Improving the specificity of high-throughput ortholog prediction

Background  

Orthologs (genes that have diverged after a speciation event) tend to have similar function, and so their prediction has become an important component of comparative genomics and genome annotation. The gold standard phylogenetic analysis approach of comparing available organismal phylogeny to gene phylogeny is not easily automated for genome-wide analysis; therefore, ortholog prediction for large genome-scale datasets is typically performed using a reciprocal-best-BLAST-hits (RBH) approach. One problem with RBH is that it will incorrectly predict a paralog as an ortholog when incomplete genome sequences or gene loss is involved. In addition, there is an increasing interest in identifying orthologs most likely to have retained similar function.     

Distribution of putative neurotransmitters in the brain of the European corn borer, Ostrinia nubilalis.

Radioautographic localization of three putative neurotransmitters in the brain of larvae of the European corn borer was studied by electron microscopy. Acetylcholine and dopamine were found to be accumulated in median neurosecretory cells. Both acetylcholine and dopamine were preferentially found in glial cells as compared to neuronal cells. This may be indicative of active participation of glial cells in a blood-brain barrier in the intact brain. Gamma-aminobutyric acid was not accumulated by any particular cell in the brain, but was apparently excluded to the periphery of the ganglion.It is suggested that dopamine, or more likely an immediate metabolite may be involved in an endogenous time measuring system and/or diapause induction-termination.     

Macroalgae exhibit diverse responses to human disturbances on coral reefs

Scientists and managers rely on indicator taxa such as coral and macroalgal cover to evaluate the effects of human disturbance on coral reefs, often assuming a universally positive relationship between local human disturbance and macroalgae. Despite evidence that macroalgae respond to local stressors in diverse ways, there have been few efforts to evaluate relationships between specific macroalgae taxa and local human-driven disturbance. Using genus-level monitoring data from 1205 sites in the Indian and Pacific Oceans, we assess whether macroalgae percent cover correlates with local human disturbance while accounting for factors that could obscure or confound relationships. Assessing macroalgae at genus level revealed that no genera were positively correlated with all human disturbance metrics. Instead, we found relationships between the division or genera of algae and specific human disturbances that were not detectable when pooling taxa into a single functional category, which is common to many analyses. The convention to use percent cover of macroalgae as an indication of local human disturbance therefore likely obscures signatures of local anthropogenic threats to reefs. Our limited understanding of relationships between human disturbance, macroalgae taxa, and their responses to human disturbances impedes the ability to diagnose and respond appropriately to these threats.     

International Society for Reef Studies (ISRS)

International Society for Reef Studies (ISRS)     

International Society for Reef Studies

International Society for Reef Studies     

Protein synthesis during hormonally induced meiotic maturation and fertilization in starfish oocytes

Uptake of radioactive amino acids and their incorporation into protein were examined during 1-methyladenine-induced maturation and subsequent fertilization of oocytes of the starfish Patiria miniata. The initial response to the hormone was a nearly immediate decrease in permeability to amino acids, indicating that the site of action of the hormone is on the cell surface. Protein synthesis began to increase starting about 12 min after 1-methyladenine stimulation and prior to germinal vesicle breakdown. It continued to rise throughout the first meiotic division. This protein synthesis was not required for assembly or initial functioning of the meiotic apparatus, although it was necessary for the completion of meiosis. Fertilization had no effect on the rate of protein synthesis.Oocytes of P. miniata provide an example of hormonal stimulation of protein synthesis in an invertebrate system.     

Midgut ultrastructure of Culex tarsalis (Diptera:Culcidae) before and after a bloodmeal

The midgut ultrastructure of raisin- and blood-fed female mosquitoes, Culex tarsalis Coquillett, was examined. The raisin-fed midgut is characterized by: (1) large nuclei, (2) small mitochondria, (3) short segments of rough endoplasmic reticulum, (4) rough endoplasmic reticular vesicles in the posterior midgut only, and (5) increased autophagic activity with age. Blood feeding elicits drastic changes in midgut epithelial structures: (1) nuclei are smaller, (2) mitochondria are much enlarged, (3) rough endoplasmic reticular vesicles disappear, (4) rough endoplasmic reticular whorls appear, (5) residual lyosomal figures are abundant, and (6) an intercellular accumulation of an electron-opaque material is noted. The significance of rough endoplasmic reticular whorls and vesicles in bloodmeal digestion is discussed. In addition, the concept of a functional host ‘gut barrier’ to infection by pathogens is examined as related to a possible by-pass mechanism.     

Development and validation of the spiral Salmonella assay: an automated approach to bacterial mutagenicity testing

Since its development by Dr. Bruce Ames and his colleagues more than a decade ago, the Salmonella/mammalian microsome mutagenicity assay has become a widely accepted tool to assist in the identification of chemicals with mutagenic and carcinogenic potential. Several automated approaches to Salmonella testing have been proposed in recent years but have failed to gain acceptance in the scientific community due to poor performance or lack of demonstrated usefulness. In this paper we report on an automated system that successfully generates dose-response data and, moreover, reduces the labor, materials, and sample mass required to obtain such information. In the standard plate-incorporation assay, dose-response relationships are defined by testing discrete doses of the test agent on a series of agar plates. In contrast, the spiral Salmonella assay generates dose-response data from a continuous concentration gradient on a single agar plate. Upon analysis, each spiral plate yields a dose-response curve consisting of 13 data points that span a concentration range of about 15:1, which is equivalent to 5 two-fold serial dilutions. The performance of the spiral Salmonella assay was compared to that of the conventional plate-incorporation assay using 13 mutagens and 7 nonmutagens selected from a variety of chemical classes. Concordant qualitative responses were obtained for all compounds tested, and comparable dose-response relationships were generated by all mutagens with the exception of sodium azide and cyclophosphamide, which are highly water-soluble and, thus, are unable to maintain a well-defined concentration gradient on a spiral plate due to rapid diffusion. In general, toxicity was expressed at a lower dose in the spiral assay, and the mutagenic potencies (slopes of the dose-response curves) were greater in the spiral assay relative to the plate-incorporation assay. These differences will be discussed, as will the applicability of the spiral plating technique to routine screening and its relevancy to future mutagenesis testing.