Low-coverage massively parallel pyrosequencing of cDNAs enables proteomics in non-model species: comparison of a species-specific database generated by pyrosequencing with databases from related species for proteome analysis of pea chloroplast envelopes

Proteomics is a valuable tool for establishing and comparing the protein content of defined tissues, cell types, or subcellular structures. Its use in non-model species is currently limited because the identification of peptides critically depends on sequence databases. In this study, we explored the potential of a preliminary cDNA database for the non-model species Pisum sativum created by a small number of massively parallel pyrosequencing (MPSS) runs for its use in proteomics and compared it to comprehensive cDNA databases from Medicago truncatula and Arabidopsis thaliana created by Sanger sequencing. Each database was used to identify proteins from a pea leaf chloroplast envelope preparation. It is shown that the pea database identified more proteins with higher accuracy, although the sequence quality was low and the sequence contigs were short compared to databases from model species. Although the number of identified proteins in non-species-specific databases could potentially be increased by lowering the threshold for successful protein identifications, this strategy markedly increases the number of wrongly identified proteins. The identification rate with non-species-specific databases correlated with spectral abundance but not with the predicted membrane helix content, and strong conservation is necessary but not sufficient for protein identification with a non-species-specific database. It is concluded that massively parallel sequencing of cDNAs substantially increases the power of proteomics in non-model species.     

Neuroendocrine hormones such as growth hormone and prolactin are integral members of the immunological cytokine network

Neuroendocrine hormones such as growth hormone (GH) and prolactin (PRL) have been demonstrated to accelerate the recovery of the immune response after chemotherapy and bone marrow transplantation and to enhance the restoration of immunity in individuals infected with HIV and in normal individuals with compromised immune systems associated with aging. As the mechanism of action of these hormones has been elucidated, it has become clear that they are integral members of the immunological cytokine/chemokine network and share regulatory mechanisms with a wide variety of cytokines and chemokines. The members of this cytokine network induce and can be regulated by members of the suppressor of cytokine signaling (SOCS) family of intracellular proteins. In order to take advantage of the potential beneficial effects of hormones such as GH or PRL, it is essential to take into consideration the overall cytokine network and the regulatory effects of SOCS proteins.     

Repeat-protein folding: new insights into origins of cooperativity, stability, and topology

Although our understanding of globular protein folding continues to advance, the irregular tertiary structures and high cooperativity of globular proteins complicates energetic dissection. Recently, proteins with regular, repetitive tertiary structures have been identified that sidestep limitations imposed by globular protein architecture. Here we review recent studies of repeat-protein folding. These studies uniquely advance our understanding of both the energetics and kinetics of protein folding. Equilibrium studies provide detailed maps of local stabilities, access to energy landscapes, insights into cooperativity, determination of nearest-neighbor interaction parameters using statistical thermodynamics, relationships between consensus sequences and repeat-protein stability. Kinetic studies provide insight into the influence of short-range topology on folding rates, the degree to which folding proceeds by parallel (versus localized) pathways, and the factors that select among multiple potential pathways. The recent application of force spectroscopy to repeat-protein unfolding is providing a unique route to test and extend many of these findings.     

Influence of delayed isotopic equilibration in urine on the accuracy of the (2)H(2)(18)O method in the elderly.

Isotopic determination of total energy expenditure (TEE) by the doubly labeled water (DLW) method may be affected by urine retention in the elderly. The isotopic enrichments in urine and plasma sampled simultaneously 4 h post-DLW dose were compared in a subset of 281 subjects [139 women, 142 men, 75 +/- 3 (SD) yr] of the 3,075 participants in the Health, Aging, and Body Composition study. Based on analytic precisions, a +/- 2% urine-plasma difference was set as the cut-off value. Ten percent of the population presented a difference lower than -2%, suggesting a delay in urine isotopic equilibration. This -13 +/- 10% urine-plasma difference was not linked to analytic errors, illnesses, the sampling time, or the time and quantity of water intake, suggesting that urine retention may be the main factor. The consequences are an 18 +/- 13 and 21 +/- 16% overestimation of the total body water and the TEE, respectively. Unexpectedly, 21% of the population presented a urine-plasma difference higher than +/- 2% that resulted, however, in a nonsignificant TEE underestimation of -3 +/- 5%. In conclusion, the delayed isotopic equilibration observed in urine reduces the accuracy of the DLW method in the elderly. It is recommended, when blood sampling is impossible, to adopt the intercept method with urine sampling 24 h postdose.     

A study of spatial variability of domoic acid in razor clams: recommendations for resource management on the Washington coast

Domoic acid (DA) levels in Washington State razor clams (Siliqua patula) have been extremely variable and unpredictable, resulting in emergency closures of harvest areas in 1991, 1998, and 1999. Information concerning toxin variability relative to sampling location is important in developing a more reliable plan for managing DA outbreaks. In November 1998, record levels of DA in razor clams (up to 295 ppm) were reported at Kalaloch beach, Washington. A razor clam resource survey conducted there during the summer of 1999, along with the long retention time of DA in the clams, permitted a study of DA levels as a function of tidal elevation and north-south beach location. During the summer low tides (28–31 July 1999) razor clams were collected from six east-west transects, approximately 1.6 km apart. Each clam was individually analyzed for DA to determine the distribution of toxin between (interspecific variability) and within (intraspecific variability) transects. While average DA levels were similar between transects, toxin levels varied substantially among individual clams. The coefficient of variation among all samples (n=445) was 122%, indicating that harvest closures based upon composite analyses of only six clams could be in error. Here we recommend a sampling strategy of razor clams for regulatory purposes that will result in DA measurements more representative of total population toxin values.     

Circadian communication between unicells?

Populations ofGonyaulax polyedra, in two different phases, about 11 h apart, were mixed, and the intensity of their spontaneous bioluminescence glow recorded for about 2 wk under conditions of constant dim (35±3 μE/m²/s) white light and constant temperature (19.0±0.3°C). The phases and amplitudes of glow signals recorded from mixed cultures were compared with those obtained from the arithmetic sum of the intensity data from two control vials. Peaks in control cultures generally remained separate, but there was a spontaneous increase in the period beginning 6–11 d after the onset of constant conditions. This did not occur in cultures in which the medium was exchanged with fresh medium every 2 d. In the actual mixes of two cultures there was a merging of the two subpeaks in the signal, which did not occur when the medium was exchanged. The results indicate that conditioning of the medium by cells may affect the period of the circadian rhythm and that this might result in a type of communication. Supported by the Deutsche Forschungsgemeinschaft; present address     

Slow and steady is the key to β-cell replication

The β-cells of the pancreas are responsible for insulin production and their destruction results in type I diabetes. β-cell maintenance, growth and regenerative repair is thought to occur predominately, if not exclusively, through the replication of existing β-cells, not via an adult stem cell. It was recently found that all β-cells contribute equally to islet growth and maintenance. The fact that all β-cells replicate homogeneously makes it possible to set up straightforward screens for factors that increase β-cell replication either In vitro or in vivo . It is possible that a circulating factor may be capable of increasing β-cell replication or that intrinsic cell cycle regulators may affect β-cell growth. An improved understanding of the in vivo maintenance and growth of β-cells will facilitate efforts to expand β-cells In vitro and may lead to new treatments for diabetes.