Dual-labeled telomere sensing probes for quantification of telomerase activity assay

The present study describes an empirically discovered phenomenon that might be useful for development of a sensitive and rapid methodology for quantification of telomerase activity assay with simple data acquisition and possibility for calculation of telomerase product in absolute units. The method is based on the design and application of two single-stranded telomere sensing probes consisting of dual-labeled 16-mer oligonucleotides (fluorescent Cy3/Cy3-labeled and non-fluorescent IowaBlack/BHQ-labeled) that can simultaneously hybridize on the primary product of the telomerase reaction.     

Performance of high-throughput DNA quantification methods

Background

The accuracy and precision of estimates of DNA concentration are critical factors for efficient use of DNA samples in high-throughput genotype and sequence analyses. We evaluated the performance of spectrophotometric (OD) DNA quantification, and compared it to two fluorometric quantification methods, the PicoGreen^® assay (PG), and a novel real-time quantitative genomic PCR assay (QG) specific to a region at the human BRCA1 locus. Twenty-Two lymphoblastoid cell line DNA samples with an initial concentration of ~350 ng/uL were diluted to 20 ng/uL. DNA concentration was estimated by OD and further diluted to 5 ng/uL. The concentrations of multiple aliquots of the final dilution were measured by the OD, QG and PG methods. The effects of manual and robotic laboratory sample handling procedures on the estimates of DNA concentration were assessed using variance components analyses.

Results

The OD method was the DNA quantification method most concordant with the reference sample among the three methods evaluated. A large fraction of the total variance for all three methods (36.0–95.7%) was explained by sample-to-sample variation, whereas the amount of variance attributable to sample handling was small (0.8–17.5%). Residual error (3.2–59.4%), corresponding to un-modelled factors, contributed a greater extent to the total variation than the sample handling procedures.

Conclusion

The application of a specific DNA quantification method to a particular molecular genetic laboratory protocol must take into account the accuracy and precision of the specific method, as well as the requirements of the experimental workflow with respect to sample volumes and throughput. While OD was the most concordant and precise DNA quantification method in this study, the information provided by the quantitative PCR assay regarding the suitability of DNA samples for PCR may be an essential factor for some protocols, despite the decreased concordance and precision of this method.

     

How advancement in biological network analysis methods empowers proteomics

Proteomics provides important information--that may not be inferable from indirect sources such as RNA or DNA--on key players in biological systems or disease states. However, it suffers from coverage and consistency problems. The advent of network-based analysis methods can help in overcoming these problems but requires careful application and interpretation. This review considers briefly current trends in proteomics technologies and understanding the causes of critical issues that need to be addressed--i.e., incomplete data coverage and inter-sample inconsistency. On the coverage issue, we argue that holistic analysis based on biological networks provides a suitable background on which more robust models and interpretations can be built upon; and we introduce some recently developed approaches. On consistency, group-based approaches based on identified clusters, as well as on properly integrated pathway databases, are particularly useful. Despite that protein interactions and pathway networks are still largely incomplete, given proper quality checks, applications and reasonably sized data sets, they yield valuable insights that greatly complement data generated from quantitative proteomics.     

The role of telomere trimming in normal telomere length dynamics

Telomeres consist of repetitive DNA and associated proteins that protect chromosome ends from illicit DNA repair. It is well known that telomeric DNA is progressively eroded during cell division, until telomeres become too short and the cell stops dividing. There is a second mode of telomere shortening, however, which is a regulated form of telomere rapid deletion (TRD) termed telomere trimming that is reviewed here. Telomere trimming appears to involve resolution of recombination intermediate structures, which shortens the telomere by release of extrachromosomal telomeric DNA. This has been detected in human and in mouse cells and occurs both in somatic and germline cells, where it sets an upper limit on telomere length and contributes to a length equilibrium set-point in cells that have a telomere elongation mechanism. Telomere trimming thus represents an additional mechanism of telomere length control that contributes to normal telomere dynamics and cell proliferative potential.     

Recent developments in quantification methods for metallothionein.

The metallothioneins (MT), a family of proteins with relatively low molecular weight (6-7 kDa), are characterised by the intrinsic presence of 20 cysteinyl groups in their structure, which confers unique metal binding properties to the molecule. Since MT are involved in biological roles, quantification of MT remains an important task. To date, a large number of determination methods have been developed. In this paper recent developments, from 1995 to the present, in methodology employed in quantification studies of total MT and MT polymorphism are described. Different fields were taken into consideration, such as (i) separation techniques and hyphenated systems, (ii) electrochemical methods, (iii) immunological methods and (iv) quantification of MT mRNA. The data presented are based on our own and published results. A brief overview of the use of metallothionein as a biomarker is included as a relevant example of the importance of MT quantification. Finally, general problems associated with determination and evaluation of obtained results within the above four topics are mentioned.     

Vesiculation of bovine erythrocyte membranes: two methods of quantification

Two simple methods of quantification of the relative concentration of vesicles released from bovine erythrocyte membranes are described. Turbidimetric and nephelometric measurements need only a typical spectrophotometer and spectrofluorimeter and could be employed for studying not only vesicles, but the turbidity of various suspensions.     

受体活性修饰蛋白研究进展

受体活性修饰蛋白(receptor activity-modifying proteins,RAMPs)属于单跨膜蛋白家族,分三个结构域,RAMP的N端和跨膜区决定本身的功能和受体表型,胞内C端对于配体的信号传导和受体循环有重要作用。目前发现有三个成员:RAMP1、RAMP2和RAMP3。RAMPs通过改变G蛋白偶联受体的糖基化,作用于配体结合区域来调节受体表型。RAMP1与降钙素受体样受体(calcitonin receptor like receptor,CRLR)结合表现出降钙素基因相关肽(calcitonin gene-related peptide,CGRP)受体表型:RAMP2和RAMP3与CRLR结合则对肾上腺髓质素(adrenomedullin,AM)表现高亲和力,与降钙素受体(calcitonin receptor,CTR)结合则作为胰淀粉样酶(amylin,AMY)受体。由此可见,RAMPs不仅调节受体与配体结合,还影响细胞内的蛋白相互作用调节细胞内信号传导来影响细胞的增殖、迁移、分化等生物学特性。RAMPs还对心血管系统的病理生理有重要调节作用。     

Different chain length specificity among three polyphosphate quantification methods

Polyphosphate is ubiquitous among living organisms and has a variety of biochemical functions. Arbuscular mycorrhizal fungi have been known to accumulate polyphosphate as a key compound for their function. However, an enzymatic assay using polyphosphate kinase (PPK) reverse reaction, in which polyphosphate is converted to adenosine triphosphate (ATP) and quantified by luciferase assay, failed to detect accumulation of polyphosphate in some mycorrhizal root. When yeast exopolyphosphatase (PPX) was applied to these samples, a much higher polyphosphate level was detected than when the PPK assay was applied. Detailed analysis of substrate chain length specificity of these methods using polyphosphate chain length standards revealed that the PPX method was the most appropriate to detect short-chain polyphosphate. The average chain length of the shortest polyphosphate fraction that could be quantified with more than 50% efficiency was 3 for the PPX method and 38 for the PPK method. It was also suggested that the ratio of the PPK value to the PPX value may be useful as a simple and relative index to compare polyphosphate chain length distribution in different samples.     

Real-time PCR quantification of Dehalococcoides populations: methods and applications

Dehalococcoides species are responsible for the reductive dehalogenation of an impressive range of common, persistent environmental contaminants. These microorganisms are difficult to both obtain and grow in pure culture, and so are often studied while they exist in consortia using molecular techniques. In particular, a significant number of quantitative real-time PCR (qPCR) assays targeting Dehalococcoides spp. have been reported. Initial qPCR methods targeted the 16S rRNA gene, however, because strains with the same 16S rRNA gene sequence can have different dehalogenating abilities, reductive dehalogenase genes are now emerging as the most appropriate qPCR target. Quantitative PCR has been critical to our current understanding of Dehalococcoides populations; it has provided information on their growth characteristics, dehalogenating abilities and effective use in bioremediation efforts. Future qPCR research directions will likely involve method standardization, as well as continued research on the functional genes associated with Dehalococcoides populations.     

Comparison of four methods for quantification of biofilms in biphasic cultures

Three methods for determining the total biofilm amount in biphasic cultures have been compared: dry weight by filtration after solvent treatment, optical density with a biomass probe and protein content. The activity of the biofilm was estimated through mineral nitrogen consumption. Calculation of the coefficients of variation shows that these parameters could be used to characterise such a biofilm. The optical density by biomass probe was the most reliable one (repeatability <0.5%) to quantify total biofilm and a linear relation was verified against dry weight. © Rapid Science Ltd. 1998     

Critical assessment of current adeno-associated viral vector production and quantification methods

Adeno-associated viral vectors have emerged as one of the most studied vectors for gene therapy. Numerous production methods have been described, each with its advantages and disadvantages. A challenge in assessing the current state of the art exists in comparing yields from one production system to the next due to the wide variety of quantification techniques. In this review, AAV vector production methods are summarized and the yields of the different processes are standardized to the number of harvested cells. Titers are further streamlined into five categories: transduction units, enhanced transduction units, infectious particles, DNase-resistant particles and total particles, and the importance of each type of measure is discussed.     

The telomere bouquet controls the meiotic spindle

Bouquet formation, in which telomeres gather to a small region of the nuclear membrane in early meiosis, has been observed in diverse eukaryotes, but the function of the bouquet has remained a mystery. Here, we demonstrate that the telomere bouquet plays a crucial role in controlling the behavior of the fission yeast microtubule-organizing center (known as the spindle pole body or SPB) and the meiotic spindle. Using mutations that specifically disrupt the bouquet, we analyze chromosome, SPB, and spindle dynamics throughout meiosis. If the bouquet fails to form, the SPB becomes fragmented at meiosis I, leading to monopolar, multiple, and mislocalized spindles. Correct SPB and spindle behavior require not only the SPB recruitment of telomere proteins but also that the proteins are properly bound to telomeric DNA. This discovery illuminates an unanticipated level of communication between chromosomes and the spindle apparatus that may be widely conserved among eukaryotes.     

Posttranslational control of telomere maintenance and the telomere damage response

Telomeres help maintain genome integrity by protecting natural chromosome ends from being recognized as damaged DNA. When telomeres become dysfunctional, they limit replicative lifespan and prevent outgrowth of potentially cancerous cells by activating a DNA damage response that forces cells into senescence or apoptosis. On the other hand, chromosome ends devoid of proper telomere protection are subject to DNA repair activities that cause end-to-end fusions and, when cells divide, extensive genomic instability that can promote cancer. While telomeres represent unique chromatin structures with important roles in cancer and aging, we have limited understanding of the way telomeres and the response to their malfunction are controlled at the level of chromatin. Accumulating evidence indicates that different types of posttranslational modifications act in both telomere maintenance and the response to telomere uncapping. Here, we discuss the latest insights on posttranslational control of telomeric chromatin, with emphasis on ubiquitylation and SUMOylation events.