Biological sample collection and processing for molecular epidemiological studies

Molecular epidemiology uses biomarkers and advanced technology to refine the investigation of the relationship between environmental exposures and diseases in humans. It requires careful handling and storage of precious biological samples with the goals of obtaining a large amount of information from limited samples, and minimizing future research costs by use of banked samples. Many factors, such as tissue type, time of collection, containers used, preservatives and other additives, transport means and length of transit time, affect the quality of the samples and the stability of biomarkers and must be considered at the initial collection stage. An efficient study design includes provisions for further processing of the original samples, such as cryopreservation of isolated cells, purification of DNA and RNA, and preparation of specimens for cytogenetic, immunological and biochemical analyses. Given the multiple uses of the samples in molecular epidemiology studies, appropriate informed consent must be obtained from the study subjects prior to sample collection. Use of barcoding and electronic databases allow more efficient management of large sample banks. Development of standard operating procedures and quality control plans is a safeguard of the samples' quality and of the validity of the analyses results. Finally, specific state, federal and international regulations are in place regarding research with human samples, governing areas including custody, safety of handling, and transport of human samples, as well as communication of study results.Here, we focus on the factors affecting the quality and the potential future use of biological samples and some of the provisions that must be made during collection, processing, and storage of samples, based on our experience in the Superfund Basic Research Program and Children's Environmental Health Center, at the University of California, Berkeley.     

Malignant fibrous histiocytoma,giant cell type,of the breast mimicking metaplastic carcinoma. A case report

BACKGROUND: We report a case of malignant fibrous histiocytoma, giant cell type (MFHGC), of the breast. A review of the literature failed to reveal cytology-based reports on this entity. The cytologic similarity of breast MFHGC on fine needle aspiration biopsy (FNAB) to other malignant breast neoplasms, including carcinoma with osteoclastlike giant cells, metaplastic carcinoma and breast sarcomas, as well as benign reactive processes, makes the recognition of this tumor challenging. CASE: A 72-year-old woman presented with a 5-month history of an enlarging breast mass. FNAB of the mass showed a hypercellular smear composed of cohesive, branching clusters of spindle cells with ovoid, focally hyperchromatic nuclei and inconspicuous nucleoli. Interspersed osteoclastlike giant cells, some associated with clusters of spindle cells, were uniformly seen throughout the smear. The background was hemorrhagic, with cellular debris and occasional spindle cells and lymphocytes. No ductal epithelial or myoepithelial cells were seen. An incisional biopsy was performed, followed by radical mastectomy. The histologic examination was diagnostic of MFHGC. The diagnosis was supported by immunohistochemical and electron microscopic studies. CONCLUSION: MFHGC, also called primary giant cell tumor of soft tissues, is composed of a mixture of histiocytes, fibroblasts and bland-appearing osteoclastlike giant cells with a multinodular growth pattern. Although MFHGC rarely occurs in the breast and the definitive diagnosis is difficult based on cytology alone, the diagnosis can be considered when a cytologic examination reveals a hypercellular, spindle cell smear with osteoclastlike giant cells in the absence of ductal epithelial or myoepithelial cells.     

Altering substrate specificity of phosphatidylcholine-preferring phospholipase C of Bacillus cereus by random mutagenesis of the headgroup binding site

PLC(Bc) is a 28.5 kDa monomeric enzyme that catalyzes the hydrolysis of the phosphodiester bond of phosphatidylcholine, phosphatidylethanolamine, and phosphatidylserine to provide a diacylglycerol and the corresponding phosphorylated headgroup. Because single replacements of Glu4, Tyr56, and Phe66 in the headgroup binding pocket led to changes in substrate specificity [Martin et al. (2000) Biochemistry 39, 3410-3415], a combinatorial library of approximately 6000 maltose binding protein-PLC(Bc) fusion protein mutants containing random permutations of these three residues was generated to identify PLC(Bc) mutants with altered specificity profiles and high catalytic activities. Members of this library were screened for hydrolytic activity toward the water soluble substrates C6PC, C6PE, and C6PS using a novel protocol that was conducted in a 96-well format and featured the in situ cleavage of the fusion protein to release the mutant PLC(Bc)s. Ten mutant enzymes that exhibited significant preferences toward C6PE or C6PS were selected and analyzed by steady-state kinetics to determine their specificity constants, k(cat)/K(M). The C6PS selective clones E4G, E4Q/Y56T/F66Y, and E4K/Y56V exhibited higher specificity constants toward C6PS than wt, whereas Y56T, F66Y, and Y56T/F66Y were C6PE selective and had comparable or higher specificity constants than wt for C6PE. The corresponding wt residues were singly reinserted back into the E4Q/Y56T/F66Y and E4K/Y56V mutants via site-directed mutagenesis, and the E4Q/F66Y mutant thus obtained exhibited a 10-fold higher specificity constant toward C6PS than wt, a value significantly higher than other PLC(Bc) mutants. On the basis of available data, an aromatic residue at position 66 appears important for significant catalytic activity toward all three substrates, especially C6PC and C6PE. The charge of residue 4 also appears to be a determinant of enzyme specificity as a negatively charged residue at this position endows the enzyme with C6PC and C6PE preference, whereas a polar neutral or positively charged residue results in C6PS selectivity. Replacing Tyr56 with Val, Ala, Thr, or Ser greatly reduces activity toward C6PC. Thus, the substrate specificity of PLC(Bc) can be modulated by varying three of the amino acid residues that constitute the headgroup binding pocket, and it is now apparent that this enzyme is not evolutionarily optimized to hydrolyze phospholipids with ethanolamine or serine headgroups.     

Glucose and mannitol diffusion in human dura mater

An in vitro experimental study of the control of the human dura mater optical properties at administration of aqueous solutions of glucose and mannitol has been presented. The significant increase of the dura mater optical transmittance under action of immersion liquids has been demonstrated. Diffusion coefficients of glucose and mannitol in the human dura mater tissue at 20 degrees C have been estimated as (1.63 +/- 0.29) x 10(-6)cm(2)/s and as (1.31 +/- 0.41) x 10(-6) cm(2)/s, respectively. Experiments show that administration of immersion liquids allows for the effective control of tissue optical characteristics that make dura mater more transparent, thereby increasing the ability of light penetration through the tissue.     

Maternal effects on offspring depend on female mating pattern and offspring environment in yellow dung flies

Abstract Direct costs and benefits to females of multiple mating have been shown to have large effects on female fecundity and longevity in several species. However, with the exception of studies examining genetic benefits of polyandry, little attention has been paid to the possible effects on offspring of multiple mating by females. We propose that nongenetic effects of maternal matings on offspring fitness are best viewed in the same context as other maternal phenotype effects on offspring that are well known even in species lacking parental care. Hence, matings can exert effects on offspring in the same way as other maternal environment variables, and are likely to interact with such effects. We have conducted a study using yellow dung flies ( Scathophaga stercoraria ), in which we independently manipulated female mating rate, number of mates and maternal thermal environment and measured subsequent fecundity, hatching success, and offspring life-history traits. To distinguish between direct effects of matings and potential genetic benefits of polyandry we split broods and reared offspring at three different temperature regimes. This allowed us to demonstrate that although we could not detect any simple benefits or costs to matings, there are effects of maternal environment on offspring and these effects interact with female mating regime affecting offspring fitness. Such interactions between female phenotype and the costs and benefits of matings have potentially broad implications for understanding female behavior.     

Steady-state assemblages of phytoplankton in four temperate lakes (NE U.S.A.)

For four temperate lakes (Northeast U.S.A.) we identify periods of persistent phytoplankton assemblages and investigate the ecological conditions that correlate to these persistent assemblages. Periods of persistent assemblages, here considered as steady-state phases, were defined according to equilibrium criteria (two or three coexisting species, contributing to 80% of the standing biomass, for at least 2 weeks) defined by Sommer et al. (1993, Hydrobiologia 249: 1–7). For all four lakes, samples were taken weekly during the ice-free season and phytoplankton attributes (biomass, assemblages, diversity, species richness, change rates) and abiotic variables (temperature, I^* – as light mean in the mixing zone – z_mix, and nutrients) were analysed. Chodikee (CH), an eutrophic and rapidly flushed lake, did not show any persistent phase. The remaining three lakes showed single steady-state phases that occurred at varying times during the ice-free season. Steady-state phases occurred during early stratification in late spring in the stably stratified oligotrophic Mohonk Lake (MO), in the late summer stratification in the meso-eutrophic Stissing Lake (ST), and during spring mixing in Wononscopomuc Lake (WO). MO showed a 3-week period with dominance of F assemblage (Botryococcus braunii, Willea wilhelmii and Eutetramorus planctonicus), characteristic for clear epilimnia, tolerant to low nutrient and sensitive to high turbidity. For three weeks, ST had a stable assemblage with dominance of Lo(Woronichinia sp.), common assemblage in summer epilimnion of mesotrophic lakes and sensitive to prolonged or deep mixing; and P, assemblage able to live in eutrophic epilimnia with mild light and sensitive to stratification and silica depletion. In contrast, the mesotrophic Wononscopomuc Lake (WO) showed persistent assemblages during a 4-week period of spring circulation, when a dinoflagellate (Lo) was co-dominant with Nitzschia acicularis (C). The latter species is characteristic for mesotrophic lakes, tolerant to low light and sensitive to stratification and silica depletion. Both Lo and P assemblages, among seven others, had before been quoted, in literature, as dominant in maturing stages. We could not find consistent statistical differences between the periods classified as steady-state and non-steady-state. However, the data demonstrated that prolonged period of both mixing and stratification can maintain dominant assemblages. Although, historically sensed as opposite mechanisms, both mixing and stratification, if persistent, were observed maintaining dominant assemblages because both scenarios are characterized by environmental constancy.     

Structure of a new 2-deoxy-2-[(R)-3-hydroxybutyramido]-D-glucose-containing O-specific polysaccharide from the lipopolysaccharide of Citrobacter gillenii PCM 1542

The O-specific polysaccharide of Citrobacter gillenii PCM 1542 from serotype O-12a,12 b is composed of one residue each of D-glucose, D-GlcNAc, 2-deoxy-2-[(R)-3-hydroxybutyramido]-D-glucose (D-GlcNAcyl) and two GalNAc residues. On the basis of sugar and methylation analyses of the intact and Smith degraded polysaccharides, along with 1D and 2D 1H and 13C NMR spectroscopy, the following structure of the branched pentasaccharide repeating unit of the O-specific polysaccharide was established:This structure differs significantly from that of the O-specific polysaccharide of C. gillenii PCM 1544 from the same serotype O-12a,12 b, which has been established earlier (Kübler-Kielz.shtsls;b, J. et al. Carbohydr. Res. 2001, 331, 331-336). Serological studies confirmed that the two O-antigens are not related and suggested that strains PCM 1542 and 1544 should be classified into different O-serogroups.