On the Species Specificity of Acceptor RNA and Attachment Enzymes

One of the steps in protein biosynthesis appears to be the attachment of each amino acid to a specific acceptor (SRNA) molecule. According to the adaptor hypothesis, each SRNA molecule would then fit to a specific complementary base sequence on a linear RNA template, specifying the sequence of amino acids in the resultant protein [1,2]. An adaptor molecule thus could have two specificities: one recognizing the correct amino acid and activating enzyme; the other, the proper position on the template. The correctness of the amino-acid sequence therefore would depend upon the precision and constancy of the adaptors. However, the structures of the enzymes and adaptors are presumably under the genetic control of the organism and might be subject to heritable modifications. It is therefore conceivable that one or both ends of an adaptor might change sufficiently to cause occasional errors and, in the long run, an alteration of the genetic code might evolve. This notion, prompted by genetic observations [3] which suggested that mutation of a bacterium might modify its translation of genetic information, lead to the present comparison of the specificities of the acceptor RNA and activating enzymes of different organisms. Several differences in specificity have been reported previously. Berg et al. [4] demonstrated that SRNA from Escherichia coli contains two distinguishable acceptors for methionine. An enzyme prepared from yeast could attach methionine to one of these, while the enzyme from E. coli could attach to both. Webster found, in pig liver, a difference between the nuclear and cytoplasmic attachment enzymes for alanine. Rendi and Ochoa [6] noted that, for leucine, the enzymes in yeast and in E. coli could attach only to their homologous SRNA. Furthermore, in the case of leucine, rat liver enzyme and SRNA were interchangeable with those from E. coli. The observations presented below show that whether the enzymes and/or acceptors from two organisms are interchangeable depends upon not only the organisms in question but also the particular amino aci

Lice, Mites, and Ticks of Southeastern Wisconsin Mammals

Seventeen species of southeastern Wisconsin mammals were found to 6e infected with arthropod ectoparasites other than fleas. One host species was infested with one species of biting lice (Mallophaga), five with five species of sucking lice (Anoplura), ten with at least 16 species of mites (Acari) and nine with six species of hard ticks (Ixodidae). Many new state and/or host records are reported. Host specificity was very pronounced in lice but less marked in ticks and mites particularly in the more common species, ex. Androlaelaps fahrenholzi (Berlese) and Ixodes cookei Packard, respectively

Transcriptomic footprints disclose specificity of reactive oxygen species signaling in Arabidopsis

Reactive oxygen species ( ROS) are key players in the regulation of plant development, stress responses, and programmed cell death. Previous studies indicated that depending on the type of ROS ( hydrogen peroxide, superoxide, or singlet oxygen) or its subcellular production site ( plastidic, cytosolic, peroxisomal, or apoplastic), a different physiological, biochemical, and molecular response is provoked. We used transcriptome data generated from ROS-related microarray experiments to assess the specificity of ROS-driven transcript expression. Data sets obtained by exogenous application of oxidative stress-causing agents ( methyl viologen, Alternaria alternata toxin, 3-aminotriazole, and ozone) and from a mutant ( fluorescent) and transgenic plants, in which the activity of an individual antioxidant enzyme was perturbed ( catalase, cytosolic ascorbate peroxidase, and copper/zinc superoxide dismutase), were compared. In total, the abundance of nearly 26,000 transcripts of Arabidopsis ( Arabidopsis thaliana) was monitored in response to different ROS. Overall, 8,056, 5,312, and 3,925 transcripts showed at least a 3-, 4-, or 5- fold change in expression, respectively. In addition to marker transcripts that were specifically regulated by hydrogen peroxide, superoxide, or singlet oxygen, several transcripts were identified as general oxidative stress response markers because their steady-state levels were at least 5- fold elevated in most experiments. We also assessed the expression characteristics of all annotated transcription factors and inferred new candidate regulatory transcripts that could be responsible for orchestrating the specific transcriptomic signatures triggered by different ROS. Our analysis provides a framework that will assist future efforts to address the impact of ROS signals within environmental stress conditions and elucidate the molecular mechanisms of the oxidative stress response in plants

Identification of plasma lipid biomarkers for prostate cancer by lipidomics and bioinformatics

Background: Lipids have critical functions in cellular energy storage, structure and signaling. Many individual lipid molecules have been associated with the evolution of prostate cancer; however, none of them has been approved to be used as a biomarker. The aim of this study is to identify lipid molecules from hundreds plasma apparent lipid species as biomarkers for diagnosis of prostate cancer. Methodology/Principal Findings: Using lipidomics, lipid profiling of 390 individual apparent lipid species was performed on 141 plasma samples from 105 patients with prostate cancer and 36 male controls. High throughput data generated from lipidomics were analyzed using bioinformatic and statistical methods. From 390 apparent lipid species, 35 species were demonstrated to have potential in differentiation of prostate cancer. Within the 35 species, 12 were identified as individual plasma lipid biomarkers for diagnosis of prostate cancer with a sensitivity above 80%, specificity above 50% and accuracy above 80%. Using top 15 of 35 potential biomarkers together increased predictive power dramatically in diagnosis of prostate cancer with a sensitivity of 93.6%, specificity of 90.1% and accuracy of 97.3%. Principal component analysis (PCA) and hierarchical clustering analysis (HCA) demonstrated that patient and control populations were visually separated by identified lipid biomarkers. RandomForest and 10-fold cross validation analyses demonstrated that the identified lipid biomarkers were able to predict unknown populations accurately, and this was not influenced by patient's age and race. Three out of 13 lipid classes, phosphatidylethanolamine (PE), ether-linked phosphatidylethanolamine (ePE) and ether-linked phosphatidylcholine (ePC) could be considered as biomarkers in diagnosis of prostate cancer. Conclusions/Significance: Using lipidomics and bioinformatic and statistical methods, we have identified a few out of hundreds plasma apparent lipid molecular species as biomarkers for diagnosis of prostate cancer with a high sensitivity, specificity and accuracy

Nearest Neighbor Methods for Testing Reflexivity and Species-Correspondence

Nearest neighbor (NN) methods are employed for drawing inferences about spatial patterns of points from two or more classes. We consider Pielou's test of niche specificity which is defined using a contingency table based on the NN relationships between the data points. We demonstrate that Pielou's contingency table for niche specificity is actually more appropriate for testing reflexivity in NN structure, hence we call this table as NN reflexivity contingency table (NN-RCT) henceforth. We also derive an asymptotic approximation for the distribution of the entries of the NN-RCT and consider variants of Fisher's exact test on it. Moreover, we introduce a new test of class- or species-correspondence inspired by spatial niche/habitat specificity and the associated contingency table called species-correspondence contingency table (SCCT). We also determine the appropriate null hypotheses and the underlying conditions appropriate for these tests. We investigate the finite sample performance of the tests in terms of empirical size and power by extensive Monte Carlo simulations and the methods are illustrated on a real-life ecological data set.Comment: 23 pages, 1 figur

Development of a species-specific coproantigen ELISA for human taenia solium taeniasis

Taenia solium causes human neurocysticercosis and is endemic in underdeveloped countries where backyard pig keeping is common. Microscopic fecal diagnostic methods for human T. solium taeniasis are not very sensitive, and Taenia saginata and Taenia solium eggs are indistinguishable under the light microscope. Coproantigen (CoAg) ELISA methods are very sensitive, but currently only genus (Taenia) specific. This paper describes the development of a highly species-specific coproantigen ELISA test to detect T. solium intestinal taeniasis. Sensitivity was maintained using a capture antibody of rabbit IgG against T. solium adult whole worm somatic extract, whereas species specificity was achieved by utilization of an enzyme-conjugated rabbit IgG against T. solium adult excretory-secretory (ES) antigen. A known panel of positive and negative human fecal samples was tested with this hybrid sandwich ELISA. The ELISA test gave 100% specificity and 96.4% sensitivity for T. solium tapeworm carriers (N = 28), with a J index of 0.96. This simple ELISA incorporating anti-adult somatic and anti-adult ES antibodies provides the first potentially species-specific coproantigen test for human T. solium taeniasis

Scale insects (Hemiptera: Coccoidea) of ornamental plants from Sao Carlos, Sao Paulo, Brazil

A list of 35 scale insects collected from 72 ornamental plant species in Sao Carlos, Sao Paulo, Brazil is provided. Regarding host specificity, 30 scale insects were polyphagous, 4 oligophagous, and 1 monophagous. A total of 102 coccoid/plant associations are recorded, 29 of which are new host records for the species; 60 are new host records for the species in Brazil. Pulvinaria urbicola Cockerell, 1893 (Coccidae), Phenacoccus similis Granara de Willink, 1983 (Pseudococcidae), and Orthezia molinarii (Morrison, 1952) (Ortheziidae) are recorded for the first time in Brazil. In addition, we describe the injury caused by scale insects on ornamental plants

Species Authentication of Dog, Cat, and Tiger Using Cytochrome Β Gene

Adulteration of animal food products for economic reason has happened during the last decades. Species identification method development was needed to prevent falsification information. The objective of this research was to study species authentication (dog, cat, and tiger) to ensure animal origin in products using cyt β gene specific marker. DNA extraction and fragment amplification were conducted using phenol-chloroform and multiplex PCR (Polymerase Chain Reaction) method, respectively. This research showed that fragment length of amplification for species tested (dog, cat, and tiger) were 523, 331, 319 bp, respectively. Species specificity was also indicated by high reverse primers homology percentage. Multiplex PCR technique succeed to amplify DNA fragment from species tested, but has a limitation to amplify total DNA composite of mix DNA

Epiparasitic plants specialized on arbuscular mycorrhizal fungi

Over 400 non-photosynthetic species from 10 families of vascular plants obtain their carbon from fungi and are thus defined as myco-heterotrophs. Many of these plants are epiparasitic on green plants from which they obtain carbon by 'cheating' shared mycorrhizal fungi. Epiparasitic plants examined to date depend on ectomycorrhizal fungi for carbon transfer and exhibit exceptional specificity for these fungi, but for most myco-heterotrophs neither the identity of the fungi nor the sources of their carbon are known. Because many myco-heterotrophs grow in forests dominated by plants associated with arbuscular mycorrhizal fungi (AMF; phylum Glomeromycota), we proposed that epiparasitism would occur also between plants linked by AMF. On a global scale AMF form the most widespread mycorrhizae, thus the ability of plants to cheat this symbiosis would be highly significant. We analysed mycorrhizae from three populations of Arachnitis uniflora (Corsiaceae, Monocotyledonae), five Voyria species and one Voyriella species (Gentianaceae, Dicotyledonae), and neighbouring green plants. Here we show that non-photosynthetic plants associate with AMF and can display the characteristic specificity of epiparasites. This suggests that AMF mediate significant inter-plant carbon transfer in nature

The evolution of complex gene regulation by low specificity binding sites

Transcription factor binding sites vary in their specificity, both within and between species. Binding specificity has a strong impact on the evolution of gene expression, because it determines how easily regulatory interactions are gained and lost. Nevertheless, we have a relatively poor understanding of what evolutionary forces determine the specificity of binding sites. Here we address this question by studying regulatory modules composed of multiple binding sites. Using a population-genetic model, we show that more complex regulatory modules, composed of a greater number of binding sites, must employ binding sites that are individually less specific, compared to less complex regulatory modules. This effect is extremely general, and it hold regardless of the regulatory logic of a module. We attribute this phenomenon to the inability of stabilising selection to maintain highly specific sites in large regulatory modules. Our analysis helps to explain broad empirical trends in the yeast regulatory network: those genes with a greater number of transcriptional regulators feature by less specific binding sites, and there is less variance in their specificity, compared to genes with fewer regulators. Likewise, our results also help to explain the well-known trend towards lower specificity in the transcription factor binding sites of higher eukaryotes, which perform complex regulatory tasks, compared to prokaryotes