Slot Blot Hybridization Research Articles

Novel selectively amplified DNA sequences in the germline genome of the Japanese hagfish, Eptatretus burgeri

In the Japanese hagfish Eptatretus burgeri, 16 chromosomes (eliminated [E]-chromosomes) have been lost in somatic cells (2n = 36), which is equivalent to approx. 21% of the genomic DNA in germ cells (2n = 52). At least seven of the 12 eliminated repetitive DNA families isolated in eight hagfish species were selectively amplified in the germline genome of this species. One of them, EEEb1 (eliminated element of E.burgeri 1) is exclusively localized on all E-chromosomes. Herein, we identified four novel eliminated repetitive DNA families (named EEEb3-6) through PCR amplification and suppressive subtractive hybridization (SSH) combined with Southern-blot hybridization. EEEb3 was mosaic for 5S rDNA and SINE elements. EEEb4 was GC-rich repeats and has one pair of direct and inverted repeats, whereas EEEb5 and EEEb6 were AT-rich repeats with one pair and two pairs of sub-repeats, respectively. Interestingly, all repeat classes except EEEb3 were transcribed in the testes, although no open reading frames (ORF) were identified. We conducted fluorescence in situ hybridization (FISH) to examine the chromosomal localizations of EEEb3-6 and EEEb2, which was previously isolated from the germline genome of E. burgeri. All sequences were only found on all EEEb1-positive E-chromosomes. Copy number estimation of the repeated elements by slot-blot hybridization revealed that (i) the EEEb1-6 family members occupied 39.9% of the total eliminated DNA, and (ii) a small number of repeats were retained in somatic cells, suggesting that there is incomplete elimination of the repeated elements. These results provide new insights into the mechanisms involved in the chromosome elimination and the evolution of E-chromosomes.

Trans-splicing of plastid rps12 transcripts, mediated by AtPPR4, is essential for embryo patterning in Arabidopsis thaliana.

AtPPR4-mediated trans-splicing of plastid rps12 transcripts is essential for key embryo morphogenetic events such as development of cotyledons, determination of provascular tissue, and organization of the shoot apical meristem (SAM), but not for the formation of the protodermal layer. Members of the pentatricopeptide repeat (PPR) containing protein family have emerged as key regulators of the organelle post-transcriptional processing and to be essential for proper plant embryo development. In this study, we report the functional characterization of the AtPPR4 (At5g04810) gene encoding a plastid nucleoid PPR protein. In-situ hybridization analysis reveals the presence of AtPPR4 transcripts already at the transition stage of embryo development. As a consequence, embryos lacking the AtPPR4 protein arrest their development at the transition/early-heart stages and show defects in the determination of the provascular tissue and organization of SAM. This complex phenotype is due to the specific role of AtPPR4 in the trans-splicing of the plastid rps12 transcripts, as shown by northern and slot-blot hybridizations, and the consequent defect in 70S ribosome accumulation and plastid protein synthesis, in agreement with the role proposed for the maize orthologue, ZmPPR4.

Transcriptional profiles of Rhizobium vitis-inoculated and salicylic acid-treated ‘Tamnara’ grapevines based on microarray analysis

The transcriptional profiles of ``Tamnara`` grapevine (Vitis labruscana L.) to Rhizobium vitis were determined using 12,000 gene oligonucleotide microarray chips constructed with 6,776 unigenes based on the EST sequencing. Among them, 95 clones were up-regulated more than three times and 90 were down-regulated more than 5-times in the R. vitis-inoculated grapevines relative to the control vines. Treatment of salicylic acid showed that 337 clones were upregulated and 52 clones were down regulated in grapevines. Microarray analysis, reverse transcription-polymer chain reaction, and slot blot hybridization analysis revealed that 5, 14, and 64 clones were up-regulated and 10, 12, and 61 clones were down-regulated in wounded, salicylic acidtreated, and R. vitis-inoculated ``Tamnara`` grapevine leaves, respectively. The expression patterns of β-1,3-glucanase, proline-rich protein, and lipoxygenase genes of ``Tamnara`` moderately resistant to R. vitis were similar to those of resistant ``Concord`` and ``Delaware`` grapevines. However, chalcone synthase genes in ``Tamnara`` grapevines showed similar expression patterns to susceptible grapevines ``Neomuscat`` and ``Rizamat``. Further expression studies with various clones for each gene should be conducted to elucidate their roles in resistant responses against pathogens or other stimuli in grapevines. These results could provide better resources for understanding the mechanism of defense responses against crown gall disease and clues for identifying new genes that may play a role in defense against R. vitis in grapevines.

Functional characterization of a serine-threonine protein kinase from Bambusa balcooathat implicates in cellulose overproduction and superior quality fiber formation

BackgroundMolecular markers allow rapid identification of biologically important germplasm/s having desired character. Previously we have reported a genotype specific molecular marker, Balco1128 [GenBank ID EU258678] of Bambusa balcooa containing an ORF (375 bp) having high similarity with receptor like cytoplasmic kinase of Arabidopsis and Oryza. Balco1128 was found to be associated only with bamboo genotypes endowed with high cellulose and low lignin contents of fibers. Under the above backdrop, it was necessitated to characterize this genetic marker for better understanding of its biological significance in context of superior quality fiber development.ResultsThe full length cDNA (3342 bp) of BbKst, a serine-threonine protein kinase was isolated from B. balcooa comprising of six LRR domains at the N-terminal end and a kinase domain at the C-terminal end. Bacteria-expressed BbKst-kinase domain (3339 bp long) showed Mg2+ dependent kinase activity at pH 7.0, 28°C. Bioinformatics study followed by phospho-amino analysis further confirmed that BbKst-kinase belongs to the serine/threonine protein kinase family. Transcript analysis of the BbKst gene following RNA slot blot hybridization and qPCR revealed higher expression of BbKst during initiation and elongation stages of fiber development. Tissue specific expression studies showed much higher expression of BbKst transcript in stems and internodes of B. balcooa than in leaves and rhizomes. Southern analysis revealed single copy insertion of BbKst in most of the Agrobacterium mediated transgenic tobacco plants. Real-time PCR detected 150-200 fold enhanced expression of BbKst in different T1 tobacco lines than that of the vector transformed plants. Heterologous expression of BbKst under control of 35S promoter in transgenic tobacco showed high cellulose deposition in the xylem fibers. Number of xylary fibers was higher in transgenic T0 and T1 plants than that of empty-vector transformed tobacco plants offering enhanced mechanical strength to the transgenic plants, which was also substantiated by their strong upright phenotypes, significantly higher cellulose contents, flexibility coefficient, slenderness ratio, and lower Runkel ratio of the fibers.ConclusionsThis finding clearly demonstrated that BbKst gene (GenBank ID JQ432560) encodes a serine/threonine protein kinase. BbKst induced higher cellulose deposition/synthesis in transgenic tobacco plants, an important attribute of fiber quality bestowing additional strength to the plant.

A method to overcome the waxy surface, cell wall thickening and polyphenol induced necrosis at wound sites - the major deterrents to Agrobacterium mediated transformation of bamboo, a woody monocot

The method is the first successful report of Agrobacterium mediated genetic transformation of the commercially important bamboo, Dendrocalamus hamiltonii. It shows how the resistance provided by the somatic embryos of this woody monocot can be overcome using a simple and effective method. The method thus standardized can be also used for the genetic transformation of other important bamboos. Identification of the factors responsible for the resistance of the somatic embryos to Agrobacterium infection was an absolute requirement for devising a successful method. Necrosis due to polyphenol oxidation, lack of differentiation due to cell wall thickening at wound sites, waxy surfaces of somatic embryos with anti-microbial properties were found to prevent Agrobacterium attachment and infection. Therefore, the somatic embryos were transformed with fresh overnight grown Agrobacterium culture containing 500 mg/l polyvinylpyrrolidone (PVP) and 0.01 % Tween-20 as surfactant followed by co-cultivation on Murashige and Skoog (MS) medium containing the vir gene inducer acetosyringone (100 μM) and 1 mg/l 6-Benzylaminopurine BAP for 2 days. Persistent GUS expression and strong positive signals in PCR, slot blot and Southern hybridization confirmed successful genetic transformation.

Human CST Has Independent Functions during Telomere Duplex Replication and C-Strand Fill-In

Human CST (CTC1-STN1-TEN1) is an RPA-like complex that is needed for efficient replication through the telomere duplex and genome-wide replication restart after fork stalling. Here, we show that STN1/CST has a second function in telomere replication during G-overhang maturation. Analysis of overhang structure after STN1 depletion revealed normal kinetics for telomerase-mediated extension in S phase but a delay in subsequent overhang shortening. This delay resulted from a defect in C-strand fill-in. Short telomeres exhibited the fill-in defect but normal telomere duplex replication, indicating that STN1/CST functions independently in these processes. Our work also indicates that the requirement for STN1/CST in telomere duplex replication correlates with increasing telomere length and replication stress. Our results provide direct evidence that STN1/CST participates in C-strand fill-in. They also demonstrate that STN1/CST participates in two mechanistically separate steps during telomere replication and identify CST as a replication factor that solves diverse replication-associated problems.

Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments

Members of the highly diverse Miscellaneous Crenarchaeotal Group (MCG) are globally distributed in various marine and continental habitats. In this study, we applied a polyphasic approach (rRNA slot blot hybridization, quantitative PCR (qPCR) and catalyzed reporter deposition FISH) using newly developed probes and primers for the in situ detection and quantification of MCG crenarchaeota in diverse types of marine sediments and microbial mats. In general, abundance of MCG (cocci, 0.4 μm) relative to other archaea was highest (12-100%) in anoxic, low-energy environments characterized by deeper sulfate depletion and lower microbial respiration rates (P=0.06 for slot blot and P=0.05 for qPCR). When studied in high depth resolution in the White Oak River estuary and Hydrate Ridge methane seeps, changes in MCG abundance relative to total archaea and MCG phylogenetic composition did not correlate with changes in sulfate reduction or methane oxidation with depth. In addition, MCG abundance did not vary significantly (P>0.1) between seep sites (with high rates of methanotrophy) and non-seep sites (with low rates of methanotrophy). This suggests that MCG are likely not methanotrophs. MCG crenarchaeota are highly diverse and contain 17 subgroups, with a range of intragroup similarity of 82 to 94%. This high diversity and widespread distribution in subsurface sediments indicates that this group is globally important in sedimentary processes.

Quantitative Detection of Residual E. coli Host Cell DNA by Real-Time PCR

E. coli has been widely used as a host system to manufacture recombinant proteins for human therapeutic use. Among impurities to be eliminated during the downstream process, residual host cell DNA is a major interest for safety. Residual E. coli host cell DNA in the final products are usually determined using conventional slot blot hybridization assay or total DNA Threshold assay, although these methods are time consuming, expensive, and relatively insensitive. Therefore a sensitive real-time PCR assay for specific detection of residual E. coli DNA was developed and compared with slot blot hybridization assay and Threshold assay to validate the overall capability of these methods. Specific primer pair for amplification of the E. coli 16S rRNA gene was selected to improve the sensitivity, and E. coli host cell DNA was quantified by use of SYBR Green 1. The detection limit of real-time PCR assay in the optimized condition was calculated to be 0.042 pg genomic DNA, which is much higher than those of slot blot hybridization assay and Threshold assay of which detection limit were 2.42 and 3.73 pg genomic DNA, respectively. The real-time PCR assay was validated to be more reproducible, accurate, and precise than slot blot hybridization assay and Threshold assay. The real-time PCR assay may be a useful tool for quantitative detection and clearance validation of residual E. coli DNA during the manufacturing process for recombinant therapeutics.

Identification and quantitative evaluation of nitrogen-converting organisms in a full-scale leachate treatment plant

The presence of ammonia nitrogen in landfill leachates poses a significant problem for treatment plant operators. The nitrification–denitrification process mostly carries out the nitrogen conversion in biological treatment systems. However, recent research shows that other processes by anaerobic ammonia-oxidizing bacteria (Anammox) and ammonia-oxidizing archaea (AOA) were also responsible for the removal of nitrogen in biological systems. In this study, the nitrogen-converting microorganisms in the Bursa Hamitler Leachate Treatment Plant were identified and monitored by using molecular tools. Fluorescent in situ hybridization (FISH) and slot-blot hybridization results showed that the Nitrosomonas and Nitrospira species were the dominant ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), respectively. Quantitative real-time PCR results indicated that AOB, NOB, AOA and Anammox bacteria exist in the leachate treatment plant. However, the removal of ammonia can be ascribed mainly to nitrification because AOB (1.5%) and NOB (11.3%) were predominant among all nitrogen-converting bacteria. The results of the phylogenetic analysis based on amoA and 16S rDNA gene revealed that the uncultured bacterium clone 4-24, Kuenenia stuttgartiensis genome fragment KUST_E and the uncultured Crenarchaeota clone NJYPZT-C1 belong to AOB, Anammox and AOA populations, respectively, and were the dominant species in their cluster.

Co-occurrence of nitrogen-converting organisms in full-scale treatment plants

This study provides insights into nitrogen-converting microorganisms in three full-scale wastewater treatment plants (WWTPs), which were investigated and monitored according to their nitrification performance and the presence of ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), ammonia-oxidizing archaea (AOA), and Anammox bacteria based on different molecular tools: fluorescent in situ hybridization (FISH), slot-blot hybridization, and quantitative real-time PCR. In situ hybridization clearly showed the Nitrosomonas species as the prevailing AOB, and Nitrospira-related species as the dominant NOB. Real-time PCR results exposed the Istanbul Pasakoy, Bursa West, and Bursa East WWTPs as harboring diverse nitrogen-converting microbial communities that include AOB, NOB, AOA, and Anammox bacteria. Nitrospira species had the highest fraction of nitrogen-converting organisms, which was up to 39.3% in the WWTPs throughout the two-year monitoring period. This study is the first molecular analysis of the simultaneous occurrence of these microorganisms.

Suppression subtractive hybridization analysis of low-protein diet- and vitamin D-induced gene expression from rat kidney inner medullary base

Protein restriction and hypercalcemia result in a urinary concentrating defect in rats and humans. Previous tubular perfusion studies show that there is an increased active urea transport activity in the initial inner medullary (IM) collecting duct in low-protein diet (LPD) and vitamin D (Vit D) animal models. To investigate the possible mechanisms that cause the urinary concentrating defect and to clone the new active urea transporter, we employed a modified two-tester suppression subtractive hybridization (ttSSH) approach and examined gene expression induced by LPD and Vit D in kidney IM base. Approximately 600 clones from the subtracted library were randomly selected; 150 clones were further confirmed to be the true positive genes by slot blot hybridization with subtracted probes from LPD and Vit D and sent for DNA sequencing. We identified 10 channel/transporter genes that were upregulated in IM base in LPD and Vit D animal models; 8 were confirmed by real-time PCR. These genes include aquaporin 2 (AQP2), two-pore calcium channel protein 2, brain-specific organic cation transporter, Na(+)- and H(+)-coupled glutamine transporter, and solute carrier family 25. Nine genes are totally new, and twelve are uncharacterized hypothetical proteins. Among them, four genes were shown to be new transmembrane proteins as judged by Kyte-Doolittle hydrophobic plot analysis. ttSSH provides a useful method to identify new genes from two conditioned populations.

Analysis of transposons and repeat composition of the sunflower (Helianthus annuus L.) genome

A sample-sequencing strategy combined with slot-blot hybridization and FISH was used to study the composition of the repetitive component of the sunflower genome. One thousand six hundred thirty-eight sequences for a total of 954,517 bp were analyzed. The fraction of sequences that can be classified as repetitive using computational and hybridization approaches amounts to 62% in total. Almost two thirds remain as yet uncharacterized in nature. Of those characterized, most belong to the gypsy superfamily of LTR-retrotransposons. Unlike in other species, where single families can account for large fractions of the genome, it appears that no transposon family has been amplified to very high levels in sunflower. All other known classes of transposable elements were also found. One family of unknown nature (contig 61) was the most repeated in the sunflower genome. The evolution of the repetitive component in the Helianthus genus and in other Asteraceae was studied by comparative analysis of the hybridization of total genomic DNAs from these species to the sunflower small-insert library and compared to gene-based phylogeny. Very little similarity is observed between Helianthus species and two related Asteraceae species outside of the genus. Most repetitive elements are similar in annual and perennial Helianthus species indicating that sequence amplification largely predates such divergence. Gypsy-like elements are more represented in the annuals than in the perennials, while copia-like elements are similarly represented, attesting a different amplification history of the two superfamilies of LTR-retrotransposons in the Helianthus genus.

Molecular characterization of the Indian strain of Apple mosaic virus isolated from apple (Malus domestica)

Apple mosaic virus (ApMV) is an important virus of apple worldwide. Surveys were conducted in the states of Himachal Pradesh (HP) and Jammu & Kashmir (J&K), India, to determine the prevalence of ApMV and to develop ways for its early diagnosis. Symptomatic leaf samples, bud and bark were collected during spring and late summer. DAS-ELISA revealed the presence of ApMV in 13/198 samples from four districts in HP, indicating a disease incidence of approximately 6.5%. The sequence of amplicons produced by reverse transcription-polymerase chain reaction (RT-PCR) using virus-specific primers confirmed the ELISA results. Comparison of the sequences of three amplicons with nine complete available sequences of ApMV coat protein (CP) (from apple) at amino acid level revealed a maximum of 96% homology to a Korean isolate of ApMV (AY125977). Comparison of the amino acid sequence of the CP of the Indian isolate with the amino acid sequence of the CP from different hosts showed that the Indian isolate clustered most closely with an isolate found in pear and originating from Czechoslovakia. Cloned DNA was reliably used for diagnosis of the virus and was a useful tool for screening at nursery level using slot blot hybridization. This study confirms the presence of ApMV at the molecular level in India and reveals sequence information.

Loss of all plastid ndh genes in Gnetales and conifers: extent and evolutionary significance for the seed plant phylogeny

The exact phylogenetic position of Gnetales, a small, highly modified group of gymnosperms with an accelerated rate of molecular evolution, is one of the most challenging issues for seed plant systematics. Recent results from entire plastid genome (ptDNA) sequencing revealed the absence of the entire suite of plastid ndh genes in several species of Gnetales and the pine family (Pinaceae) potentially highlighting a major structural feature linking these two groups-concerted loss of all plastid genes for the NADH dehydrogenase complex. However, the precise extent of ndh gene loss in gymnosperms has not been surveyed. Using a slot-blot hybridization method, we probed all 11 ndh genes in 162 species from 70 of 85 gymnosperm genera. We find that all ndh genes are absent across Gnetales and Pinaceae, but not in any other group of gymnosperms. This feature represents either a major synapomorphy for a clade consisting of these two lineages or, less likely, a convergent loss. Our survey substantially extends previous inferences based on more limited sampling and, if the former evolutionary interpretation is correct, it provides additional support for the contentious "gnepine" hypothesis, which places Gnetales as sister to Pinaceae.

Duplication of MER115 on chromosome 4 in patients with primary biliary cirrhosis

Primary biliary cirrhosis (PBC) is a complex disease with genetic and environmental influences. The disease is more prevalent in families with PBC and candidate gene case-control studies have linked PBC with DRB1(*)08 human leucocyte antigen class II alleles. The goal of this study was to characterize a MER115 intergenic region on chromosome 4 as a putative genetic variant associated with PBC. This region was incidentally identified during investigations to discover candidate microbial agents using representational difference analysis (RDA) with liver samples from patients with PBC and primary sclerosing cholangitis (PSC). blast search analysis of all the RDA products from the PBC liver revealed genomic sequences, whereas Escherichia coli, mycoplasma and hepatitis B virus DNA were found in the PSC liver. We identified one of the PBC RDA products as an ancestral repeat, referred to as MER115. Southern blot analysis with the PBC product uncovered a restriction fragment length polymorphism in PBC patients' liver. Southern blot hybridization signal showed increased signal intensity in PBC vs. control patients' DNA (P<0.005) and slot blot hybridization studies confirmed a copy number variation of the MER115 in hepatic DNA of PBC vs. control patients (P=0.02). Further comparative genetic studies will be required to determine the extent of genomic duplication associated with MER115 and provide data on the possible copy number variants of genes close to this intergenic region in patients with PBC.

Molecular studies on Tomato aspermy virus isolates infecting chrysanthemums

Tomato aspermy virus (TAV), an important viral pathogen of chrysanthemums, was detected by double antibody sandwich-enzyme linked immunosorbent assay (DAS-ELISA) from chrysanthemums exhibiting mottling and deformed inflorescence grown in various states of India. Out of 15 cultivars (cvs.) tested, 11 (73.3%) were found to be positive for TAV. On sap inoculation the virus produced local lesions on Chenopodium spp. and Cucumis sativus. Nicotiana clevelandii, N. glutinosa, N. megalosiphon and N. tabacum reacted systemically to the virus producing severe mosaic, leaf deformation and characteristic leaf enations. Tomato plants produced malformed fruits (2-3/plant) with a few seeds. Myzus persicae and Aphis gossypii transmitted the virus non-persistently. Electron microscopy of partially purified viral preparations revealed polyhedral virions (ca. 29 nm dia). Cytopathology of infected leaves of N. clevelandii showed crystalline inclusions containing virions in the central vacuole of infected cells. The virions showed very good clumping with antiserum to TAV in liquid phase immuno-electron microscopy. Slot blot hybridization was performed to detect the virus in various chrysanthemum cultivars. The virus positivity was confirmed by reverse transcription-polymerase chain reaction (RT-PCR) and nucleotide sequencing of coat protein gene (CP). The amplified 657 bp fragment was about 97% identical with respect to CP sequences of other TAV isolates available in the database. In terms of derived amino acid sequence similarity, the homology value was 99%. In order to amplify RNA 1, RNA 2 and RNA 3, multiplex RT-PCR was performed. High genetic similarities of CP gene of TAV Indian isolates with that of other isolates of TAV indicate their probable common ancestry.

Lactobacillus plantarum response to inorganic carbon concentrations: PyrR2-dependent and -independent transcription regulation of genes involved in arginine and nucleotide metabolism

Lactobacillus plantarum susbp. plantarum is a capnophilic Gram-positive heterotroph with optimal growth in 4 % CO(2)-enriched air. At low inorganic carbon (C(i)) concentrations, the pyr genes encoding the enzymes of the pyrimidine biosynthetic pathway were overexpressed, in agreement with a previous study showing that these genes are regulated at the transcription level in response to C(i) via a PyrR(2)-mediated mechanism. A previous study of high-CO(2)-requiring (HCR) mutants revealed an unknown genetic link between arginine regulation and C(i)-dependent nutritional needs. To better understand L. plantarum's adaptation to C(i) availability, additional C(i)-responsive genes were sought in the arginine biosynthetic pathway (arg and car genes) using slot-blot hybridization and a proteomic differential 2D gel electrophoresis (DIGE) global approach. Besides the nine pyr-encoded proteins, 16 new Icr (inorganic-carbon-regulated) proteins accumulated differentially in response to C(i) availability, suggesting that the C(i) response involves several metabolic pathways and adaptation processes. Among these Icr proteins only argininosuccinate lyase, encoded by argH, was involved in arginine biosynthesis. Three proteins involved in the purine biosynthetic pathway and nucleotide conversion, adenylate kinase (Adk), GMP synthase (GuaA), and IMP dehydrogenase (GuaB), accumulated differentially in response to changes in C(i) levels. Expression of the Icr protein-encoding genes argH and guaB was regulated at the transcription level or by RNA stability in response to C(i) availability, as previously demonstrated for the pyr genes. However, PyrR(2) was not essential for the C(i)-regulated transcription of argH and guaB, demonstrating that PyrR(2) modulates only a subset of C(i)-regulated genes. These results suggest that the C(i) response may involve at least two regulatory mechanisms in L. plantarum.

Characterization of high-capacity adenovirus production by the quantitative real-time polymerase chain reaction: a comparative study of different titration methods

High-capacity adenoviruses (HC-Ad) hold great promise for the treatment of many diseases. The major drawbacks for the clinical application of this vector concern difficulties with respect to large-scale production, and the absence of standardized methods for production and titration. In the present study, we compare the different methods found in the literature for characterizing HC-Ad production. Two productions of the HC-Ad carrying murine IL-12 gene were obtained. The viral titer and adenovirus-helper contamination as well as viral particle concentration of both productions were determined using different methods: (i) quantification of total viral particles by spectrophotometry and plaque assay to estimate first-generation (FG)-helper-Ad contamination; (ii) quantification of HC-Ad and FG-helper-Ad genomes by the quantitative polymerase chain reaction (qPCR) directly from viral stock; (iii) quantification of viral genomes after cell infection by the slot-blot hybridization assay and (iv) qPCR. Dramatic differences with respect to viral titer were found depending on the method used. The first method overestimates HC-Ad titer and underestimates FG-helper-Ad contamination and no information on the infectivity of the HC-Ad is obtained. qPCR analysis of viral stock is more sensitive and accurate, but information about infectivity remains unknown and FG-helper-Ad contamination is overestimated. Quantification of HC-Ad and FG-helper-Ad infectious units by-slot blot DNA hybridization and qPCR assay are found to be equally sensitive and accurate. The results of the present study demonstrate that a standardized method should be developed for HC-Ad characterization for future clinical applications of this vector. Quantification of HC-Ad production by qPCR is a fast, safe and reliable method for determining HC-Ad and FG-helper-Ad particles and infectious units.

Significant contribution of Archaea to extant biomass in marine subsurface sediments

Deep drilling into the marine sea floor has uncovered a vast sedimentary ecosystem of microbial cells. Extrapolation of direct counts of stained microbial cells to the total volume of habitable marine subsurface sediments suggests that between 56 Pg (ref. 1) and 303 Pg (ref. 3) of cellular carbon could be stored in this largely unexplored habitat. From recent studies using various culture-independent techniques, no clear picture has yet emerged as to whether Archaea or Bacteria are more abundant in this extensive ecosystem. Here we show that in subsurface sediments buried deeper than 1 m in a wide range of oceanographic settings at least 87% of intact polar membrane lipids, biomarkers for the presence of live cells, are attributable to archaeal membranes, suggesting that Archaea constitute a major fraction of the biomass. Results obtained from modified quantitative polymerase chain reaction and slot-blot hybridization protocols support the lipid-based evidence and indicate that these techniques have previously underestimated archaeal biomass. The lipid concentrations are proportional to those of total organic carbon. On the basis of this relationship, we derived an independent estimate of amounts of cellular carbon in the global marine subsurface biosphere. Our estimate of 90 Pg of cellular carbon is consistent, within an order of magnitude, with previous estimates, and underscores the importance of marine subsurface habitats for global biomass budgets.

Comparison of five DNA quantification methods

Six commercial preparations of human genomic DNA were quantified using five quantification methods: UV spectrometry, SYBR-Green dye staining, slot blot hybridization with the probe D17Z1, Quantifiler™ Human DNA Quantification kit and RB1 rt-PCR. All methods measured higher DNA concentrations than expected based on the information by the manufacturers. UV spectrometry, SYBR-Green dye staining, slot blot and RB1 rt-PCR gave 39, 27, 11 and 12%, respectively, higher concentrations than expected based on the manufacturers’ information. The DNA preparations were quantified using the Quantifiler™ Human DNA Quantification kit in two experiments. The measured DNA concentrations with Quantifiler were 125 and 160% higher than expected based on the manufacturers’ information. When the Quantifiler™ human DNA standard (Raji cell line) was replaced by the commercial human DNA preparation G147A (Promega) to generate the DNA standard curve in the Quantifiler™ Human DNA Quantification kit, the DNA quantification results of the human DNA preparations were 31% higher than expected based on the manufacturers’ information. The results indicate a calibration problem with the Quantifiler™ human DNA standard for its use with the Quantifiler™ Human DNA Quantification kit. The possible reasons for the problem are discussed and a solution is suggested. The results emphasise the need for standard reference DNA material and standard methods for DNA quantification.