Cell cycle population effects in perturbation studies

Growth condition perturbation or gene function disruption are commonly used strategies to study cellular systems. Although it is widely appreciated that such experiments may involve indirect effects, these frequently remain uncharacterized. Here, analysis of functionally unrelated Saccharyomyces cerevisiae deletion strains reveals a common gene expression signature. One property shared by these strains is slower growth, with increased presence of the signature in more slowly growing strains. The slow growth signature is highly similar to the environmental stress response (ESR), an expression response common to diverse environmental perturbations. Both environmental and genetic perturbations result in growth rate changes. These are accompanied by a change in the distribution of cells over different cell cycle phases. Rather than representing a direct expression response in single cells, both the slow growth signature and ESR mainly reflect a redistribution of cells over different cell cycle phases, primarily characterized by an increase in the G1 population. The findings have implications for any study of perturbation that is accompanied by growth rate changes. Strategies to counter these effects are presented and discussed.     

The Impact of Simvastatin on Pulmonary Effectors of Pseudomonas aeruginosa Infection

The statin family of cholesterol-lowering drugs is known to have pleiotropic properties which include anti-inflammatory and immunomodulatory effects. Statins exert their pleiotropic effects by altering expression of human immune regulators including pro-inflammatory cytokines. Previously we found that statins modulate virulence phenotypes of the human pathogen Pseudomonas aeruginosa, and sought to investigate if simvastatin could alter the host response to this organism in lung epithelial cells. Simvastatin increased the expression of the P. aeruginosa target genes KLF2, KLF6, IL-8 and CCL20. Furthermore, both simvastatin and P. aeruginosa induced alternative splicing of KLF6. The novel effect of simvastatin on wtKLF6 expression was found to be responsible for induction of the KLF6 regulated genes CCL20 and iNOS. Simvastatin also increased the adhesion of P. aeruginosa to host cells, without altering invasion or cytotoxicity. This study demonstrated that simvastatin had several novel effects on the pulmonary cellular immune response.     

Biologically relevant effects of mRNA amplification on gene expression profiles

Background  

Gene expression microarray technology permits the analysis of global gene expression profiles. The amount of sample needed limits the use of small excision biopsies and/or needle biopsies from human or animal tissues. Linear amplification techniques have been developed to increase the amount of sample derived cDNA. These amplified samples can be hybridised on microarrays. However, little information is available whether microarrays based on amplified and unamplified material yield comparable results.     

High-level production of animal-free recombinant transferrin from Saccharomyces cerevisiae

Background

Microorganisms that are exposed to pollutants in the environment, such as metals/metalloids, have a remarkable ability to fight the metal stress by various mechanisms. These metal-microbe interactions have already found an important role in biotechnological applications. It is only recently that microorganisms have been explored as potential biofactories for synthesis of metal/metalloid nanoparticles. Biosynthesis of selenium (Se⁰) nanospheres in aerobic conditions by a bacterial strain isolated from the coalmine soil is reported in the present study.

Results

The strain CM100B, identified as Bacillus cereus by morphological, biochemical and 16S rRNA gene sequencing [GenBank:GU551935.1] was studied for its ability to generate selenium nanoparticles (SNs) by transformation of toxic selenite (SeO₃ ^2-) anions into red elemental selenium (Se⁰) under aerobic conditions. Also, the ability of the strain to tolerate high levels of toxic selenite ions was studied by challenging the microbe with different concentrations of sodium selenite (0.5 mM-10 mM). ESEM, AFM and SEM studies revealed the spherical Se⁰ nanospheres adhering to bacterial biomass as well as present as free particles. The TEM microscopy showed the accumulation of spherical nanostructures as intracellular and extracellular deposits. The deposits were identified as element selenium by EDX analysis. This is also indicated by the red coloration of the culture broth that starts within 2-3 h of exposure to selenite oxyions. Selenium nanoparticles (SNs) were further characterized by UV-Visible spectroscopy, TEM and zeta potential measurement. The size of nanospheres was in the range of 150-200 nm with high negative charge of -46.86 mV.

Conclusions

This bacterial isolate has the potential to be used as a bionanofactory for the synthesis of stable, nearly monodisperse Se⁰ nanoparticles as well as for detoxification of the toxic selenite anions in the environment. A hypothetical mechanism for the biogenesis of selenium nanoparticles (SNs) involving membrane associated reductase enzyme(s) that reduces selenite (SeO₃ ^2-) to Se⁰ through electron shuttle enzymatic metal reduction process has been proposed.     

Cephenniini with prothoracic glands and internal cavities: new taxa,enigmatic characters and phylogeny of the Cephennomicrus group of genera (Coleoptera,Staphylinidae, Scydmaeninae)

Genera of the Cephennomicrus group of the Cephenniini (Scydmaenitae) are revised, and the following new taxa are described: Trichokrater gen.n. , Trichokrater ekkentros sp.n. (type species of Trichokrater) (Borneo), Cephennococcus gen.n. , Cephennococcus kuchingensis sp.n. (type species of Cephennococcus) (Borneo), Cephennococcus kenyirensis sp.n. (West Malaysia), Cephennococcus crassus sp.n. (Borneo), Cephennococcus minutissimus sp.n. (West Malaysia), Pomphopsilla gen.n. , Pomphopsilla luhya sp.n. (type species of Pomphopsilla) (Kenya) and Pomphopsilla soror sp.n. (Kenya). Unique subcuticular pockets with setose openings on the pronotum of Trurlia and Trichokrater are identified as glandular structures. Enigmatic internal prothoracic cavities are described for the first time in Scydmaeninae (in Cephennococcus, Pomphopsilla and a female of an undescribed genus from Sulawesi); their fine structure and function remain unknown. Parsimony‐based cladistic analysis of the adult morphology of genera of Cephenniini provided robust evidence for a monophyly of the Cephennomicrus group, composed of Cephennomicrus, Cephennula, Lathomicrus, Pomphopsilla, Cephennococcus, Trurlia, Trichokrater and two undescribed Oriental genera known from females only; this distinct and well‐supported lineage is a sister group of Cephennodes + Hlavaciellus. The genus Cephennomicrus represented in the analysis by species belonging to three previously postulated species groups is not monophyletic, and a comprehensive study comprising more taxa is necessary to reclassify this heterogeneous group.     

Infants' exploration of scented toys: effects of prior experiences

To evaluate breastfed infants' responses to scented objects, we videotaped the facial and bodily reactions of sixty-three infants as they explored, in succession, three toys that were identical in appearance but different in their characteristic odor. Two of the toys were scented with odorants previously shown to be transmitted to human milk, one with ethanol and the other with vanilla, whereas the third toy was unscented. Each videotape was subjected to frame-by-frame analysis to measure a variety of behaviors that are considered either to be exploratory in nature in that they lead to perceptual information about the object or to reflect the infants' hedonic reaction. Analyses of these behaviors revealed that the infants looked more and vocalized less in the presence of the vanilla-scented toy and spent less time manipulating the ethanol-scented toy when compared with the unscented toy. Moreover, differential exposure to the odors of ethanol and vanilla, as indicated by differential consumption of alcohol by a parent or use of vanilla-scented product by the mother, was related to differential responses to these odors. These findings suggest that human infants are able to detect and retain information about the chemical features of their environment.      

Phylogeny of a new supertribe Cephenniitae with generic review of Eutheiini and description of a new tribe Marcepaniini (Coleoptera: Staphylinidae: Scydmaeninae)

Genera of Eutheiini are reviewed and Eutheimorphus is removed from this tribe of ant‐like stone beetles (Scydmaeninae) and transferred to Cephenniini. A monogeneric Marcepaniini trib.n. is described to accommodate Marcepania gen.n. from Malaysia, with five species: M. semengohensis sp.n. (the type species of Marcepania), M. tuberculata sp.n. , M. seramaensis sp.n. , M. minutissima sp.n. and M. elongata sp.n. A phylogenetic analysis of all genera of Cephenniini, Eutheiini and Marcepaniini based on adult morphological characters resulted in recovering a well‐supported monophyletic clade Eutheiini + (Marcepaniini + Cephenniini) and these tribes are included in Cephenniitae stat.n. (Eutheiini and Cephenniini are therefore removed from Scydmaenitae). Only a weak support for monophyly of Eutheiini was found, but morphological characters allow for maintaining this presumably relic group as a separate tribe. Previously proposed monophyletic groups within Cephenniini were recovered as such, but after inclusion of Eutheimorphus, a sister taxon to the ‘Cephennomicrus group’, the latter lineage gained weak statistical support. The evolutionary history of Cephenniitae is discussed, with focus on known northern hemisphere fossils classified in Scydmaenitae and Hapsomelitae, but possibly closely allied to Cephenniitae. Establishing the supertribe Cephenniitae is the first step toward a profound reclassification of Scydmaeninae on a robust phylogenetic basis. This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:B0E1B12D-9587-4C4F-A908-A12A0C424A8C .