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Unique features of Plasmids among different Citrobacter species
Full text linkThe _Citrobacter_ plasmids are supposed to represent the host genetic association within the living bacterial cell. The plasmids impart various beneficial characteristics to the host, helping it to retain suitable characteristics for adaptation as well as evolution. The study aims at understanding the role of prophage in influencing host functional characteristics by horizontal gene transfer or as whole plasmids. The _Citrobacter_ plasmid can be understood by analyzing many hypothetical protein sequences within its genome. Our study included 82 hypothetical proteins in 5 _Citrobacter_ plasmids genomes. The function predictions in 31 hypothetical proteins and 3-D structures were predicted for 11 protein sequences using PS2 server. The probable function prediction was done by using Bioinformatics web tools like CDD-BLAST, INTERPROSCAN, PFAM and COGs by searching sequence databases for the presence of orthologous enzymatic conserved domains in the hypothetical sequences. This study identified many uncharacterized proteins, whose roles are yet to be discovered in _Citrobacter_ plasmids. These results for unknown proteins within plasmids can be used in linking the genetic interactions of _Citrobacter_ species and their functions in different environmental conditions
Historical temporal trends in groundwater levels from British Columbia, Canada
Full text linkA time trend study of groundwater monitoring well levels was conducted in British Columbia, Canada. Trend data was available for a total of 210 groundwater monitoring well stations throughout the province with end-of-month water levels over the period of record. Significant temporal trends in groundwater levels were found at 67 stations (40.4% of all stations amenable to statistical examination, and 31.9% of all available stations). Of these 67 stations, 10 had increasing groundwater level trends and the remaining 57 had declining groundwater level trends. Thus, 34.3% of stations with a sufficiently long time series for analysis displayed declining groundwater level trends, while 6.0% have increasing trends, and 59.6% of these stations appear to have no significant temporal variation in groundwater levels. Geographic distinctions in groundwater level time trends are difficult to make owing to the unbalanced distribution of monitoring sites throughout the province. Based on percentages of total stations with a sufficiently long monitoring record for statistical analysis, it appears that the semi-arid Thompson/Nicola and Okanagan zones of British Columbia are most likely to have declining groundwater levels. Overall, a substantial proportion of groundwater monitoring wells in British Columbia - which have been operated with varying record lengths dating from recent installations to sites with records back to the 1950s - are exhibiting declining levels. At a significant number of other sites in the monitoring network, records are too short and/or poorly populated to facilitate statistical analysis
The Evolutionary Seesaw: Origins of biodiversity?
Full text linkI consider the problem of evolutionary branching in adaptive dynamics without applying the limits of separation of timescales between ecological and evolutionary processes. I derive expressions for the waiting time for a branching event to occur and survive in terms of both ecological and evolutionary parameters, and show how demographic stochasticity alone can result in the frequent failure of adaptive branching
New insight into DNA damage by cisplatin at the atomic scale
Full text linkCisplatin is cis-diamminedichloroplatinum (II) of chemical formula, Pt(NH3)Cl2, abbreviated as cis-DDP and known commercially as platinol. It is used widely as an anticancer drug for various types of cancer, ever since its discovery two centuries ago and has become a target of extensive researches. Transplatin, trans-DDP on the other hand, is found to be less or ineffective to treat cancers. Cisplatin is known to interact mainly with the N(7) nitrogen of guanine in nucleic acids, after a water molecule takes away one of the chlorines by hydrolysis. This initiates the damage of nucleic acids and eventually leads to apoptosis. However the way how this happens and why transplatin is less effective is not completely clear. Here the author brings some new insights, using the precise structures of these molecules at the atomic level, how cisplatin can interact with the nitrogen of guanine and adenine and rupture the hydrogen bonding in the Watson Crick base pairs and damage the structure of DNA. It is hoped that the results presented here will contribute to a better atomistic insight into the structure, bonding and feasibility of the biochemical reactions involving these compounds and their derivates for the alleviation of cancer
Studies on the Accumulation of Chromium in Fenugreek
Full text linkStudying Cr uptake by Fenugreek, we note that the maximum concentration of Cr takes place in the shells of the pods followed by leaves, stems and seeds in that order. Interestingly, applied higher doses of Cr does not increase accumulation of Cr in the stems, rather Cr content in the stems levels off. However, the maximum dispersal/distribution of Cr taken up is in the leaves
Biotransformation of artemisinin mediated through fungal strains for obtaining derivatives with novel activities
Full text linkArtemisinin, a sesquiterpene lactone, is the active antimalarial constituent of Artemisia annua. Several fungal strains Saccharomyces cerevisiae, Aspergillus flavus, Aspergillus niger and Picchia pastoris were used to biotransform artemisinin. Among these strains, A. flavus was the only microorganism capable of transforming artemisinin to deoxyartemisinin in higher yields than the previous reports. The structure of deoxyartemisinin was elucidated by spectroscopy. Deoxyartemisinin showed antibacterial activity against Staphylococcus aureus, S. epidermidis and S. mutans at a minimum inhibitory concentration (MIC) of 1 mg/mL compared to artemisinin whose MIC was >2 mg/mL
Clean Coal and Spirulina maxima (Cyanobacteria) Production through Alkaline-Seawater
No full textCarbon capture and storage have involved high cost and an earthquake threat. Coal in NaOH-natural seawater (NSW) can produce clean coal, and organic carbon enriched pretreated sweater (PSWS) can be used to grow Spirulina maxima. However, with freshwater shortage, high cost CO2 feedstock incurs S. maxima biomass production, and using PSWS should be considered as an alternative. NaHCO3 and Na2CO3 were used to sediment Mg2+ and Ca2+ of NSW to resolve turbidity and decreasing phosphate solubility. Here, we show that pre-combustion coal and NaOH concentration calculated by our devised formulae for any salinity could dilute volatile matter 19.8 Kg plus CO2 116.50 to 168.89 Kg Ton^-1^ coal in NaOH-NSW by sedimentation Mg2+ and Ca2+ of 99.91% and 32.52%, respectively, and clean coal will be produced. S. maxima biomass production cost was 3.35 times lower in PSWS medium than that of the standard. This method will be used for carbon sequestration and low cost biomass production
Quantum Genetics and Quantum Automata Models of Quantum-Molecular Evolution Involved in the Evolution of Organisms and Species
Full text linkPrevious theoretical or general approaches to the problems of Quantum Genetics and Molecular Evolution are considered in this article from the point of view of Quantum Automata Theory first published by the author in 1971 and further developed in several recent articles. The representation of genomes and Interactome networks in categories of many-valued logic LMn –algebras that are naturally transformed during biological evolution, or evolve through interactions with the environment provide a new insight into the mechanisms of molecular evolution, as well as organismal evolution, in terms of sequences of quantum automata. Phenotypic changes are expressed only when certain environmentally-induced quantum-molecular changes are coupled with an internal re-structuring of major submodules of the genome and Interactome networks related to cell cycling and cell growth. Contrary to the commonly held view of 'standard’ Darwinist models of evolution, the evolution of organisms and species occurs through coupled multi-molecular transformations induced not only by the environment but actually realized through internal re-organizations of genome and interactome networks. The biological, evolutionary processes involve certain epigenetic transformations that are responsible for phenotypic expression of the genome and Interactome transformations initiated at the quantum-molecular level. It can thus be said that only quantum genetics can provide correct explanations of evolutionary processes that are initiated at the quantum--multi-molecular levels and propagate to the higher levels of organismal and species evolution.

Biological evolution should be therefore regarded as a multi-scale process which is initiated by underlying quantum (coupled) multi-molecular transformations of the genomic and interactomic networks, followed by specific phenotypic transformations at the level of organism and the variable biogroupoids associated with the evolution of species which are essential to the survival of the species. The theoretical framework introduced in this article also paves the way to a Quantitative Biology approach to biological evolution at the quantum-molecular, as well as at the organismal and species levels. This is quite a substantial modification of the 'established’ modern Darwinist, and also of several so-called `molecular evolution’ theories
Visual Molecular Dynamics Investigations of the Impact of Hydrophobic Nanoparticles on Prognosis of Alzheimer’s Disease and Cancers
Full text linkThe possible impact of hydrophobic lectin nanoparticles on the prognosis and progression of Alzheimer's disease (AD) and cancers was investigated by Visual Molecular Dynamics (VMD) computer modeling programs available from the Beckmann Advanced Research Institute at the University of Illinois at Urbana. Our results indicate the possibility of impeding pathological aggregation of certain proteins such as modified tau- or beta-amyloid that are currently being considered as possible causes of Alzheimer's disease. VMD programs serve as useful tools for investigation hydrophobic protein aggregation that may play a role in aging of human populations
Inference of population splits and mixtures from genome-wide allele frequency data
Full text linkMany aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model for inferring the patterns of population splits and mixtures in multiple populations. In this model, the sampled populations in a species are related to their common ancestor through a graph of ancestral populations. Using genome-wide allele frequency data and a Gaussian approximation to genetic drift, we infer the structure of this graph. We applied this method to a set of 55 human populations and a set of 82 dog breeds and wild canids. In both species, we show that a simple bifurcating tree does not fully describe the data; in contrast, we infer many migration events. While some of the migration events that we find have been detected previously, many have not. For example, in the human data we infer that Cambodians trace approximately 16% of their ancestry to a population ancestral to other extant East Asian populations. In the dog data, we infer that both the boxer and basenji trace a considerable fraction of their ancestry (9% and 25%, respectively) to wolves subsequent to domestication, and that East Asian toy breeds (the Shih Tzu and the Pekingese) result from admixture between modern toy breeds and ``ancient" Asian breeds. Software implementing the model described here, called _TreeMix_, is available at "http://treemix.googlecode.com":http://treemix.googlecode.com