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.

     

A new group-selection model for the evolution of homosexuality

Abstract. Scientists have long puzzled over how homosexual orientation has evolved, given the assumed low relative fitness of homosexual individuals compared to heterosexual individuals. A number of theoretical models for the evolution of homosexuality have been postulated including balance polymorphism, "Fertile females", hypervariability of DNA sequences, kin selection, and "parental manipulation". In this paper, I propose a new group-selection model for the evolution of homosexuality which offers two advantages over existing models: (1) its non-assumption of genetic determinism, and (2) its lack of dependency on an inefficient altruism relation and family dynamics theory.     

Detection and differentiation of yellow head complex viruses using monoclonal antibodies

Three monoclonal antibodies (MAbs) raised against pathogenic yellow head virus (YHV) from Thailand were tested against tissues of shrimp from Thailand, Australia, Ecuador and India that were purported to be infected with yellow head complex viruses. MAbs V-3-2B and Y-18 were specific to gp116 and gp64 envelope proteins, respectively, while Y-19 was specific to a 20 kDa putative nucleoprotein p20. As a preliminary step, the site of reactivity of the 3 MAbs in YHV was determined by immuno-electron microscopy using ultra-thin sections of YHV-infected shrimp tissue and negatively stained, semi-purified YHV particles. As expected, MAb Y-19 reacted with viral nucleocapsids in ultra-thin sections but not with negatively stained, whole virions; MAb V-3-2B did react with negatively stained, whole virions, but not with virions or nucleocapsids in ultra-thin sections. Unexpectedly, MAb Y-18 did not react with whole or sectioned virions. By immunohistochemistry, MAbs Y-19 and Y-18 reacted with Penaeus monodon tissues infected with either YHV or with gill-associated virus (GAV) from Australia, while MAb V-3-2B reacted with YHV only. In addition, all the YHV and GAV tissue samples gave positive in situ hybridization reactions with a cDNA probe specific to the ORF1b gene of YHV. They also gave expected differential RT-PCR results for YHV and GAV. By contrast, 2 natural Thai shrimp specimens with no gross signs of disease gave similar immunohistochemical reactions and RT-PCR reactions to GAV. However, sequencing of their RT-PCR products showed that they shared 92.7% identity with GAV, but only 79.0% identity with YHV. Although specimens from Ecuador and India displayed histopathology suggestive of YHV infection, they gave negative immunohistochemical reactions with all 3 Mabs, and negative in situ hybridization results. Additional work is required to determine whether a virus from the yellow head complex was responsible for their observed histopathology. These data show that the 3 YHV MAbs could be used in diagnostic situations to differentiate some viruses in the yellow head virus complex.     

POTS to broadband ... cable modems

There have been 3 columns talking about broadband communications and now at the very end when it's time to compare using a telco or cableco, I'm asking does it really matter? So what if I can actually get the whole 30 Mbps with a cable network when the website I'm connecting to is running on an ISDN line at 128 Kbps? Broadband offers a lot more bandwidth than the connections many Internet servers have today. Except for the biggest websites, many servers connect to the Internet with a switched 56-Kbps, ISDN, or fractional T1 line. Even with the big websites, my home network only runs a 10 Mbps Ethernet connection to my cable modem. Maybe it doesn't matter that the cable lines are shared or that I can only get 8 Mbps from an ADSL line. Maybe the ISP that I use has a T1 line connection to the Internet so my new ADSL modem has a fatter pipe than my provider! (See table 1). It all makes me wonder what's in store for us in the future. PC technology has increased exponentially in the last 10 years with super fast processor speeds, hard disks of hundreds of gigabytes, and amazing video and audio. Internet connection speeds have failed to keep the same pace. Instead of hundreds of times better or faster--modem speeds are barely 10 times faster. Broadband connections offer some additional speed but still not comparable growth as broadband connections are still in their infancy. Rather than trying to make use of existing communication paths, maybe we need a massive infrastructure makeover of something new. How about national wireless access points so we can connect anywhere, anytime? To use the latest and fastest wireless technology you will simply need to buy another $9.95 WLAN card or download the latest super slick WLAN compression/encryption software. Perhaps it is time for a massive infra-restructuring. Consider the past massive infrastructure efforts. The telcos needed to put in their wiring infrastructure starting in the 1870s before telephones were useful to the masses. CATV was a minor player in the TV broadcast business before they installed their cabling infrastructure and went national. Even automobiles were fairly useless until roads were paved and the highway infrastructure was built!     

Cyclic amine sulfonamides as linkers in the design and synthesis of novel human beta(3) adrenergic receptor agonists

Piperidine, pyrrolidine, and azetidine sulfonamides were examined as linkers in designing novel human beta(3) adrenergic receptor (beta(3)-AR) agonists. The azetidine derivative 37, and piperidine derivatives 7, 8, and 13 were found to be potent beta(3)-AR agonists and have good selectivity against beta(1)- and beta(2)-AR.     

Analysis of HPC1, HPCX, and PCaP in Icelandic hereditary prostate cancer

Putative prostate cancer susceptibility loci have recently been identified by genetic linkage analysis on chromosomes 1q24-25 (HPC1). 1q44.243 (PCaP), and Xq27-28 (HPCX). In order to estimate the genetic linkage in Icelandic prostate cancer families, we genotyped 241 samples from 87 families with eleven markers in the HPC1 region, six markers at PCaP, and eight at HPCX. Concurrently, we assessed allelic imbalance at the HPC1 and PCaP loci in selected tumors from the patients. For each of the candidate regions, the combined parametric and non-parametric LOD scores were strongly negative. Evidence for linkage allowing for genetic heterogeneity was also insignificant for all the regions. The results were negative irrespective of whether calculations were performed for the whole material or for a selected set of early age at onset families. The prevalence of allelic imbalance was relatively low in both the HPC1 (0%-9%) and PCaP (5%-20%) regions and was not elevated in tumors from positively linked families. Our studies indicate that the putative cancer susceptibility genes at chromosomes 1q24-25, 1q44.2-43, and Xq27-28 are unlikely to contribute significantly to hereditary prostate cancer in Iceland and that selective loss of the HPC1 and PCaP loci is a relatively rare somatic event in prostate cancers.     

Apoptosis occurs in a new model of thermal brain injury

Apoptosis has been implicated recently as a prominent response of the brain to a variety of insults, such as ischemia and trauma. In this study, we demonstrate that apoptosis is a prominent part of the brain's response to a thermal insult. To examine the brain's response to a thermal insult, a new model of thermal brain injury in the laboratory rat was developed. Water heated to 60 degrees C was passed over an area of thinned calvarium for 1 min. This resulted in an actual brain temperature of 47-48 degrees C. A uniform area of 2,3,5-triphenyl-tetrazolium chloride pallor was demonstrated and pyknotic neurons were seen in the area of injury by hematoxylin-eosin staining. Apoptosis was demonstrated by the characteristic DNA fragmentation seen by agarose gel electrophoresis, ApopTag in situ staining and electron microscopy. The findings of apoptosis were localized to the area of thermal injury and were time dependent, starting 6 h after the insult and peaking approximately 18 h after the insult. This represents one of the first demonstrations that apoptosis occurs in the brain in response to a thermal injury.     

Optimization of transient gene expression in mammalian cells and potential for scale-up using flow electroporation

The goals of this study were to identify mammalian cell lines which could be efficiently transiently-transfected and scaled-up for protein production. The transfection efficiencies of eight cell lines (NSO, NSO-TAg, CV-1, COS-7, CHO, CHO-TAg, HEK 293, and 293-EBNA) were measured using electroporation for DNA delivery and green fluorescent protein (Evans, 1996) as the reporter gene. In addition, we have evaluated the effects of stable expression of viral proteins, cell cycle manipulation, and butyrate post-treatment in small scale experiments. The cell lines varied widely in their GFP transfection efficiencies. Stable expression of simian virus 40 large T-antigen or Epstein Barr nuclear antigen failed to significantly increase transfection efficiency above that seen in the parental lines. Aphidicolin (a DNA polymerase inhibitor), which blocked cells from S or G2/M, brought about an increase in transfection efficiency in two cell lines. The primary effect of butyrate (a histone deacetylase inhibitor) post-treatment was an increased intensity of the fluorescent signal of green fluorescent protein, as measured by flow cytometry (1.0 to 4.2-fold, depending on the cell line). The combined use of aphidicolin pretreatment followed by butyrate treatment post- electroporation yielded increases in fluorescence intensities ranging from 0.9 to 6.8-fold. Based on their high transfection efficiencies in small scale experiments, rapid growth, and ability to grow in suspension culture, CHO, CHO-TAg, and 293-EBNA were selected to assess the feasibility of using flow electroporation for large-scale transfections. Using secreted placental alkaline phosphatase as a reporter, 293-EBNA cells produced the highest protein levels in both the presence and absence of butyrate. These data indicate that flow electroporation provides an efficient method of DNA delivery into large numbers of cells for mammalian protein production. This revised version was published online in August 2006 with corrections to the Cover Date.     

Application of conformationally restricted peptidomimetics to modeling the bound conformation of peptide antagonists with the IL-1 receptor

A collection of complementary peptide caricatures that closely mimic low-energy (presumably highly populated) conformations of amino acids of interest would constitute a valuable tool set to study the interactions of small peptide ligands with their biological targets. Our general strategy for the design, synthesis and application of peptidomimetics is presented. An illustration of how structural information from mimetics combined with cutting edge biophysical data can be used to derive a model for the bound conformation of an 11-mer peptide antagonist with the IL-1 receptor is given.