Studies on normal human bone marrow cultures in controlled environment thin-film culture systems

Summary Two thin film culture systems, the controlled environment steady state system (SS) and the rocker tube configuration of that system (RT), were used to identify some of the conditions that appear to maintain morphologic and functional characteristics of cells of human bone marrow explants in vitro. The systems configuration assured continual gassing, control and easy monitoring of the cultures. Cytocentrifuge preparations of media of specimens cultured in RT disclosed, though in decreasing numbers, various hematopoietic cells for periods exceeding one month. Hematopoietic cells shed from specimens cultured in the SS system were retained in the culture tubes; cells of the myelocytic series predominated for the first 2 weeks while an increasing number of monocytes and macrophages appeared in the media of older cultures. Histologic examination of cultured explants disclosed preservation of the marrow architecture and the persistence of hematopoietic cells. Specimens cultured in RT tubes tended to be less cellular than similar cultures placed in dialysis bags or as cultured in the SS system. Immunoglobulins (Ig) were released into the culture media at a constant rate throughout the period of culture. Specimens that were cultured at a controlled pH of 7.4 released 2 to more than 4 times as much Ig as similar specimens maintained at a pH level of 7.1. There were no definitive differences in Ig levels in the cultures maintained at comparable pH levels and overlaid with various CO₂ concentrations, i.e. 2%, 5%, 10%; similarly, no differences in Ig levels were found in specimens cultured in media containing fetal bovine sera as opposed to horse sera. Supported by U.S.P.H.S. Grant CA-5834 from the National Cancer Institute. Department of Medicine A. Department of Cell Physiology Department of Immunology and Immunochemistry.     

Do antibody binding techniques identify polysomes synthesizing a specific protein?

Specific binding of antibody directed against MOPC-21 myeloma protein to MOPC-21 polysomes has been demonstrated. It was also shown that this same antibody bound specifically to the ribosomal subunits of these polysomes, suggesting that the antibody is not binding exclusively to the nascent polypeptide chains on the polysomes. The antibody was bound specifically to polysomes of a nonproducing variant XC1 which had been isolated in the presence of MOPC-21 myeloma protein while the antibody was not bound to XC1 polysomes isolated in the absence of myeloma protein. This suggests that the myeloma protein is adsorbed to the polysomes during the isolation procedure.     

Effects of nicotinamide on NAD and poly (ADP-ribose) metabolism in DNA-damaged human lymphocytes

The effect of nicotinamide on unscheduled DNA synthesis was studied in resting human lymphocytes. In cells treated with UV irradiation or with MNNG, nicotinamide caused a two-fold stimulation of unscheduled DNA synthesis and retarded the rate of NAD⁺ lowering caused by these treatments. Nicotinamide also reduced the burst of poly(ADP-ribose) synthesis caused by MNNG treat-ment. Thus under conditions that it enhances unscheduled DNA synthesis, nicotinamide causes marked effects on the metabolism of NAD⁺ and poly(ADP-ribose). The effect of nicotinamide on unscheduled DNA synthesis was shown to be independent of protein or polyamine synthesis.     

Anthropogenic noise reduces avian feeding efficiency and increases vigilance along an urban–rural gradient regardless of species’ tolerances to urbanisation

Anthropogenic noise can adversely impact urban bird populations by interfering with vocal communication. Less research has addressed if anthropogenic noise masks the adventitious sounds that birds use to aid predator detection, which may lead to increased vigilance and reduced feeding efficiency. We test this hypothesis using a controlled playback experiment along an urban–rural gradient in Sheffield (UK). We also test the related predictions that anthropogenic noise has the greatest impacts on vigilance and feeding efficiency in rural populations, and on species that are more sensitive to urbanisation. We focus on six passerines, in order from most to least urbanised (based on how urbanisation influences population densities): blue tit Cyanistes caeruleus, robin Erithacus rubeculla, great tit Parus major, chaffinch Fringilla coelebs, coal tit Periparus ater and nuthatch Sitta europaea. We used play-back of anthropogenic urban noise and a control treatment at 46 feeding stations located along the urban–rural gradient. We assess impacts on willingness to visit feeders, feeding and vigilance rates. Exposure to anthropogenic noise reduced visit rates to supplementary feeding stations, reduced feeding rates and increased vigilance. Birds at more urban sites exhibit less marked treatment induced reductions in feeding rates, suggesting that urban populations may be partially habituated or adapted to noisy environments. There was no evidence, however, that more urbanised species were less sensitive to the impacts of noise on any response variable. Our results support the adventitious sound masking hypothesis. Urban noise may thus interfere with the ability of birds to detect predators, reducing their willingness to use food rich environments and increase vigilance rates resulting in reduced feeding rates. These adverse impacts may compromise the quality of otherwise suitable foraging habitats in noisy urban areas. They are likely to be widespread as they arise in a range of species including common urban birds.     

The Bio3D packages for structural bioinformatics

Bio3D is a family of R packages for the analysis of biomolecular sequence, structure, and dynamics. Major functionality includes biomolecular database searching and retrieval, sequence and structure conservation analysis, ensemble normal mode analysis, protein structure and correlation network analysis, principal component, and related multivariate analysis methods. Here, we review recent package developments, including a new underlying segregation into separate packages for distinct analysis, and introduce a new method for structure analysis named ensemble difference distance matrix analysis (eDDM). The eDDM approach calculates and compares atomic distance matrices across large sets of homologous atomic structures to help identify the residue wise determinants underlying specific functional processes. An eDDM workflow is detailed along with an example application to a large protein family. As a new member of the Bio3D family, the Bio3D‐eddm package supports both experimental and theoretical simulation‐generated structures, is integrated with other methods for dissecting sequence‐structure–function relationships, and can be used in a highly automated and reproducible manner. Bio3D is distributed as an integrated set of platform independent open source R packages available from: http://thegrantlab.org/bio3d/ .     

Combined effects of formalin fixation and tissue processing on immunorecognition

Abstract

It is accepted that aldehyde-based fixation of cells can affect immunodetection of antigens; however, the effects of tissue processing on immunodetection have not been analyzed systematically. We investigated the effects of aldehyde-based fixation and the various cumulative steps of tissue processing on immunohistochemical detection of specific antigens. DU145 (prostate) and SKOV3 (ovarian) cancer cell lines were cultured as monolayers on microscope slides. Immunohistochemical detection of Ki67/MIB-1 and proliferating cell nuclear antigen (PCNA) was evaluated after various fixation times in 10% neutral buffered formalin and after each of the several cumulative steps of tissue processing. The effect of antigen retrieval (AR) was evaluated concomitantly as an additional variable. Our results indicate that in addition to fixation, each of the tissue processing steps has effects on immunorecognition of the epitopes recognized by these antibodies. Extensive dehydration through ethanols to absolute ethanol had only modest effects, except for the detection of Ki67/MIB-1 in SKOV-3 cells where the effect was stronger. In general, however, establishment of a hydrophobic environment by xylene resulted in the greatest decrease in immunorecognition. AR compensated for most, but not all, of the losses in staining following fixation and exposure to xylene; however, AR gave consistent results for most steps of tissue processing, which suggests that AR also should be used for staining PCNA. The cellular variations that were observed indicate that the effects of fixation and other steps of tissue processing may depend on how antigens are packaged by specific cells.     

Assigning fossil specimens to a given recent classification when the distribution of character variation is not normal

To help assign fossil material to Recent taxa we present a methodology that offers systematic quantitative tools to explore several continuous characters. It also enables the quantitative determination of which characters amongst several alternatives give results more consistent with a given classification.

The Gini Mean Difference ('Gini') is the expected absolute difference between two randomly drawn observations. In a fossil assemblage comprising several taxa, the Gini of the overall assemblage may be decomposed into three components: the weighted sum of intra‐taxon Gini, the index of overlap, and the inter‐taxon Gini. The parameter that is additional to alternative methods is the overlap index, which serves as a quantitative measure for evaluating the quality of identification. The Gini is advantageous in that it does not require the assumption of a normal distribution in character variation.

The Gini methodology is described in both mathematical and non‐mathematical terms. We demonstrate it by application to a hypothetical gastropod genus consisting of five species, in which we show in orderly, quantitative terms that one character is better for identification of the various species than another character.     

Patterns of DNA methylation in the normal colon vary by anatomical location,gender, and age

Alterations in DNA methylation have been proposed to create a field cancerization state in the colon, where molecular alterations that predispose cells to transformation occur in histologically normal tissue. However, our understanding of the role of DNA methylation in field cancerization is limited by an incomplete characterization of the methylation state of the normal colon. In order to determine the colon’s normal methylation state, we extracted DNA from normal colon biopsies from the rectum, sigmoid, transverse, and ascending colon and assessed the methylation status of the DNA by pyrosequencing candidate loci as well as with HumanMethylation450 arrays. We found that methylation levels of repetitive elements LINE-1 and SAT-α showed minimal variability throughout the colon in contrast to other loci. Promoter methylation of EVL was highest in the rectum and progressively lower in the proximal segments, whereas ESR1 methylation was higher in older individuals. Genome-wide methylation analysis of normal DNA revealed 8388, 82, and 93 differentially methylated loci that distinguished right from left colon, males from females, and older vs. younger individuals, respectively. Although variability in methylation between biopsies and among different colon segments was minimal for repetitive elements, analyses of specific cancer-related genes as well as a genome-wide methylation analysis demonstrated differential methylation based on colon location, individual age, and gender. These studies advance our knowledge regarding the variation of DNA methylation in the normal colon, a prerequisite for future studies aimed at understanding methylation differences indicative of a colon field effect.