Hydroxymethanesulfonate from Volcanic Sulfur Dioxide: A "Mineral" Reservoir for Formaldehyde and Other Simple Carbohydrates in Prebiotic Chemistry.

While formaldehyde (HCHO) was likely generated in Earth's prebiotic atmosphere by ultraviolet light, electrical discharge, and/or volcano-created lightning, HCHO could not have accumulated in substantial amounts in prebiotic environments, including those needed for prebiotic processes that generate nucleosidic carbohydrates. HCHO at high concentrations in alkaline solutions self-reacts in the Cannizzaro reaction to give methanol and formate, neither having prebiotic value. Here, we explore the possibility that volcanic sulfur dioxide (SO2) might have generated a reservoir for Hadean HCHO by a reversible reaction with HCHO to give hydroxymethanesulfonate (HMS). We show that salts of HMS are stable as solids at 90°C and do not react with themselves in solution, even at high (>8 M) concentrations. This makes them effective stores of HCHO, since the reverse reaction slowly delivers HCHO back into an environment where it can participate in prebiotically useful reactions. Specifically, we show that in alkaline borate solutions, HCHO derived from HMS allows formation of borate-stabilized carbohydrates as effectively as free HCHO, without losing material to Cannizzaro products. Further, we show that SO2 can perform similar roles for glycolaldehyde and glyceraldehyde, two intrinsically unstable carbohydrates that are needed by various models as precursors for RNA building blocks. Zircons from the Hadean show that the Hadean mantle likely provided volcanic SO2 at rates at least as great as the rates of atmospheric HCHO generation, making the formation of Hadean HMS essentially unavoidable. Thus, hydroxymethylsulfonate adducts of formaldehyde, glycolaldehyde, and glyceraldehyde, including the less soluble barium, strontium, and calcium salts, are likely candidates for prebiotically useful organic minerals on early Earth.

Detecting ultralow-frequency mutations by Duplex Sequencing.

Duplex Sequencing (DS) is a next-generation sequencing methodology capable of detecting a single mutation among >1 × 10(7) wild-type nucleotides, thereby enabling the study of heterogeneous populations and very-low-frequency genetic alterations. DS can be applied to any double-stranded DNA sample, but it is ideal for small genomic regions of <1 Mb in size. The method relies on the ligation of sequencing adapters harboring random yet complementary double-stranded nucleotide sequences to the sample DNA of interest. Individually labeled strands are then PCR-amplified, creating sequence 'families' that share a common tag sequence derived from the two original complementary strands. Mutations are scored only if the variant is present in the PCR families arising from both of the two DNA strands. Here we provide a detailed protocol for efficient DS adapter synthesis, library preparation and target enrichment, as well as an overview of the data analysis workflow. The protocol typically takes 1-3 d.

APOBEC3B mutagenesis in cancer.

Recent evidence has implicated APOBEC3B as a source of mutations in cervical, bladder, lung, head and neck, and breast cancers. APOBEC enzymes normally function in innate immune responses, including those that target retroviruses, suggesting links between mutagenesis, immunity and viral infection in the process of cancer development.

Disintegration of nascent replication bubbles during thymine starvation triggers RecA- and RecBCD-dependent replication origin destruction.

Thymineless death strikes cells unable to synthesize DNA precursor dTTP, with the nature of chromosomal damage still unclear. Thymine starvation stalls replication forks, whereas accumulating evidence indicates the replication origin is also affected. Using a novel DNA labeling technique, here we show that replication slowly continues in thymine-starved cells, but the newly synthesized DNA becomes fragmented and degraded. This degradation apparently releases enough thymine to sustain initiation of new replication bubbles from the chromosomal origin, which destabilizes the origin in a RecA-dependent manner. Marker frequency analysis with gene arrays 1) reveals destruction of the origin-centered chromosomal segment in RecA(+) cells; 2) confirms origin accumulation in the recA mutants; and 3) identifies the sites around the origin where destruction initiates in the recBCD mutants. We propose that thymineless cells convert persistent single-strand gaps behind replication forks into double-strand breaks, using the released thymine for new initiations, whereas subsequent disintegration of small replication bubbles causes replication origin destruction.

Stalled replication fork repair and misrepair during thymineless death in Escherichia coli.

Starvation for DNA precursor dTTP, known as 'thymineless death' (TLD), kills bacterial and eukaryotic cells alike. Despite numerous investigations, toxic mechanisms behind TLD remain unknown, although wrong nucleotide incorporation with subsequent excision dominates the explanations. We show that kinetics of TLD in Escherichia coli is not affected by mutations in DNA repair, ruling out excision after massive misincorporation as the cause of TLD. We found that the rate of DNA synthesis in thymine-starved cells decreases exponentially, indicating replication fork stalling. Processing of stalled replication forks by recombinational repair is known to fragment the chromosome, and we detect significant chromosomal fragmentation during TLD. Moreover, we report that, out of major recombinational repair functions, only inactivation of recF and recO relieves TLD, identifying the poisoning mechanism. Inactivation of recJ and rep has slight effect, while the recA, recBC, ruvABC, recG and uvrD mutations all accelerate TLD, identifying the protection mechanisms. Our epistatic analysis argues for two distinct pathways protecting against TLD: RecABCD/Ruv repairs the double-strand breaks, whereas UvrD counteracts RecAFO-catalyzed toxic single-strand gap processing.

Induction of microRNAs, mir-155, mir-222, mir-424 and mir-503, promotes monocytic differentiation through combinatorial regulation.

Acute myeloid leukemia (AML) involves a block in terminal differentiation of the myeloid lineage and uncontrolled proliferation of a progenitor state. Using phorbol myristate acetate (PMA), it is possible to overcome this block in THP-1 cells (an M5-AML containing the MLL-MLLT3 fusion), resulting in differentiation to an adherent monocytic phenotype. As part of FANTOM4, we used microarrays to identify 23 microRNAs that are regulated by PMA. We identify four PMA-induced microRNAs (mir-155, mir-222, mir-424 and mir-503) that when overexpressed cause cell-cycle arrest and partial differentiation and when used in combination induce additional changes not seen by any individual microRNA. We further characterize these pro-differentiative microRNAs and show that mir-155 and mir-222 induce G2 arrest and apoptosis, respectively. We find mir-424 and mir-503 are derived from a polycistronic precursor mir-424-503 that is under repression by the MLL-MLLT3 leukemogenic fusion. Both of these microRNAs directly target cell-cycle regulators and induce G1 cell-cycle arrest when overexpressed in THP-1. We also find that the pro-differentiative mir-424 and mir-503 downregulate the anti-differentiative mir-9 by targeting a site in its primary transcript. Our study highlights the combinatorial effects of multiple microRNAs within cellular systems.

Cyanide, peroxide and nitric oxide formation in solutions of hydroxyurea causes cellular toxicity and may contribute to its therapeutic potency.

Hydroxyurea (HU) is a potent remedy against a variety of ailments and an efficient inhibitor of DNA synthesis, yet its pharmacology is unclear. HU acts in Escherichia coli by the same mechanism as it does in eukaryotes, via inhibition of ribonucleotide reductase. When examining a controversy about concentrations of HU that prevent thymineless death in E. coli, we found instability in HU solutions that avoided prior detection due to its peculiar nature. In contrast to freshly dissolved HU, which did not affect respiration and was bacteriostatic, 1-day-old HU solutions inhibited respiration and were immediately bactericidal. Respiration was inhibited by two gases, hydrogen cyanide (HCN) and nitric oxide (NO), whose appearance we detected in "aged" HU stocks by gas chromatography-mass spectrometry; however, neither gas was bactericidal. While determining the cause of toxicity, we found that HU damages DNA directly. We also demonstrated accumulation of peroxides in HU solutions by enzymatic assays, which explains the toxicity, as both NO and HCN are known to kill bacteria when combined with hydrogen peroxide. Remarkably, we found that bactericidal effects of NO+H(2)O(2) and HCN+H(2)O(2) mixtures were further synergistic. Accumulation of decomposition products in solutions of HU may explain the broad therapeutic effects of this drug.

Micro-Magnetocardiography System With a Single-Chip SQUID Magnetometer Array for QT Analysis and Diagnosis of Myocardial Injury in Small Animals.

Development of drugs requires electrophysiological studies of small animals like mice, rats or guinea pigs. Electrocardiography (ECG) of hirsute animals is time-consuming. We have developed a micro magnetometer array with a 9-channel superconducting quantum interference device (SQUID) with a 2.5-mm diameter pickup-coil for noncontacting measurement of magnetocardiograms (MCGs) in small animals. The micro-MCG successfully recorded the PQRST complex in mice, rats and guinea pigs. A regional myocardial injury was made in rat hearts with a cryoinjury probe, and the characteristic pattern of the injury was recorded in the MCG. An anterior myocardial injury created a QS pattern in the MCG, and a posterior myocardial injury created a QR pattern in the MCG. Quinidine-induced QT prolongation was successfully detected by micro-MCG in mice and rats. Simultaneous recording of ECG and MCG was conducted after intraperitoneal administration of quinidine (60 mg/kg) in guinea pigs. QT interval corrected for heart rate (QTc) in both ECG and MCG correlated well. The newly developed micro-MCG may facilitate electrophysiological studies of small animals, and may enable high-throughput screening of drug-induced QT abnormality.

Wavelength-dependent fragmentation and clustering observed after femtosecond laser ablation of solid C60.

We report here the resonance effect in femtosecond laser ablation of solid C60 by investigating wavelength and fluence dependence of product ion species. When the ablation laser wavelength is far from the molecular absorption band of C60, we observe both C60-2n+ fragment ions and C60+2n+ cluster ions as well as C60+ parent ion. Delayed ionization of C60 is not significant. When the ablation laser wavelength is near resonant with the molecular absorption, we observe C60+ and some amount of C60-2n+ fragment ions depending on the laser fluence. Delayed ionization of C60 is significant in this case, which indicates high internal energy of C60 molecule. From the observations, we confirm the strong coupling of femtosecond laser energy with C60 molecule when the molecular absorption is high at the ablation laser wavelength.

Ionization and fragmentation of solid C60 by femtosecond laser ablation.

Ionization and fragmentation of solid C(60) dispersed on a silicon plate are investigated by femtosecond laser ablation. Bimodal mass distribution with large fragment ions C(60-2n) (+) (0< or =n< or =11) and small fragment ions C(n) (+) (13< or =n< or =28), formation of dimer ion (C(60))(2) (+), and delayed ionization of C(60) have been observed as reported in gas phase experiments with nanosecond laser excitation. Metastable dissociation of small fragment ions C(n) (+) has been observed for the first time, which suggests different structures of fragment ions compared with those of well-studied carbon cluster ions. From these observations, strong coupling of laser energy to electronic degrees of freedom of solid C(60) has been revealed for femtosecond laser ablation as compared with excitation in the gas phase.

A set of polymorphic trinucleotide and tetranucleotide microsatellite markers for the Japanese flounder (Paralichthys olivaceus).

We have developed the first set of trinucleotide and tetranucleotide markers for the Japanese flounder, Paralichthys olivaceus. One hundred and sixty-seven polymorphic trinucleotide and tetranucleotide microsatellites were isolated using clones derived from two libraries. Of almost 200,000 clones analysed, 0.5% presented trinucleotide or tetranucleotide repeat regions. Among the trinucleotide repeats analysed in this study, the most frequent one was (CAG)(n) and the most common tetranucleotide repeat was (GATA)(n). The position of the new markers in the genetic linkage map was determined. Markers were evenly distributed along the P. olivaceus linkage groups, without distinction between the kinds of repeats and library of origin. The markers isolated in this study contribute significantly to the genetic linkage map of the Japanese flounder.

Antisense transcription in the mammalian transcriptome.

Antisense transcription (transcription from the opposite strand to a protein-coding or sense strand) has been ascribed roles in gene regulation involving degradation of the corresponding sense transcripts (RNA interference), as well as gene silencing at the chromatin level. Global transcriptome analysis provides evidence that a large proportion of the genome can produce transcripts from both strands, and that antisense transcripts commonly link neighboring "genes" in complex loci into chains of linked transcriptional units. Expression profiling reveals frequent concordant regulation of sense/antisense pairs. We present experimental evidence that perturbation of an antisense RNA can alter the expression of sense messenger RNAs, suggesting that antisense transcription contributes to control of transcriptional outputs in mammals.

Comparison of left atrial size by freehand scanning three-dimensional echocardiography and two-dimensional echocardiography.

AIMS: As the left ventricular (LV) dimension is a poor indicator of LV volume, there are well-known limitations of left atrial (LA) antero-posterior dimensions as indicators of chamber size. LA volume has been shown to provide a more accurate assessment of LA size than LA dimension. To evaluate two-dimensional (2D)-derived LA volume in assessing LA size, we compared LA dimension and 2D LA volume with three-dimensional (3D)-derived LA volume. METHODS: We performed transthoracic freehand scanning 3D echocardiography (3D EchoTech, Germany) using magnetic fields and a harmonic imaging system in 32 patients. We collected a series of LA tomograms by slowly tilting the probe (fan-like scanning) in the parasternal position. The 3D LA volume was calculated by using the multiplanar Simpson's method. The 2D LA volume was measured by using the modified biplane Simpson's rule. RESULTS: LA antero-posterior dimensions and 2D volumes showed a significant positive correlation with 3D LA volumes. However, the correlation coefficient was significantly greater for the relationship between 2D LA volumes and 3D LA volumes than for that between LA dimensions and 3D LA volume. CONCLUSIONS: The 2D LA volumes provide a more accurate measure of the true size of the LA and are more sensitive to changes in LA size.

Comprehensive sequence analysis of translation termination sites in various eukaryotes.

Recent investigations into the translation termination sites of various organisms have revealed that not only stop codons but also sequences around stop codons have an effect on translation termination. To investigate the relationship between these sequence patterns and translation as well as its termination efficiency, we analysed the correlation between strength of consensus and translation efficiency, as predicted according to Codon Adaptation Index (CAI) value. We used RIKEN full-length mouse cDNA sequences and ten other eukaryotic UniGene datasets from NCBI for the analyses. First, we conducted sequence profile analyses following translation termination sites. We found base G and A at position +1 as a strong consensus for mouse cDNA. A similar consensus was found for other mammals, such as Homo sapiens, Rattus norvegicus and Bos taurus. However, some plants had different consensus sequences. We then analysed the correlation between the strength of consensus at each position and the codon biases of whole coding regions, using information content and CAI value. The results showed that in mouse cDNA, CAI value had a positive correlation with information content at positions +1. We also found that, for positions with strong consensus, the strength of the consensus is likely to have a positive correlation with CAI value in some other eukaryotes. Along with these observations, biological insights into the relationship between gene expression level, codon biases and consensus sequence around stop codons will be discussed.

Removal of polyA tails from full-length cDNA libraries for high-efficiency sequencing.

We have developed a method to overcome sequencing problems caused by the presence of homopolymer stretches, such as polyA/T, in cDNA libraries. PolyA tails are shortened by cleaving before cDNA cloning with type IIS restriction enzymes, such as GsuI, placed next to the oligo-dT used to prime the polyA tails of mRNAs. We constructed four rice Cap-Trapper-selected, full-length normalized cDNA libraries, of which the average residual polyA tail was 4 bases or shorter in most of the clones analyzed Because of the removal of homopolymeric stretches, libraries prepared with this method can be used for direct sequencing and transcriptional sequencing without the slippage observed for libraries prepared with currently available methods, thus improving sequencing accuracy, operations, and throughput.

Computational analysis of full-length mouse cDNAs compared with human genome sequences.

Although the sequencing of the human genome is complete, identification of encoded genes and determination of their structures remain a major challenge. In this report, we introduce a method that effectively uses full-length mouse cDNAs to complement efforts in carrying out these difficult tasks. A total of 61,227 RIKEN mouse cDNAs (21,076 full-length and 40,151 EST sequences containing certain redundancies) were aligned with the draft human sequences. We found 35,141 non-redundant genomic regions that showed a significant alignment with the mouse cDNAs. We analyzed the structures and compositional properties of the regions detected by the full-length cDNAs, including cross-species comparisons, and noted a systematic bias of GENSCAN against exons of small size and/or low GC-content. Of the cDNAs locating the 35,141 genomic regions, 3,217 did not match any sequences of the known human genes or ESTs. Among those 3,217 cDNAs, 1,141 did not show any significant similarity to any protein sequence in the GenBank non-redundant protein database and thus are candidates for novel genes.

[Three-dimensional transesophageal echocardiographic measurement of left ventricular volumes using the average rotation method: comparison with the disk summation method].

OBJECTIVES: Three-dimensional(3-D) echocardiography accurately calculates left ventricular volumes without geometric assumptions. Conventional 3-D echocardiography using the disk summation method is limited in practical use because of the long analysis time. This study validated the average rotation method for rapid and accurate left ventricular volume measurement compared with the conventional disk summation method. METHODS: 3-D data acquisition using multiplane transesophageal echocardiography was performed in 13 patients. Left ventricular volumes and ejection fraction were calculated by the disk summation method with 20 parallel short-axis tomograms and by the average rotation method with 3, 6, 9 and 12 apical long-axis tomograms. RESULTS: 3-D left ventricular volumes and ejection fraction by the average rotation method in each subgroup of slice resolution had excellent correlation and close limits of agreement with those by the disk summation method. Intraobserver variability and interobserver variability were < or = 11%. With the use of three component tomograms, analysis time required for left ventricular volume measurement by the average rotation method was < or = 2 min. CONCLUSIONS: Transesophageal 3-D echocardiography using the average rotation method is a clinically useful tool for accurate and rapid measurement of left ventricular volume and function.

Correlation between sequence conservation of the 5' untranslated region and codon usage bias in Mus musculus genes.

The codon adaptation index (CAI) values of all protein-coding sequences of the full-length cDNA libraries of Mus musculus were computed based on the RIKEN mouse full-length cDNA library. We have also computed the extent of consensus in flanking sequences of the initiator ATG codon based on the 'relative entropy' values of respective nucleotide positions (from -20 to +12 bp relative to the initiator ATG codon) for each group of genes classified by CAI values. With regard to the two nucleotides positions (-3 and +4) known to be highly conserved in Kozak's consensus sequence, a clear correlation between CAI values and relative entropy values was observed at position -3 but this was not significant at position +4, although a significant correlation was found at position -1 of the consensus sequence. Further, although no correlation was observed at any additional positions, relative entropy values were very high at positions -4, -6, and -8 in genes with high CAI values. These findings suggest that the extent of conservation in the flanking sequence of the initiator ATG codon including Kozak's consensus sequence was an important factor in modulation of the translation efficiency as well as synonymous codon usage bias particularly in highly expressed genes.

New stable neutral radical with intramolecular hydrogen bonding: synthesis and characterization of 2,5,8-tri-tert-butyl-7-hydroxy-6-oxophenalenoxyl.

A new stable neutral radical with intramolecular hydrogen bonding, 2,5,8-tri-tert-butyl-7-hydroxy-6-oxophenalenoxyl, was synthesized from the corresponding dihydroxyphenalenone and isolated as a stable solid under air atmosphere at room temperature. The structure was unequivocally determined by means of IR spectra, ESR/ENDOR techniques, and DFT calculations.

Identification of the chemical states of phosphorus in atmospheric aerosols by XANES spectrometry.

Depth selective XAFS spectrometry was applied to determine the chemical states of phosphorus in atmospheric aerosols. Atmospheric aerosols were collected on aluminum foils and polyethylene films using a 4-stage cascade impactor and a 12-stage low pressure Andersen sampler, respectively. Samplings were performed at Uji (urban area) and Sakurajima (near a volcano). We measured X-ray fluorescence yield (XFY) and total electron yield (sample current) simultaneously to obtain the X-ray absorption near edge structure (XANES) spectra of the atmospheric aerosols. X-ray absorption in the vicinities of P K-edges was measured on the beamline BL-11B at the Photon Factory, High Energy Accelerator Research Organization, Tsukuba, Japan. The Sakurajima aerosol samples showed only a P5+ peak and the peak was remarkable in coarse mode. In case of the Uji samples, the P5+ peak was dominant and a slight P3+ peak was detected for sample current measurement.