A highly sensitive assay for adenosine triphosphate employing an improved firefly luciferase reagent

An improved firefly luciferase reagent allowed reliable detection of as little as 80 fmo1/1 adenosine triphosphate (ATP). Contamination by ATP of the deionized water diluent limited the sensitivity of the assay in some laboratories. The reagent can be used to measure ATP from less than ten bacterial cells if care is taken to eliminate ATP from equipment and reagents.     

Peppy: A virtual reality environment for exploring the principles of polypeptide structure

A key learning outcome for undergraduate biochemistry classes is a thorough understanding of the principles of protein structure. Traditional approaches to teaching this material, which include two‐dimensional (2D) images on paper, physical molecular modeling kits, and projections of 3D structures into 2D, are unable to fully capture the dynamic 3D nature of proteins. We have built a virtual reality application, Peppy, aimed at facilitating teaching of the principles of protein secondary structure. Rather than attempt to model molecules with the same fidelity to the underlying physical chemistry as existing, research‐oriented molecular modelling approaches, we took the more straightforward approach of harnessing the Unity video game physics engine. Indeed, the simplicity and limitations of our model are strengths in a teaching context, provoking questions and thus deeper understanding. Peppy allows exploration of the relative effects of hydrogen bonding (and electrostatic interactions more generally), backbone φ/ψ angles, basic chemical structure, and steric effects on a polypeptide structure in an accessible format that is novel, dynamic, and fun to use. Apart from describing the implementation and use of Peppy, we discuss the outcomes of deploying Peppy in undergraduate biochemistry courses.     

Embryonal carcinoma cell induction of miRNA and mRNA changes in co-cultured prostate stromal fibromuscular cells

The prostate stromal mesenchyme controls organ-specific development. In cancer, the stromal compartment shows altered gene expression compared to non-cancer. The lineage relationship between cancer-associated stromal cells and normal tissue stromal cells is not known. Nor is the cause underlying the expression difference. Previously, the embryonal carcinoma (EC) cell line, NCCIT, was used by us to study the stromal induction property. In the current study, stromal cells from non-cancer (NP) and cancer (CP) were isolated from tissue specimens and co-cultured with NCCIT cells in a trans-well format to preclude heterotypic cell contact. After 3 days, the stromal cells were analyzed by gene arrays for microRNA (miRNA) and mRNA expression. In co-culture, NCCIT cells were found to alter the miRNA and mRNA expression of NP stromal cells to one like that of CP stromal cells. In contrast, NCCIT had no significant effect on the gene expression of CP stromal cells. We conclude that the gene expression changes in stromal cells can be induced by diffusible factors synthesized by EC cells, and suggest that cancer-associated stromal cells represent a more primitive or less differentiated stromal cell type.     

Assessing the Susceptibility of Transgenic Mice Overexpressing Deer Prion Protein to Bovine Spongiform Encephalopathy

Several transgenic mouse models have been developed which facilitate the transmission of chronic wasting disease (CWD) of cervids and allow prion strain discrimination. The present study was designed to assess the susceptibility of the prototypic mouse line, Tg(CerPrP)1536^+/−, to bovine spongiform encephalopathy (BSE) prions, which have the ability to overcome species barriers. Tg(CerPrP)1536^+/− mice challenged with red deer-adapted BSE resulted in 90% to 100% attack rates, and BSE from cattle failed to transmit, indicating agent adaptation in the deer.     

Two Paralogous Genes Encoding Small Subunits of ADP-glucose Pyrophosphorylase in Maize, <Emphasis Type="Italic">Bt2</Emphasis> and <Emphasis Type="Italic">L2</Emphasis>, Replace the Single Alternatively Spliced Gene Found in Other Cereal Species

Two types of gene encoding small subunits (SSU) of ADP-glucose pyrophosphorylase, a starch-biosynthetic enzyme, have been found in cereals and other grasses. One of these genes encodes two SSU proteins. These are targeted to different subcellular compartments and expressed in different organs of the plant: the endosperm cytosol and the leaf plastids. The SSU gene encoding two proteins evolved from an ancestral gene encoding a single protein by the acquisition of an alternative first exon. Prior to the work reported here, this type of SSU gene had been found in all grasses examined except maize. In maize, two separate genes, Bt2 and L2, were known to have the same roles as the alternatively spliced gene found in other grasses. The evolutionary origin of these maize genes and their relationship to the SSU genes in other grasses were unclear. Here we show that Bt2 and L2 are paralogous genes that arose as a result of the tetraploidization of the maize genome. Both genes derive from an ancestral alternatively spliced SSU gene orthologous to that found in other grasses. Following duplication, the Bt2 and L2 genes diverged in function. Each took a different one of the two functions of the ancestral gene. Now Bt2 encodes the endosperm cytosolic SSU but does not contribute significantly to leaf AGPase activity. Similarly, L2 has lost the use of one of its two alternative first exons. It can no longer contribute to the endosperm cytosolic SSU but is probably responsible for the bulk of the leaf AGPase SSU. Reviewing Editor: Dr. Patrick Keeling Sequences have been deposited in GenBank under accession numbers AY727927, DQ118037, and DQ118038.     

Decorticate, decerebrate and opisthotonic posturing and seizures in Kenyan children with cerebral malaria

Background

Intermittent preventive treatment of malaria during pregnancy (IPTp) is a key intervention in the national strategy for malaria control in Tanzania. SP, the current drug of choice, is recommended to be administered in the second and third trimesters of pregnancy during antenatal care (ANC) visits. To allow for a proper design of planned scaling up of IPT services in Tanzania it is useful to understand the IPTp strategy's acceptability to health managers, ANC service providers and pregnant women. This study assesses the knowledge, attitudes and practices of these groups in relation to malaria control with emphasis on IPTp services.

Methods

The study was conducted in February 2004, in Korogwe District, Tanzania. It involved in-depth interviews with the district medical officer (DMO), district hospital medical officer in charge and relevant health service staff at two peripheral dispensaries, and separate focus group discussions (FGDs) with district Council Health Management Team members at district level and pregnant women at dispensary and community levels.

Results

Knowledge of malaria risks during pregnancy was high among pregnant women although some women did not associate coma and convulsions with malaria. Contacting traditional healers and self-medication with local herbs for malaria management was reported to be common. Pregnant women and ANC staff were generally aware of SP as the drug recommended for IPTp, albeit some nurses and the majority of pregnant women expressed concern about the use of SP during pregnancy. Some pregnant women testified that sometimes ANC staff allow the women to swallow SP tablets at home which gives a room for some women to throw away SP tablets after leaving the clinic. The DMO was sceptical about health workers' compliance with the direct observed therapy in administering SP for IPTp due to a shortage of clean water and cups at ANC clinics. Intensified sensitization of pregnant women about the benefits of IPTp was suggested by the study participants as an important approach for improving IPTp compliance.

Conclusion

The successful implementation of the IPTp strategy in Tanzania depends on the proper planning of, and support to, the training of health staff and sustained sensitization of pregnant women at health facility and community levels about the benefits of IPTp for the women and their unborn babies.     

Character state‐based taxa erected to accommodate fossil and extant needle stoneflies (Leuctridae – Leuctrida tax.n.) and close relatives

In order to accommodate a newly discovered fossil specimen related to a subset of extant needle stoneflies (Leuctridae sensu Zwick, 2000), we provide a comparative analysis of the wing venation of these insects, and of their close relatives, primarily based on extant material. A number of character states potentially supporting monophyletic taxa are identified, and are used to erect taxon names under the cladotypic nomenclatural procedure. We introduce a new standard definition in which the mention of the antonym of the defining character state is applied. The proposed taxa, and taxa inclusiveness, are as follows: Nemouromorpha > Capniida/Leuctrida/‘Nemouridae s.l.’, and Leuctrida > Exeleuctrida > Mioleuctrida & Eleuctrida > Collaleuctrida. This scheme allowed us to tentatively accommodate several fossil species described earlier and the new specimen, left undetermined at the genus and species levels, but assigned to Collaleuctrida. To optimize retrieval of hierarchical information, we introduce the use of ‘nec’ (Latin for ‘but not’) into the taxonomic address to indicate exclusion from a taxon. For example, Mioleuctrida nec Collaleuctrida ?yehae indicates that ?yehae can be assigned to Mioleuctrida but can also be conclusively excluded from Collaleuctrida. Based on the investigated case, it is finally argued that the cladotypic nomenclatural procedure is optimal regarding name use and numbers, and allows adequate treatment of homoplasy.