Dyes from a twenty-first century perspective

In June 2008, the Biological Stain Commission sponsored A Seminar on Dyes and Staining the purpose of which was twofold: first, to show that very useful information applicable to biomedical dyes and staining is available from unrelated disciplines and second, to summarize modern thinking on how dyes, solvents, and tissues interact to produce selective staining. In this introduction to the papers from the symposium, we acknowledge that biomedical dye research has declined as newer technologies have gained importance. We should point out, however, that dyes and staining still are vitally important. Moreover, needs abound for innovative studies concerned with dye analysis, synthesis, and mode of action. Concepts and tools from unrelated fields hold promise for significant breakthroughs in many areas of interest.     

Pattern of serum immunoreactivity against breast cancer cell lysates may predict severity of disease in breast cancer patients

Humoral tumor-specific immunity has been investigated as a potential tool to identify tumor-associated antigens and evaluate cancer diagnosis and prognosis. Using SDS-PAGE and western blotting techniques we investigated the humoral immune response against tumor cell antigens in 36 breast cancer patients, 17 node-positive (NP) and 19 node-negative (NN). As a source of antigens, we prepared protein lysates from four breast cancer cell lines (AU565, BT474, MCF-7 and MDA-MB-231) which in vitro exhibit different features of invasion, estrogen receptor/progesterone receptor status and HER2/neu expression thereby potentially representing mild to aggressive forms of clinical disease. A higher number of immunocomplexes Ag–Ab were formed when serum from NN patients was immunoreacted against lysates from AU565 and MCF-7 in comparison to serum from NP patients (P < 0.01). BT474 cells were not a good antigenic source. MDA-MB-231 cells could not significantly discriminate between NN and NP patients since both groups showed higher amounts of reactivity against the lysate. However, comparative analysis of protein preparations purified from MCF-7 and MDA-MB-231 cells and immunodetected concomitantly with the same serum samples showed that serum from patients with cancers with worse prognosis (stage, nodality, HER2/neu and hormonal status) reacted more intensely to proteins purified from the relatively more invasive cell line MDA-MB-231 compared to MCF-7. These findings suggest that the study of serum antibody reactivity to antigens purified from breast cancer cell lines with different invasive properties should be further investigated for its potential in providing beneficial prognostic information in breast cancer. Supported by the United States Military Cancer Institute and the Department of Clinical Investigation at Walter Reed Army Medical Center. The opinions or assertions contained herein are the private views of the authors and are not to be construed as official or reflecting the views of the Department of the Army or the Department of Defense.     

Isolation and characterisation of a variant allele of the gene for human apolipoprotein E

Size-selected human DNA fragments enriched in the Apolipoprotein E (ApoE) gene sequence were cloned from an individual of known ApoE phenotype, E2/E2. The clone bank was screened using a human cDNA clone for the ApoE locus (1), and a single genomic clone was isolated. Sequence data obtained from appropriate subcloned fragments confirmed that the codon for Arg-158 (CGC) in the E3 allele is altered to the codon for Cys (TGC) in the E2 allele. Hybridisation data indicated the presence of at least one intron in the ApoE gene, consistent with the structure of an independently isolated human ApoE4 allele (2).     

Factors regulating the contributions of fixed nitrogen by pasture and crop legumes to different farming systems of eastern Australia

On-farm and experimental measures of the proportion (%Ndfa) and amounts of N₂ fixed were undertaken for 158 pastures either based on annual legume species (annual medics, clovers or vetch), or lucerne (alfalfa), and 170 winter pulse crops (chickpea, faba bean, field pea, lentil, lupin) over a 1200 km north-south transect of eastern Australia. The average annual amounts of N₂ fixed ranged from 30 to 160 kg shoot N fixed ha^–1 yr^–1 for annual pasture species, 37–128 kg N ha^–1 yr^–1 for lucerne, and 14 to 160 kg N ha^–1 yr^–1 by pulses. These data have provided new insights into differences in factors controlling N₂ fixation in the main agricultural systems. Mean levels of %Ndfa were uniformly high (65–94%) for legumes growing at different locations under dryland (rainfed) conditions in the winter-dominant rainfall areas of the cereal-livestock belt of Victoria and southern New South Wales, and under irrigation in the main cotton-growing areas of northern New South Wales. Consequently N₂ fixation was primarily regulated by biomass production in these areas and both pasture and crop legumes fixed between 20 and 25 kg shoot N for every tonne of shoot dry matter (DM) produced. Nitrogen fixation by legumes in the dryland systems of the summer-dominant rainfall regions of central and northern New South Wales on the other hand was greatly influenced by large variations in %Ndfa (0–81%) caused by yearly fluctuations in growing season (April–October) rainfall and common farmer practice which resulted in a build up of soil mineral-N prior to sowing. The net result was a lower average reliance of legumes upon N₂ fixation for growth (19–74%) and more variable relationships between N₂ fixation and DM accumulation (9–16 kg shoot N fixed/t legume DM). Although pulses often fixed more N than pastures, legume-dominant pastures provided greater net inputs of fixed N, since a much larger fraction of the total plant N was removed when pulses were harvested for grain than was estimated to be removed or lost from grazed pastures. Conclusions about the relative size of the contributions of fixed N to the N-economies of the different farming systems depended upon the inclusion or omission of an estimate of fixed N associated with the nodulated roots. The net amounts of fixed N remaining after each year of either legume-based pasture or pulse crop were calculated to be sufficient to balance the N removed by at least one subsequent non-legume crop only when below-ground N components were included. This has important implications for the interpretation of the results of previous N₂ fixation studies undertaken in Australia and elsewhere in the world, which have either ignored or underestimated the N present in the nodulated root when evaluating the contributions of fixed N to rotations.     

Hip joint replacement surgery for idiopathic osteoarthritis aggregates in families

In order to determine whether there is a genetic component to hip or knee joint failure due to idiopathic osteoarthritis (OA), we invited patients (probands) undergoing hip or knee arthroplasty for management of idiopathic OA to provide detailed family histories regarding the prevalence of idiopathic OA requiring joint replacement in their siblings. We also invited their spouses to provide detailed family histories about their siblings to serve as a control group. In the probands, we confirmed the diagnosis of idiopathic OA using American College of Rheumatology criteria. The cohorts included the siblings of 635 probands undergoing total hip replacement, the siblings of 486 probands undergoing total knee replacement, and the siblings of 787 spouses. We compared the prevalence of arthroplasty for idiopathic OA among the siblings of the probands with that among the siblings of the spouses, and we used logistic regression to identify independent risk factors for hip and knee arthroplasty in the siblings. Familial aggregation for hip arthroplasty, but not for knee arthroplasty, was observed after controlling for age and sex, suggesting a genetic contribution to end-stage hip OA but not to end-stage knee OA. We conclude that attempts to identify genes that predispose to idiopathic OA resulting in joint failure are more likely to be successful in patients with hip OA than in those with knee OA.     

The contributions of nitrogen-fixing crop legumes to the productivity of agricultural systems

Data collated from around the world indicate that, for every tonne of shoot dry matter produced by crop legumes, the symbiotic relationship with rhizobia is responsible for fixing, on average on a whole plant basis (shoots and nodulated roots), the equivalent of 30–40 kg of nitrogen (N). Consequently, factors that directly influence legume growth (e.g. water and nutrient availability, disease incidence and pests) tend to be the main determinants of the amounts of N₂ fixed. However, practices that either limit the presence of effective rhizobia in the soil (no inoculation, poor inoculant quality), increase soil concentrations of nitrate (excessive tillage, extended fallows, fertilizer N), or enhance competition for soil mineral N (intercropping legumes with cereals) can also be critical. Much of the N₂ fixed by the legume is usually removed at harvest in high-protein seed so that the net residual contributions of fixed N to agricultural soils after the harvest of legumegrain may be relatively small.Nonetheless, the inclusion of legumes in a cropping sequence generally improves the productivity of following crops. Whilesome of these rotational effects may be associated with improvements in availability of N in soils, factors unrelated to N also play an important role. Recent results suggest that one such non-N benefit may be due to the impact on soil biology of hydrogenemitted from nodules as a by-product of N₂, fixation.     

Genes for the CPE Receptor (CPETR1) and the Human Homolog of RVP1 (CPETR2) Are Localized within the Williams–Beuren Syndrome Deletion

Williams–Beuren syndrome (WBS) is a neurodevelopmental disorder affecting multiple systems. Haploinsufficiency of genes deleted in chromosomal region 7q11.23 is the likely cause for this syndrome. We now report the localization of the genes for the CPE-R (Clostridium perfringensenterotoxin receptor,CPETR1) and the human homolog of RVP1 (rat ventral prostate 1 protein,CPETR2), both previously mapped to 7q11, to the WBS critical region. A single nucleotide polymorphism (SNP) present inCPETR1has been identified and was used to determine parental origin of the deleted allele in five informative families. The mouse homologsCpetr1andCpetr2were identified and mapped to the conserved syntenic region on mouse chromosome 5. Northern blot analysis ofCPETR1demonstrates tissue specificity, with expression in kidney, lung, thyroid, and gastrointestinal tissues. In mouse,Cpetr1is expressed in the early embryo, appears to be developmentally upregulated during gestation, and is present in adult tissues. Our results suggest a role for CPE-R in internal organ development and function during pre- and postnatal life.     

Detection of a Reproducible,Single-Member Shift in Soil Bacterial Communities Exposed to Low Levels of Hydrogen

Soil is exposed to hydrogen when symbiotic rhizobia in legume root nodules cannot recycle the hydrogen that is generated during nitrogen fixation. The hydrogen emitted is most likely taken up by free-living soil bacteria that use hydrogen as an energy source, though the bacteria that do this in situ remain unclear. In this study, we investigated the effect of hydrogen exposure on the bacteria of two different soils in a microcosm setup designed to simulate hydrogen-emitting root nodules. Although the size and overall composition of the soil bacterial community did not significantly alter after hydrogen exposure, one ribotype increased in relative abundance within each soil. This single-ribotype shift was identified by generating multiple terminal restriction fragment length polymorphism (T-RFLP) profiles of 16S rRNA genes from each soil sample, with gene sequence confirmation to identify terminal restriction fragments. The increased abundance of a single ribotype after hydrogen exposure, within an otherwise similar community, was found in replicate samples taken from each microcosm and was reproducible across replicate experiments. Similarly, only one member of the soil bacterial community increased in abundance in response to hydrogen exposure in soil surrounding the root nodules of field-grown soybean (Glycine max). The ribotypes that increased after hydrogen exposure in each soil system tested were all from known hydrogen-oxidizing lineages within the order Actinomycetales. We suggest that soil actinomycetes are important utilizers of hydrogen at relevant concentrations in soil and could be key contributors to soil''s function as a sink in the global hydrogen cycle.Soil is the major sink in the global hydrogen cycle and accounts for approximately 75 to 80% of uptake from the atmosphere (7, 11). Soil is such a strong sink that the atmospheric mixing ratio of molecular hydrogen, H₂, is hemispherically asymmetric because of the greater landmass in the Northern Hemisphere (11). Many nitrogen-fixing bacteria that form symbiotic relationships with legume plants cannot recycle the H₂ that is generated during N₂ fixation (2, 13). Most of the H₂ emitted from legume root nodules is taken up by the surrounding soil, within a few centimeters of the nodule surface, and is not released to the atmosphere (20). Although the H₂ emitted by the rhizobial symbionts costs the legume approximately 5% of its daily photosynthate and “represents a significant investment by the plant” (9), there is growing evidence to suggest that soil exposed to H₂ is beneficial to plant growth, separate from the benefits derived from N₂ fixation (8, 10, 28). Previously, La Favre and Focht have hypothesized that “the hydrogen which is evolved during N₂ fixation represents an additional energy input into the plant-soil ecosystem… since metabolism of H₂ by chemolithotrophic bacteria results in an input of fixed carbon to the system” (20). A number of studies have found that when H₂ is taken up by soil, net CO₂ fixation occurs at the rate of 7 to 8 nmol CO₂ per g of soil per h (22, 34). For a legume fixing 200 kg of atmospheric N₂ per hectare, over 200,000 liters of H₂ could be released into the legume''s rhizosphere over the duration of the growing season and CO₂ fixation could result in an extra 25 kg of soil carbon fixed per hectare (9, 10, 28).Many bacteria isolated from soil are able to utilize H₂ as an energy source (2, 5-7, 21), and free-living bacteria are most likely responsible for the H₂ uptake observed by soil surrounding legume roots (22). Adding a bacterial energy source, such as H₂, could affect the microbial population size, as has been observed previously (34), but more specific shifts within the bacterial community may occur if just the microorganisms able to utilize the energy source multiply. Their activity could also have downstream consequences specifically on other members of the community. Most H₂-oxidizing cultures have required enrichment with concentrations of H₂ that are not environmentally relevant and therefore cannot be assumed to be carrying out H₂ oxidation at much lower, naturally occurring concentrations (5-7). Recent surveys of microbes present in soil samples, via their nucleic acids, have revealed many novel bacterial inhabitants that have been little studied and thus may also be contributing to the repertoire of bacterial soil processes, such as H₂ uptake (16). A recent study into the effect of H₂ on soil bacteria focused on a few groups of H₂-oxidizing, autotrophic bacteria and thus ignored many other H₂ utilizers potentially present in soil (34).There are now many ways of characterizing the entire microbial community in environmental samples, either via their entire genomic content, though metagenomic analysis of soil is difficult at present, or via analysis of the lineages present according to 16S rRNA gene sequences, or ribotypes (36). A recent study comparing high-throughput pyrosequencing of 16S rRNA genes and an easily accessible profiling method, known as terminal restriction fragment length polymorphism (T-RFLP), found the simpler profiles were appropriate for comparing the dominant ribotypes in multiple samples (24). Although T-RFLP profiles only provide a simplified snapshot of the dominant members in microbial communities, compared to the deeper analyses provided by microarrays or high-throughput sequencing technologies, T-RFLP profiling is a cost-effective, reproducible, and robust method of “fingerprinting” many soil samples rapidly and efficiently (14, 24, 25, 32).In this study, we chose to assess the dominant members of the soil bacterial community via T-RFLP profiles of ribotypes present in H₂-treated and control soils to avoid a narrow focus on well-studied H₂ oxidizers. We investigated the bacterial community structure in two different soils, utilizing a microcosm setup with concentrations of H₂ calculated to occur in the rhizosphere of N₂-fixing legumes, to determine whether common responses to H₂ exposure could be predicted from soils that differ by climate, edaphic characteristics, and starting communities. Soil in microcosms has previously been shown to have similar H₂ uptake properties to soil close to H₂-emitting legume nodules (9), but we also complemented our plant-free microcosm work with an examination of soil collected from the root systems of field-grown soybean (Glycine max (L.) Merr.).     

Assessment of immunologic response and recurrence patterns among patients with clinical recurrence after vaccination with a preventive HER2/neu peptide vaccine: from US Military Cancer Institute Clinical Trials Group Study I-01 and I-02

Background  E75, a HER2/neu immunogenic peptide, is expressed in breast cancer (BCa). We have performed clinical trials of E75 + GM-CSF vaccine in disease-free, node-positive and node-negative BCa patients at high recurrence risk and recurrences were noted in both control and vaccine groups. Methods  Among the 186 BCa patients enrolled, 177 completed the study. Patients were HLA typed; the HLA-A2⁺/A3⁺ patients were vaccinated; HLA-A2⁻/A3⁻ patients were followed as controls. Standard clinicopathological factors, immunologic response to the vaccine, and recurrences were collected and assessed. Results  The control group recurrence rate was 14.8 and 8.3% in the vaccinated group (P = 0.17). Comparing the 8 vaccinated recurrences (V-R) to the 88 vaccinated nonrecurrent patients (V-NR), the V-R group had higher nodal stage (≥N2: 75 vs. 5%, P = 0.0001) and higher grade tumors (%grade 3: 88 vs. 31%, P = 0.003). The V-R group did not fail to respond immunologically as noted by equivalent dimer responses and post-DTH responses. Compared to control recurrent patients (C-R), V-R patients trended toward higher-grade tumors and hormone-receptor negativity. C-R patients had 50% bone-only recurrences, compared to V-R patients with no bone-only recurrences (P = 0.05). Lastly, V-R mortality rate was 12.5% compared with 41.7% for the C-R group (P = 0.3). Conclusions  The vaccinated patients who recurred had more aggressive disease compared to V-NR patients. V-R patients had no difference in immune response to the vaccine either in vitro or in vivo. V-R patients, when compared to C-R patients, trended towards more aggressive disease, decreased recurrence rates, decreased mortality, and no bone-only recurrences. Supported by the United States Military Cancer Institute and the Department of Clinical Investigation at Walter Reed Army Medical Center. Funded primarily by the Clinical Breast Care Project. The opinions or assertions contained herein are the private views of the authors and are not to be construed as official or reflecting the views of the Department of the Army, the Department of the Navy, or the Department of Defense. This work represents original research that has not been submitted elsewhere for publication.