A new method for isolating pollen and spores from acetate peels for scanning electron microscopy

A procedure for precisely extracting pollen and spores from cellulose acetate peels made from Carboniferous permineralizations is described. This technique produces either whole or sectioned clean grains and allows for the correlation of morphological and ultrastructural features by scanning electron microscopy. The critical examination of pollen and spores from peels prepared for earlier studies is now possible using this technique.     

Minimotif Miner: a tool for investigating protein function

In addition to large domains, many short motifs mediate functional post-translational modification of proteins as well as protein-protein interactions and protein trafficking functions. We have constructed a motif database comprising 312 unique motifs and a web-based tool for identifying motifs in proteins. Functional motifs predicted by MnM can be ranked by several approaches, and we validated these scores by analyzing thousands of confirmed examples and by confirming prediction of previously unidentified 14-3-3 motifs in EFF-1.     

Cellular reprogramming: a novel tool for investigating autism spectrum disorders

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by impairment in reciprocal social interaction and communication, as well as the manifestation of stereotyped behaviors. Despite much effort, ASDs are not yet fully understood. Advanced genetics and genomics technologies have recently identified novel ASD genes, and approaches using genetically engineered murine models or postmortem human brain have facilitated understanding ASD. Reprogramming somatic cells into induced pluripotent stem cells (iPSCs) provides unprecedented opportunities in generating human disease models. Here, we present an overview of applying iPSCs in developing cellular models for understanding ASD. We also discuss future perspectives in the use of iPSCs as a source of cell therapy and as a screening platform for identifying small molecules with efficacy for alleviating ASD.     

siRNA as a tool for investigating organogenesis: The pitfalls and the promises

Removing the function of a specific gene from a developing organ, by making a ‘knockout’ mouse, is a powerful method for analyzing the molecular pathways that control organogenesis. The technique is expensive, though, in terms of time and money, and complex strategies for producing conditional knockouts are needed for genes that are essential for early development of the embryo, for which an unconditional knockout would be lethal before the organ of interest begins to form. Small interfering RNAs (siRNAs) offer a method of knocking down the expression of specific genes with no need for genomic manipulation. Almost as soon as they had been discovered, siRNAs began to be used to explore the molecular biology of mammalian cells in conventional, two-dimensional culture. They have now also been applied successfully, by several groups, to knock down specific genes in various organ rudiments developing in organ culture. This article reviews the basic technique of siRNA-mediated gene knockdown and how it is being applied to organ culture. It also reviews some of the current problems and challenges in the field, and the ways in which these problems are likely to be overcome.Key words: siRNA, RNAi, organ culture, organogenesis, organ development, 3D culture     

Dispersal of spores and pollen from crops

Fungal spores and pollens can be dispersed in a number of ways: by animals and insects; by water; by wind or by rain. This paper concentrates on the effects of wind on the dispersal of spores and pollen grains and the effects of rain on spore dispersal. For dispersal to be successful particles must complete three phases: removal, dispersal through the air and deposition. The biology of the organism and its environment can affect all three phases, however, once released the fate of all airborne particles largely depends on the laws of physics which govern the motion of the air. Many types of spore are actively ejected into the air while others are simply blown from the host surface. Particle size and shape affects dispersal and deposition phases. Local environmental factors such as temperature, humidity and light, as well as wind or rain, can play a key role in the removal of spores. Wind speed and turbulence or rainfall, largely determine spore dispersal, but, the size and shape of the particle, the nature of the plant canopy and the way the particles are released into the air may also be important. Particle deposition depends on both environmental and biological factors. This paper briefly considers these processes using examples and how they can be modelled.     

Fixation of microsporidian spores for electron microscopy

Fresh and frozen spores of the microsporidia Nosema apis and Nosema bombi were fixed using various fixatives at different times and temperatures. Paraformaldehyde and technical formaldehyde gave results comparable to or better than glutaraldehyde. Increased fixation temperature improved the fixation of spores from terrestrial hosts. Freezing did not destroy the cytology of the spore.     

Electron microscopy as a quantitative method for investigating tau fibrillization

Fibrillization of tau protein is a hallmark lesion in Alzheimer's disease. To clarify the utility of electron microscopy as a quantitative assay for tau fibrillization in vitro, the interaction between synthetic tau filaments and carbon/formvar-coated grids was characterized in detail. Filament adsorption onto grids was hyperbolic when analyzed as a function of time or bulk protein concentration, with no evidence for competitive displacement or elution from other components in the reaction mixture. Filament length measurements were linear with filament concentration so long as the concentration of total tau protein in the sample was held constant, suggesting that measurement of filament lengths was accurate under these conditions. Furthermore, exponential filament length distributions were not significantly affected by adsorption time or filament concentration, suggesting that preferential binding among filaments of differing lengths was minimal. However, monomeric tau protein was found to be a strong competitor of filament adsorption, indicating that comparison of filament length measurements at different bulk tau concentrations should be interpreted with caution.     

Semiautomatic microscopy as a tool for cytologists

Despite impressive advances in the application of computer image analysis to cytology, many of the identification tasks that cytologists are called on to perform remain refractory to automated image analysis. The major reason is that a large fraction of these images, though simple for a human to deal with, are too complex to yield to current image analysis methodologies. It may be years before automated computer image analysis is reduced to clinical practicality. Even then, it is not clear that all cytologic image analyses will prove amenable to automation. In the meantime, semiautomatic image analysis (computer-aided microscopy) can provide a viable alternative, especially to persistently difficult image analysis problems. In semiautomatic image analysis, the onerous tasks of data acquisition--e.g., stage movement, data entry and storage--are left to the computer, while the decision-making tasks-e.g., identifying a cell's morphologic class--are left to the observer. Such a system proves to be easy and flexible to use as well as economical to build. It can also provide a reliable data base for the later evaluation of fully automated systems as they are developed. One such semiautomatic system, the Image Combining Computer Microscope (ICCM), is described, and the range of its application is illustrated. Some of the examples of ICCM applications discussed are: neuronal cell plots, three-dimensional dendrite tracking, serial section reconstruction of axons and mapping of plaques and tangles in Alzheimer's disease. They illustrate how powerful a semiautomated system can be in handling complex image analysis problems. It is suggested that semiautomated image analysis provides a viable long-range alternative to many cytologic image analysis problems.     

Second harmonic generation microscopy: a powerful tool for bio-imaging

Second harmonic generation (SHG) microscopy is an important optical imaging technique in a variety of applications. This article describes the history and physical principles of SHG microscopy and its more advanced variants, as well as their strengths and weaknesses in biomedical applications. It also provides an overview of SHG and advanced SHG imaging in neuroscience and microtubule imaging and how these methods can aid in understanding microtubule formation, structuration, and involvement in neuronal function. Finally, we offer a perspective on the future of these methods and how technological advancements can help make SHG microscopy a more widely adopted imaging technique.     

Capsules with Lycopodium spores for absolute diatom and pollen analysis

Lycopodium spore capsules have been produced as a slight modification of the widely used Lycopodium spore tablets introduced by Stockmarr in 1971. The spore content is increased in the capsules to facilitate their use in absolute diatom analysis.     

Enhanced CellClassifier: a multi-class classification tool for microscopy images

Background  

Light microscopy is of central importance in cell biology. The recent introduction of automated high content screening has expanded this technology towards automation of experiments and performing large scale perturbation assays. Nevertheless, evaluation of microscopy data continues to be a bottleneck in many projects. Currently, among open source software, CellProfiler and its extension Analyst are widely used in automated image processing. Even though revolutionizing image analysis in current biology, some routine and many advanced tasks are either not supported or require programming skills of the researcher. This represents a significant obstacle in many biology laboratories.     

光学显微镜下细菌芽孢染色方法的探讨

由于细菌芽孢对水溶性染料具有较强的抗性,造成芽孢的染色较困难。加热、酸水解、机械摩擦等措施均可以提高芽孢的染色性能,对这些处理方法的优缺点进行分析,并对常规使用的Moeller法进行了改进,提出了一种更适合于微生物学实验课堂教学的细菌芽孢鉴别染色方法。     

Modelling germination kinetics of spores of Clostridium tyrobutyricum: a tool for predictive microbiology

Germination of spores of Clostridium tyrobutyricum between 9° and 45°C was followed by the decrease in optical density of the spore suspension. An empirical equation with three parameters is proposed to describe the time-course of spore germination. Each parameter of the model has a direct biological significance and is modelled vs temperature. In the framework of predictive microbiology, the equation may be used for the prediction of the overall lag time of growth.     

Modern pollen assemblages from Reasi (Jammu and Kashmir), India: a tool for interpreting fossil pollen records

Twenty five surface samples/moss cushions were collected for palynological analysis from open areas of Reasi District, Jammu and Kashmir (India). These samples were used to investigate the relationships between extant vegetation and modern pollen spectra, which serve as modern analogue for the reliable ecological interpretation of fossil pollen records. The present vegetation in the region comprises tropical dry deciduous forests and subtropical pine forests with scattered stands of oak. The pollen analysis reveals that Pinus sp. (average 69% in the pollen assemblages), amongst the conifers, dominates the pollen rain, which can be attributed to its high pollen productivity and exceptional pollen dispersal efficiency. Cedrus sp. and Podocarpus sp. pollen contribute with an average of 16 and 5% to the total pollen rain. Other conifers such as Picea sp., Abies sp., Juniperus sp. and Tsuga sp., as well as broad-leaved taxa such as Quercus sp., Alnus sp., Betula sp., Carpinus sp., Corylus sp., Juglans sp., Ulmus sp., Salix sp., Elaeocarpus sp., Mallotus sp. and Aesculus sp., have lower averages of 1 to 4.5% in the total pollen rain which could be either due to their poor pollen dispersal efficiency or to the poor preservation in the samples. Tubuliflorae (average 25%), Poaceae (average 6.26%), Cerealia and other crop plants (average 7.68%) are other prominent taxa in the pollen rain. The nearly complete absence of members of tropical dry deciduous forests in the pollen spectra likely is due to the fact that most species in this vegetation type are not wind pollinated.     

Photochemistry as a tool in investigating ionic channels: Photoaffinity probes

TPMP is a noncompetitive inhibitor of the nicotinic acetycholine receptor which blocks agonist-induced ion flux by directly interacting with the receptor's ion channel. By activation with UV light it can be made to react covalently with its binding site in the receptor protein. Here a method is described to perform this photolabeling with a time resolution comparable to the physiological event of channel opening and closing. By this technique structural transitions within the receptor can be visualized and transient conformational states can be labeled covalently and irreversibly.     

Mathematical modeling as a tool for investigating cell cycle control networks

Although not a traditional experimental "method," mathematical modeling can provide a powerful approach for investigating complex cell signaling networks, such as those that regulate the eukaryotic cell division cycle. We describe here one modeling approach based on expressing the rates of biochemical reactions in terms of nonlinear ordinary differential equations. We discuss the steps and challenges in assigning numerical values to model parameters and the importance of experimental testing of a mathematical model. We illustrate this approach throughout with the simple and well-characterized example of mitotic cell cycles in frog egg extracts. To facilitate new modeling efforts, we describe several publicly available modeling environments, each with a collection of integrated programs for mathematical modeling. This review is intended to justify the place of mathematical modeling as a standard method for studying molecular regulatory networks and to guide the non-expert to initiate modeling projects in order to gain a systems-level perspective for complex control systems.     

Droplet digital PCR as a tool for investigating dynamics of cryptic symbionts

Interactions among symbiotic organisms and their hosts are major drivers of ecological and evolutionary processes. Monitoring the infection patterns among natural populations and identifying factors affecting these interactions are critical for understanding symbiont–host relationships. However, many of these interactions remain understudied since the knowledge about the symbiont species is lacking, which hinders the development of appropriate tools. In this study, we developed a digital droplet PCR (ddPCR) assay based on apicomplexan COX1 gene to detect an undescribed agamococcidian symbiont. We show that the method gives precise and reproducible results and enables detecting cryptic symbionts in low target concentration. We further exemplify the assay''s use to survey seasonally sampled natural host (Pygospio elegans) populations for symbiont infection dynamics. We found that symbiont prevalence differs spatially but does not show seasonal changes. Infection load differed between populations and was low in spring and significantly increased towards fall in all populations. We also found that the symbiont prevalence is affected by host length and population density. Larger hosts were more likely to be infected, and high host densities were found to have a lower probability of infection. The observed variations could be due to characteristics of both symbiont and host biology, especially the seasonal variation in encounter rates. Our findings show that the developed ddPCR assay is a robust tool for detecting undescribed symbionts that are otherwise difficult to quantify, enabling further insight into the impact cryptic symbionts have on their hosts.