Informed consent and ethical re-use of African genomic data

Rapid advances in human genomic research are increasing the availability of genomic data for secondary analysis. Particularly in the case of vulnerable African populations, ethics and informed consent processes need to be transparent-both to ensure participant protection, as well as to share skills and to evolve best practice for informed consent from a shared knowledge base. An open dialogue between all stakeholders can facilitate this.     

Rapid assessment of insect fragments in flour milled from wheat infested with known densities of immature and adult Sitophilus oryzae (Coleoptera: Curculionidae)

Milling wheat, Triticum aestivum L., infested with low densities of internal feeding insects can result in flour containing insect fragments. The Food and Drug Administration (FDA) enforces a standard or defect action level stating that a maximum of 75 insect fragments per 50 g of flour is allowed. However, the relationship between level of infestation and number of resulting fragments is not well documented, and a more rapid method for enumerating insect fragments is needed. We characterized the number of insect fragments produced from milling small lots of wheat spiked with known densities and life stages of Sitophilus oryzae (L.) (Coleoptera: Curculionidae). Insect fragments were enumerated with near-infrared spectroscopy (NIRS), a quick nondestructive procedure, and with the industry standard flotation method. Results showed that an individual small larva, large larva, pupa, or adult produced 0.4, 0.7, 1.5, and 27.0 fragments, respectively. NIRS-predicted counts of < or =51 (from small larvae), < or =53 (from large larvae), < or =43 (from pupae), or 0 (from adults) indicated that there were <75 actual fragments in that sample, because the upper bound of associated 95% inverse prediction confidence intervals was less than the standard; NIRS-predicted counts of > or =98, > or =117, 108, or > or =225 fragments (same life stages as above) signaled that these flour samples contained >75 actual fragments. These data suggest that NIRS could be adopted for rapid assessment of insect fragments resulting from relatively low levels of infestation with immature life states, but that it was not accurate enough for enumerating insect fragments, relevant to FDA standards, resulting from adults.     

Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.).

A total of 2414 new di-, tri- and tetra-nucleotide non-redundant SSR primer pairs, representing 2240 unique marker loci, have been developed and experimentally validated for rice (Oryza sativa L.). Duplicate primer pairs are reported for 7% (174) of the loci. The majority (92%) of primer pairs were developed in regions flanking perfect repeats > or = 24 bp in length. Using electronic PCR (e-PCR) to align primer pairs against 3284 publicly sequenced rice BAC and PAC clones (representing about 83% of the total rice genome), 65% of the SSR markers hit a BAC or PAC clone containing at least one genetically mapped marker and could be mapped by proxy. Additional information based on genetic mapping and "nearest marker" information provided the basis for locating a total of 1825 (81%) of the newly designed markers along rice chromosomes. Fifty-six SSR markers (2.8%) hit BAC clones on two or more different chromosomes and appeared to be multiple copy. The largest proportion of SSRs in this data set correspond to poly(GA) motifs (36%), followed by poly(AT) (15%) and poly(CCG) (8%) motifs. AT-rich microsatellites had the longest average repeat tracts, while GC-rich motifs were the shortest. In combination with the pool of 500 previously mapped SSR markers, this release makes available a total of 2740 experimentally confirmed SSR markers for rice, or approximately one SSR every 157 kb.     

Participation of plasma membrane proteins in the formation of tight junction by cultured epithelial cells

Measurements of the transepithelial electrical resistance correlated with freeze-fracture observations have been used to study the process of tight junction formation under various experimental conditions in monolayers of the canine kidney epithelial cell line MDCK. Cells derived from previously confluent cultures and plated immediately after trypsin- EDTA dissociation develop a resistance that reaches its maximum value of several hundred ohms-cm(2) after approximately 24 h and falls to a steady-state value of 80-150 ohms- cm(2) by 48 h. The rise in resistance and the development of tight junctions can be completely and reversibly prevented by the addition of 10 μg/ml cycloheximide at the time of plating, but not when this inhibitor is added more than 10 h after planting. Thus tight junction formation consists of separable synthetic and assembly phases. These two phases can also be dissociated and the requirement for protein synthesis after plating eliminated if, following trypsinization, the cells are maintained in spinner culture for 24 h before plating. The requirement for protein synthesis is restored, however, if cells maintained in spinner culture are treated with trypsin before plating. Actinomycin D prevents development of resistance only in monolayers formed from cells derived from sparse rather than confluent cultures, but new mRNA synthesis is not required if cells obtained from sparse cultures are maintained for 24 h in spinner culture before plating. Once a steady-state resistance has been reached, its maintenance does not require either mRNA or protein synthesis; in fact, inhibition of protein synthesis causes a rise in the resistance over a 30-h period. Following treatments that disrupt the junctions in steady- state monolayers recovery of resistance also does not require protein synthesis. These observations suggest that proteins are involved in tight junction formation. Such proteins, which do not turn over rapidly under steady-state conditions, are destroyed by trypsinization and can be resynthesized in the absence of stable cell-cell or cell-substratum contact. Messenger RNA coding for proteins involved in tight junction formation is stable except when cells are sparsely plated, and can also be synthesized without intercellular contacts or cell-substratum attachment.     

The influence of serum,glucose and oxygen on intervertebral disc cell growth <Emphasis Type="Italic">in vitro</Emphasis>: implications for degenerative disc disease

Introduction  

The avascular nature of the human intervertebral disc (IVD) is thought to play a major role in disc pathophysiology by limiting nutrient supply to resident IVD cells. In the human IVD, the central IVD cells at maturity are normally chondrocytic in phenotype. However, abnormal cell phenotypes have been associated with degenerative disc diseases, including cell proliferation and cluster formation, cell death, stellate morphologies, and cell senescence. Therefore, we have examined the relative influence of possible blood-borne factors on the growth characteristics of IVD cells in vitro.     

ESTimating plant phylogeny: lessons from partitioning

Background  

While Expressed Sequence Tags (ESTs) have proven a viable and efficient way to sample genomes, particularly those for which whole-genome sequencing is impractical, phylogenetic analysis using ESTs remains difficult. Sequencing errors and orthology determination are the major problems when using ESTs as a source of characters for systematics. Here we develop methods to incorporate EST sequence information in a simultaneous analysis framework to address controversial phylogenetic questions regarding the relationships among the major groups of seed plants. We use an automated, phylogenetically derived approach to orthology determination called OrthologID generate a phylogeny based on 43 process partitions, many of which are derived from ESTs, and examine several measures of support to assess the utility of EST data for phylogenies.     

Assessment of Bioaerosols in Swine Barns by Filtration and Impaction

Bioaerosol concentrations inside one naturally ventilated and one mechanically ventilated swine finishing barn were assessed by sampling air using membrane filtration and impaction (six-stage Andersen sampler), and assayed by culture method. The barns, located on the same commercial farm in northeast Kansas, did not show any significant difference (p > 0.05) in concentrations of total and respirable airborne microorganisms. The overall mean total concentrations inside the two barns were 6.6 × 10⁴ colony forming units (CFU)/m³ (SD = 3.8 × 10⁴ CFU/m³) as measured by filtration and 8.6 × 10⁴ CFU/m³ (SD = 5.1 × 10⁴ CFU/m³) by impaction. The overall mean respirable concentrations were 9.0 × 10³ CFU/m³ (SD = 4.1 × 10³ CFU/m³) measured by filtration and 2.8 × 10⁴ CFU/m³ (SD = 2.2 × 10⁴ CFU/m³) by impaction. Total and respirable CFU concentrations measured by impaction were significantly (p < 0.05) higher than that by filtration. The persistent strains of microorganisms were various species of the following genera: Staphylococcus, Pseudomonas, Bacillus, Listeria, Enterococcus, Nocardia, Lactobacillus, and Penicillium. It appears that filtration sampling can be used for a qualitative survey of bioaerosols in swine barns while the Andersen sampler is suitable for both quantitative and qualitative assessments. Received: 2 April 2001 / Accepted: 13 June 2001