Visualizing Single-molecule DNA Replication with Fluorescence Microscopy

We describe a simple fluorescence microscopy-based real-time method for observing DNA replication at the single-molecule level. A circular, forked DNA template is attached to a functionalized glass coverslip and replicated extensively after introduction of replication proteins and nucleotides (Figure 1). The growing product double-strand DNA (dsDNA) is extended with laminar flow and visualized by using an intercalating dye. Measuring the position of the growing DNA end in real time allows precise determination of replication rate (Figure 2). Furthermore, the length of completed DNA products reports on the processivity of replication. This experiment can be performed very easily and rapidly and requires only a fluorescence microscope with a reasonably sensitive camera.     

Honey, I shrunk the DNA: DNA length as a probe for nucleic-acid enzyme activity

The replication, recombination, and repair of DNA are processes essential for the maintenance of genomic information and require the activity of numerous enzymes that catalyze the polymerization or digestion of DNA. This review will discuss how differences in elastic properties between single- and double-stranded DNA can be used as a probe to study the dynamics of these enzymes at the single-molecule level.     

The predictive value of vitamin B12 concentrations and hyperhomocysteinaemia for cardiovascular disease

Background. Cardiovascular disease has been associated with both homocysteine and vitamin B12 levels. However, little information is available about the mutual relation in cardiovascular patients. The aim of this study was to assess the prevalence of vitamin B12 deficiency in patients with cardiovascular disease, and to study the correlation with homocysteine levels. Methods. Blood samples were taken from 229 patients who had been admitted to the Coronary Care Unit of the Heart-Lung Centre of the Radboud University Medical Centre in Nijmegen, the Netherlands. Patient demographics and clinical characteristics were assessed from medical files. Adjusted logistic regression was used to study the associations between vitamin B12, homocysteine and ischaemic heart disease. Results. In 70 patients (33%) serum vitamin B12 levels were below the lower limit of normal (<203 ng/l). Sixty-nine patients (33%) had vitamin B12 concentrations in the lower normal range (between 203 and 339 ng/l). Plasma homocysteine levels above the upper limit of normal were found in 83 out of the 229 patients (36%). Adjusted odds ratios for both vitamin B12 (0.76, 95% CI 0.44-1.30) and homocysteine (1.27, 95% CI 0.74-2.18) levels did not show a statistical association with ischaemic heart disease. No association was found between serum vitamin B12 levels and plasma homocysteine. Conclusion. Our data suggest that hyperhomocysteinaemia and low serum vitamin B12 concentrations are independent and cannot be used as a diagnostic tool for ischaemic heart disease. (Neth Heart J 2007;15:291-4.)     

Major adverse cardiovascular events in older emergency department patients presenting with non-cardiac medical complaints

Netherlands Heart Journal - The risk of major adverse cardiovascular events (MACE) for older emergency department (ED) patients presenting with non-cardiac medical complaints is unknown. To apply...     

Endocytosis by random initiation and stabilization of clathrin-coated pits

Clathrin-coated vesicles carry traffic from the plasma membrane to endosomes. We report here the real-time visualization of cargo sorting and endocytosis by clathrin-coated pits in living cells. We have detected the formation of coats by monitoring incorporation of fluorescently tagged clathrin or its adaptor AP-2; we have also followed clathrin-mediated uptake of transferrin and of single LDL or reovirus particles. The intensity of a cargo-loaded clathrin cluster grows steadily during its lifetime, and the time required to complete assembly is proportional to the size of the cargo particle. These results are consistent with a nucleation-growth mechanism and an approximately constant growth rate. There are no strongly preferred nucleation sites. A proportion of the nucleation events are weak and short lived. Cargo incorporation occurs primarily or exclusively in a newly formed coated pit. Our data lead to a model in which coated pits initiate randomly but collapse unless stabilized, perhaps by cargo capture.     

The likely impact of elevated [CO2], nitrogen deposition, increased temperature and management on carbon sequestration in temperate and boreal forest ecosystems: a literature review

Temperate and boreal forest ecosystems contain a large part of the carbon stored on land, in the form of both biomass and soil organic matter. Increasing atmospheric [CO2], increasing temperature, elevated nitrogen deposition and intensified management will change this C store. Well documented single-factor responses of net primary production are: higher photosynthetic rate (the main [CO2] response); increasing length of growing season (the main temperature response); and higher leaf-area index (the main N deposition and partly [CO2] response). Soil organic matter will increase with increasing litter input, although priming may decrease the soil C stock initially, but litter quality effects should be minimal (response to [CO2], N deposition, and temperature); will decrease because of increasing temperature; and will increase because of retardation of decomposition with N deposition, although the rate of decomposition of high-quality litter can be increased and that of low-quality litter decreased. Single-factor responses can be misleading because of interactions between factors, in particular those between N and other factors, and indirect effects such as increased N availability from temperature-induced decomposition. In the long term the strength of feedbacks, for example the increasing demand for N from increased growth, will dominate over short-term responses to single factors. However, management has considerable potential for controlling the C store.     

A detailed one-dimensional model of combustion of a woody biomass particle

A detailed one-dimensional model for combustion of a single biomass particle is presented. It accounts for particle heating up, pyrolysis, char gasification and oxidation and gas phase reactions within and in the vicinity of the particle. The biomass pyrolysis is assumed to take place through three competing reactions yielding char, light gas and tar. The model is validated using different sets of experiments reported in the literature. Special emphasis is placed on examination of the effects of pyrolysis kinetic constants and gas phase reactions on the combustion process which have not been thoroughly discussed in previous works. It is shown that depending on the process condition and reactor temperature, correct selection of the pyrolysis kinetic data is a necessary step for simulation of biomass particle conversion. The computer program developed for the purpose of this study enables one to get a deeper insight into the biomass particle combustion process.     

Timing, Coordination, and Rhythm: Acrobatics at the DNA Replication Fork

In DNA replication, the antiparallel nature of the parental duplex imposes certain constraints on the activity of the DNA polymerases that synthesize new DNA. The leading-strand polymerase advances in a continuous fashion, but the lagging-strand polymerase is forced to restart at short intervals. In several prokaryotic systems studied so far, this problem is solved by the formation of a loop in the lagging strand of the replication fork to reorient the lagging-strand DNA polymerase so that it advances in parallel with the leading-strand polymerase. The replication loop grows and shrinks during each cycle of Okazaki fragment synthesis. The timing of Okazaki fragment synthesis and loop formation is determined by a subtle interplay of enzymatic activities at the fork. Recent developments in single-molecule techniques have enabled the direct observation of these processes and have greatly contributed to a better understanding of the dynamic nature of the replication fork. Here, we will review recent experimental advances, present the current models, and discuss some of the exciting developments in the field.     

Single-molecule analysis of DNA replication in Xenopus egg extracts

The recent advent in single-molecule imaging and manipulation methods has made a significant impact on the understanding of molecular mechanisms underlying many essential cellular processes. Single-molecule techniques such as electron microscopy and DNA fiber assays have been employed to study the duplication of genome in eukaryotes. Here, we describe a single-molecule assay that allows replication of DNA attached to the functionalized surface of a microfluidic flow cell in a soluble Xenopus leavis egg extract replication system and subsequent visualization of replication products via fluorescence microscopy. We also explain a method for detection of replication proteins, through fluorescently labeled antibodies, on partially replicated DNA immobilized at both ends to the surface.     

mKikGR,a Monomeric Photoswitchable Fluorescent Protein

The recent demonstration and utilization of fluorescent proteins whose fluorescence can be switched on and off has greatly expanded the toolkit of molecular and cell biology. These photoswitchable proteins have facilitated the characterization of specifically tagged molecular species in the cell and have enabled fluorescence imaging of intracellular structures with a resolution far below the classical diffraction limit of light. Applications are limited, however, by the fast photobleaching, slow photoswitching, and oligomerization typical for photoswitchable proteins currently available. Here, we report the molecular cloning and spectroscopic characterization of mKikGR, a monomeric version of the previously reported KikGR that displays high photostability and switching rates. Furthermore, we present single-molecule imaging experiments that demonstrate that individual mKikGR proteins can be localized with a precision of better than 10 nanometers, suggesting their suitability for super-resolution imaging.