot induction was observed when MS medium was supplemented with 1.0 + 2.0 mgl⁻¹ (Kn + BAP). The maximum average number of shoots 16.93 ± 2.15 and average length (3.98 ± 0.55) was recorded when MS medium have 0.5 + 2.0 mgl⁻¹ (Kn + BAP). The in vitro regenerated microshoots were rooted on MS and half strength MS medium and there was significant difference in root induction on both media under the influence of auxins (IAA, IBA, and NAA). The maximum average number (11.67 ± 3.03) and average root length (3.88 ± 0.71) was reported in half MS medium having 1.0 mgl⁻¹ IBA. The complete regenerated plantlets were acclimatized under growth chamber before transferring to the earthen pots and showed 90% survival.

Graphical abstract

     

Breeding system, colony and population structure in the weaver ant Oecophylla smaragdina

Weaver ants ( Oecophylla smaragdina ) are dominant ants in open forests from India, Australia, China and Southeast Asia, whose leaf nests are held together with larval silk. The species, together with its sole congener O. longinoda , has been important in research on biological control, communication, territoriality and colony integration. Over most of the range, only one queen has been found per colony, but the occurrence of several queens per nest has been reported for the Australian Northern Territory. The number of males mating with each queen is little known. Here we report on the colony structure of O. smaragdina using published and new microsatellite markers. Worker genotype arrays reflect the occurrence of habitual polygyny (more than one queen per colony) in 18 colonies from Darwin, Northern Australia, with up to five queens inferred per colony. Monogyny (one queen per colony) with occasional polygyny was inferred for 14 colonies from Queensland, Australia, and 20 colonies from Java, Indonesia. Direct genotyping of the sperm carried by 77 Queensland queens and worker genotypic arrays of established colonies yielded similar results, indicating that less than half of the queens mate only once and some mate up to five times. Worker genotype arrays indicated that queens from Java and the Northern Territory also often mate with more than one male, but less often than those from Queensland. A strong isolation-by-distance effect was found for Queensland samples. The variation uncovered means that O. smaragdina is a more versatile study system than previously supposed.