Image processing software for enhanced visualization of faint or noisy autoradiographic images

A computer program for digital image processing is described which can be implemented using scanning densitometer hardware pre-existing in most biology departments plus computer video hardware which may either pre-exist in the biology department or would represent a moderate upgrade over an already planned computer purchase. The primary purpose of this computer program is to provide contrast enhancement of faint or low contrast autoradiograph images and to implement background subtraction and digital smoothing methods which permit visualization of blurry electrophoresis bands against noisy backgrounds. However, the program also has modest editing capabilities that allow its use in the routine preparation of images for publication. Finally, the program has facilities for deblurring, edge enhancement and multiple image averaging, which give it usefulness in other forms of photographic analysis.     

单核苷酸多态性基因分型技术原理与进展

在基因组规模了解遗传变异与生物功能之间的关系可望为生物学带来全新的深入认识。本从等位基因分型机理、反应形式和检测方法等三个方面讨论SNP分型方法的现状,并简要介绍了目前应用的一些分型方法。     

New concepts in synaptic biology derived from single-molecule imaging

Single-molecule approaches give access to the full distribution of molecule behaviors and overcome the averaging intrinsic to bulk measurement methods. They allow access to complex processes where a given molecule can have heterogeneous properties over time. Recent developments in single-molecule imaging technologies have been followed by their wide application in cellular biology and are leading to the unraveling of new mechanisms related to molecular movements. They are shaping new concepts in the dynamic equilibria of complex biological macromolecular assemblies such as synapses. These advances were made possible thanks to improvements in visualization approaches combined with new strategies to label proteins with nanoprobes. In this primer, we will review the different approaches used to track single molecules in live neurons, compare them to bulk measurements, and discuss the different concepts that have emerged from their application to synaptic biology.     

Spatial and temporal demographic variation drives within-season fluctuations in sexual selection

Our understanding of selection in nature stems mainly from whole-season and cross-sectional estimates of selection gradients. These estimates suggest that selection is relatively constant within, but fluctuates between seasons. However, the strength of selection depends on demographics, and because demographics can vary within seasons, there is a gap in our understanding regarding the extent to which seasonal fluctuations in demographics may cause variation in selection. Here we use two populations of the golden orb-web spider (Nephila plumipes) that differ in density to examine how demographics change within a season and whether there are correlated shifts in selection. We demonstrate that there is within-season variation in sex ratio and density at multiple spatial and temporal scales. This variation led to changes in the competitive challenges that males encountered at different times of the season and was correlated with significant variation in selection gradients on male size and weight between sampling periods. We highlight the importance of understanding the biology of the organism under study to correctly determine the relevant scale in which to examine selection. We also argue that studies may underestimate the true variation in selection by averaging values, leading to misinterpretation of the effect of selection on phenotypic evolution.     

Osteoclast radicals

In biological research, new ideas arise and quickly spread to encompass the entire field. Thus, the evolution of molecular biology has significantly changed our methods of approaching our research. A similar far-reaching finding has been the advent of radical reactions into biology. Although radical chemistry has been utilzed for many technological advances that affect our daily lives, the appreciation of this same process within our cells has opened an unexplored arena for research enquiry. As cellular messengers, radical molecules seem shimsically designed: they are evanescent, rapidly and apparently indiscriminately reactive, and barely detectable bymost biological methods. Yet, our initial probing of these reactive agents in cells and organisms has led us to postulate a virtually undescribed system of communication within and among cells which may have significant effects in multiple organs. In bone, radical reactions have been attributed with an important role in the control of bone resorption.     

Molecular biology of protein kinase C signaling in cardiac myocytes

The PKC family of serine/threonine kinases have been implicated in a diverse array of cellular responses. Adult cardiac myocytes express multiple PKC isozymes, which participate in the response of muscle cells to extracellular stimuli, modulate contractile properties, and promote cell growth and survival. Recently, the classification of this ubiquitous family of signaling molecules has been expanded from three to four subfamilies. This review will focus on the application of pharmacologic and molecular approaches to explore the biology of cardiac PKC isozymes. The availability of transgenic mice and peptide PKC modulators have been instrumental in identifying target substrates for activated cardiac PKC isozymes, as well as the identification of specific isozymes linked to distinct growth characteristics and cell phenotype. The rapid growth of knowledge in the area of PKC signaling and PKC substrate interactions, may result in the development of therapeutic modalities with the potential to arrest or reverse the progression of cardiovascular diseases.     

Molecular biology of protein kinase C signaling in cardiac myocytes.

The PKC family of serine/threonine kinases have been implicated in a diverse array of cellular responses. Adult cardiac myocytes express multiple PKC isozymes, which participate in the response of muscle cells to extracellular stimuli, modulate contractile properties, and promote cell growth and survival. Recently, the classification of this ubiquitous family of signaling molecules has been expanded from three to four subfamilies. This review will focus on the application of pharmacologic and molecular approaches to explore the biology of cardiac PKC isozymes. The availability of transgenic mice and peptide PKC modulators have been instrumental in identifying target substrates for activated cardiac PKC isozymes, as well as the identification of specific isozymes linked to distinct growth characteristics and cell phenotype. The rapid growth of knowledge in the area of PKC signaling and PKC substrate interactions, may result in the development of therapeutic modalities with the potential to arrest or reverse the progression of cardiovascular diseases.     

Inferring pH from diatoms: a comparison of old and new calibration methods

Two new methods for inferring pH from diatoms are presented. Both are based on the observation that the relationships between diatom taxa and pH are often unimodal. The first method is maximum likelihood calibration based on Gaussian logit response curves of taxa against pH. The second is weighted averaging. In a lake with a particular pH, taxa with an optimum close to the lake pH will be most abundant, so an intuitively reasonable estimate of the lake pH is to take a weighted average of the pH optima of the species present.Optima and tolerances of diatom taxa were estimated from contemporary pH and proportional diatom counts in littoral zone samples from 97 pristine soft water lakes and pools in Western Europe. The optima showed a strong relation with Hustedt's pH preference groups. The two new methods were then compared with existing calibration methods on the basis of differences between inferred and observed pH in a test set of 62 additional samples taken between 1918 and 1983. The methods were ranked in order of performance as follows (between brackets the standard error of inferred pH in pH units); maximum likelihood (0.63) > weighted averaging (0.71) = multiple regression using pH groups (0.71) = the Gasse & Tekaia method (0.71) > Renberg & Hellberg's Index B (0.83) » multiple regression using taxa (2.2). The standard errors are larger than those usually obtained from surface sediment samples. The relatively large standard may be due to seasonal variation and to the effects of other factors such as humus content. The maximum likelihood method is statistically rigorous and can in principle be extended to allow for additional environmental factors. It is computer intensive however. The weighted averaging approach is a good approximation to the maximum likelihood method and is recommended as a practical and robust alternative.     

Multiple site dissimilarity quantifies compositional heterogeneity among several sites,while average pairwise dissimilarity may be misleading

Several measures of multiple site dissimilarity have been proposed to quantify the overall heterogeneity in assemblage composition among any number of sites. It is also a common practice to quantify such overall heterogeneity by averaging pairwise dissimilarities between all pairs of sites in the pool. However, pairwise dissimilarities do not account for patterns of co‐occurrence among more than two sites. In consequence, the average of pairwise dissimilarities may not accurately reflect the overall compositional heterogeneity within a pool of more than two sites. Here I use several idealized examples to illustrate why pairwise dissimilarity measures fail to properly quantify overall heterogeneity. Thereafter, the effect of this potential problem in empirical patterns is exemplified with data of world amphibians. In conclusion, when the attribute of interest is the overall heterogeneity in a pool of sites (i.e. beta diversity) or its turnover or nestedness components, only multiple site dissimilarity measures are recommended.     

Manipulation of cellular redox parameters for improving therapeutic responses in B-cell lymphoma and multiple myeloma

Developing novel combined-modality therapeutic approaches based on understanding of the involvement of redox biology in apoptosis of malignant cells is a promising approach for improving clinical responses in B-cell lymphoma and multiple myeloma. Therapeutic modalities that generate reactive oxygen species (i.e., radiation, photodynamic therapy, and specific chemotherapeutic drugs) have been shown to be selectively cytotoxic to malignant B-cells. In this review, we will discuss agents that induce apoptosis in B-cell tumors by oxidative stress. Subsequently, a novel biochemical rationale (based on fundamental differences in cancer vs. normal cell oxidative metabolism) for combining oxidative stressors with radiotherapy and chemotherapy, that may lead to designing of more effective treatment strategies for B-cell malignancies, will be discussed. Besides providing potential curative benefit, such novel therapies could also selectively target and inhibit the emergence of drug-resistance in tumor cells, which is a major determinant of treatment failure in many B-cell malignancies.     

Oppugning the assumptions of spatial averaging of segment and joint orientations

Movement scientists frequently calculate “arithmetic averages” when examining body segment or joint orientations. Such calculations appear routinely, yet are fundamentally flawed. Three-dimensional orientation data are computed as matrices, yet three-ordered Euler/Cardan/Bryant angle parameters are frequently used for interpretation. These parameters are not geometrically independent; thus, the conventional process of averaging each parameter is incorrect. The process of arithmetic averaging also assumes that the distances between data are linear (Euclidean); however, for the orientation data these distances are geodesically curved (Riemannian). Therefore we question (oppugn) whether use of the conventional averaging approach is an appropriate statistic. Fortunately, exact methods of averaging orientation data have been developed which both circumvent the parameterization issue, and explicitly acknowledge the Euclidean or Riemannian distance measures. The details of these matrix-based averaging methods are presented and their theoretical advantages discussed. The Euclidian and Riemannian approaches offer appealing advantages over the conventional technique. With respect to practical biomechanical relevancy, examinations of simulated data suggest that for sets of orientation data possessing characteristics of low dispersion, an isotropic distribution, and less than 30° second and third angle parameters, discrepancies with the conventional approach are less than 1.1°. However, beyond these limits, arithmetic averaging can have substantive non-linear inaccuracies in all three parameterized angles. The biomechanics community is encouraged to recognize that limitations exist with the use of the conventional method of averaging orientations. Investigations requiring more robust spatial averaging over a broader range of orientations may benefit from the use of matrix-based Euclidean or Riemannian calculations.     

Multimodal optical imaging

The recent resurgence of interest in the use of intravital microscopy in lung research is a manifestation of extraordinary progress in visual imaging and optical microscopy. This review evaluates the tools and instrumentation available for a number of imaging modalities, with particular attention to recent technological advances, and addresses recent progress in use of optical imaging techniques in basic pulmonary research.1 Limitations of existing methods and anticipated future developments are also identified. Although there have also been major advances made in the use of magnetic resonance imaging, positron emission tomography, and X-ray and computed tomography to image intact lungs and while these technologies have been instrumental in advancing the diagnosis and treatment of patients, the purpose of this review is to outline developing optical methods that can be evaluated for use in basic research in pulmonary biology.     

Conspecific and Heterospecific Plant Densities at Small-Scale Can Drive Plant-Pollinator Interactions

Generalist pollinators are important in many habitats, but little research has been done on small-scale spatial variation in interactions between them and the plants that they visit. Here, using a spatially explicit approach, we examined whether multiple species of flowering plants occurring within a single meadow showed spatial structure in their generalist pollinator assemblages.We report the results for eight plant species for which at least 200 individual visits were recorded. We found that for all of these species, the proportions of their general pollinator assemblages accounted for by particular functional groups showed spatial heterogeneity at the scale of tens of metres. This heterogeneity was connected either with no or only subtle changes of vegetation and flowering species composition. In five of these species, differences in conspecific plant density influenced the pollinator communities (with greater dominance of main pollinators at low-conspecific plant densities). The density of heterospecific plant individuals influenced the pollinator spectrum in one case.Our results indicate that the picture of plant-pollinator interactions provided by averaging data within large plots may be misleading and that within-site spatial heterogeneity should be accounted for in terms of sampling effort allocation and analysis. Moreover, spatially structured plant-pollinator interactions may have important ecological and evolutionary consequences, especially for plant population biology.     

Steady flow through a constricted cylinder by multiparticle collision dynamics

The flow characterization of blood through healthy and diseased flow geometries is of interest to researchers and clinicians alike, as it may allow for early detection, and monitoring, of cardiovascular disease. In this paper, we use a numerically efficient particle-based flow model called multiparticle collision dynamics (MPC for short) to study the effect of compressibility and slip of flow of a Newtonian fluid through a cylinder with a local constriction. We use a cumulative averaging method to compare our MPC results to the finite-element solution of the incompressible no-slip Navier-Stokes equations in the same geometry. We concentrate on low Reynolds number flows [ $Re \in (4,30)$ ] and quantify important differences observed between the MPC results and the Navier-Stokes solution in constricted geometries. In particular, our results show that upstream recirculating zones can form with the inclusion of slip and compressibility, which are not observed in the flow of an incompressible Newtonian fluid using the no-slip assumption, but have been observed experimentally for blood. Important flow features are also presented that could be used as indicators to observe compressibility and slip in experimental data where near-wall data may be difficult to obtain. Finally, we found that the cumulative averaging method used is ideal for steady particle-based flow methods, as macroscopic no-slip is readily obtained using the MPC bounce-back rule. Generally, a small spurious slip is seen using other averaging methods such as weighted spatial averages or averages over several runs, and the bounce-back rule has to be modified so as to achieve macroscopic no-slip. No modifications of the bounce-back rule were required for our simulations.     

Revealing instances of coordination among multiple cortical areas

Cognitive functions must involve interactions between several (perhaps many) cortical regions. The instances of such interactions may not be tightly time locked to any external cue. Thus averaging over repeated trials of brain activity or its spectrograms may miss these instances. Here, coordinated activity among multiple cortical locations is revealed in ongoing activity with millisecond accuracy without the need for averaging over time or frequencies. This is based on reconstructions of the cortical current dipole amplitudes at multiple points from MEG recordings. In these current dipole traces, instances of brief activity undulations (BAUs) are automatically detected and used to reveal where and when cortical points interact. The article shows that these BAUs truly represent the reorganization of activity at the cortex and are strongly connected to behavior.     

Multimodality Chamber for coregistered anatomical and molecular imaging of small animals

Modern imaging methods are applied extensively in translational animal research, and combined analysis of anatomical and functional imaging results is of increasing importance. Many imaging centers handle multiple independent animal colonies and use several imaging modalities, often in combination. The authors have developed and successfully tested a two-piece acrylic Multimodality Chamber that enables investigators to coregister images from two or more modalities, including microMR, microCT, microPET and optical imaging.     

Biotechnological exploitation of bacteriophage research

The experimentally amenable nature of phage and their use in testing fundamental biological questions have meant that phage research has had a profound effect on modern molecular biology. Phage research has also fuelled multiple biotechnological developments. For example, phage display has recently been harnessed in a multidisciplinary approach for the generation of novel nanotechnologies. In addition, with the emerging threat of antibiotic-resistant bacterial infections, phage have begun to provide technologies to combat these problems. Finally, recent data acquired from genome sequencing and advances in phage biology research have aided the development of phage-derived bacterial detection and treatment strategies in addition to methods to control the detrimental effects of phage in industry. Here, we examine the promising uses of phage in these important areas of biotechnology.     

小鼠S180腹水瘤细胞在细胞生物学实验教学中的应用及注意问题

摘要细胞生物学实验教学中,经常需要使用大量相同的细胞样品。通过教学实践,作者发现小鼠S180腹水瘤细胞可作为多个实验的细胞材料。该文阐述了小鼠S180腹水瘤细胞作为细胞生物学实验教学材料的优点和准备方法,可用其进行的细胞实验及具体用法等,旨在为细胞生物学实验教学中的选材提供参考。关键词小鼠腹水瘤细胞;细胞生物学实验;实验材料     

Cross-modal associations of human body odour attractiveness with facial and vocal attractiveness provide little support for the backup signals hypothesis: A systematic review and meta-analysis

Assessing the attractiveness of potential mating partners typically involves multiple sensory modalities, including the integration of olfactory, visual, and auditory cues. However, predictions diverge on how the individual modalities should relate to each other. According to the backup signals hypothesis, multimodal cues provide redundant information, whereas the multiple messages hypothesis suggests that different modalities provide independent and distinct information about an individual's mating-related quality. The backup signals hypothesis predicts a positive association between assessments based on different modalities, whereas no substantial correlation across modalities is expected under the multiple messageshypothesis. Previous studies testing the two hypotheses have provided mixed results, and a systematic evaluation is currently missing.We performed a systematic review and a meta-analysis of published and unpublished studies to examine the congruence in assessments between human body odour and facial attractiveness, and between body odour and vocal attractiveness. We found positive but weak associations between ratings of body odours and faces (r = 0.1, k = 25), and between body odours and voices (r = 0.1, k = 9). No sex differences were observed in the magnitude of effects.Compared to judgments of facial and vocal attractiveness, our results suggest that assessment of body odour provides independent and non-redundant information about human mating-related quality. Our findings thus provide little support for the backup signals hypothesis and may be better explained by the multiple messages hypothesis.