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PubMed2005

Detection of potentially novel bacterial components of the human skin microbiota using culture-independent molecular profiling.

Although the micro-organisms forming the cutaneous microbiota are considered to play important roles in the modification and prevention of skin diseases, a comprehensive analysis of their composition has not yet been carried out because of difficulties in determining yet-to-be-cultured micro-organisms in the samples. Swab-scrubbed forehead skin samples of five healthy volunteers were analysed by profiling 16S rRNA genes, as well as by conventional culture methods, to provide a profile of the cutaneous microbiota that included yet-to-be-cultured bacteria from normal human skin. Cluster analyses of the 16S rRNA gene sequences indicated a marked increase in diversity compared with that derived from the culture methods. Nineteen previously recognized species and 13 novel phylotypes were obtained from the analysis of 416 clones. In addition to well-known bacteria such as Staphylococcus epidermidis and Propionibacterium acnes, phylotype A, the 16S rRNA gene of which is 97 % similar to that of Methylophilus methylotrophus, was detected in three of the five samples, in one of which it was the predominant clone. Culture-independent genetic profiling of 16S rRNA genes for detecting human cutaneous microbiota has allowed us to detect potentially novel components of the cutaneous microbiota in humans.

Bacteria↗
PubMed2004

Significant differences in type IV pilin allele distribution among Pseudomonas aeruginosa isolates from cystic fibrosis (CF) versus non-CF patients.

Type IV pili (TFP) are important colonization factors of the opportunistic pathogen Pseudomonas aeruginosa, involved in biofilm formation and attachment to host cells. This study undertook a comprehensive analysis of TFP alleles in more than 290 environmental, clinical, rectal and cystic fibrosis (CF) isolates of P. aeruginosa. Based on the results, a new system of nomenclature is proposed, in which P. aeruginosa TFP are divided into five distinct phylogenetic groups. Each pilin allele is stringently associated with characteristic, distinct accessory genes that allow the identification of the allele by specific PCR. The invariant association of the pilin and accessory genes implies horizontal transfer of the entire locus. Analysis of pilin allele distribution among isolates from various sources revealed a striking bias in the prevalence of isolates with group I pilin genes from CF compared with non-CF human sources (P<0.0001), suggesting this particular pilin type, which can be post-translationally modified by glycosylation via the action of TfpO (PilO), may confer a colonization or persistence advantage in the CF host. This allele was also predominant in paediatric CF isolates (29 of 43; 67.4 %), showing that this bias is apparent early in colonization. Group I pilins were also the most common type found in environmental isolates tested. To the authors' knowledge, this is the first example of a P. aeruginosa virulence factor allele that is strongly associated with CF isolates.

Adolescent↗
PubMed2025

A survey of dietary effects on tRNA abundance and modifications.

Transfer RNAs (tRNAs) play a central role in protein translation and are increasingly recognized as dynamic regulators of gene expression. Both physiological and environmental signals can modulate tRNA abundance and chemical modifications, yet the impact of dietary cues on the tRNA landscape remains poorly understood. Here, we investigated the effects of two distinct dietary interventions-low-protein and high-fat diets-on tRNA abundance and modification profiles across multiple mouse tissues. We conducted a comprehensive analysis of tRNA abundance and modification changes in response to these nutritional challenges using RNA mass spectrometry and Ordered Two-Template Relay sequencing (OTTR-seq), a modified-base-sensitive tRNA sequencing method. Our results reveal both shared and tissue-specific alterations in abundance and modifications of specific nuclear and mitochondrial genome-encoded tRNAs in response to dietary conditions at isotype, isoacceptor, and isodecoder levels. As many of the tissue-specific or diet-responsive tRNA modifications have been previously reported to affect decoding efficiency or translational fidelity, these results have implications for understanding translational adaptation in response to dietary conditions.

Journal Article↗
PubMed1998

Purification and characterization of the nuclear RNase P holoenzyme complex reveals extensive subunit overlap with RNase MRP.

Ribonuclease P (RNase P) is a ribonucleoprotein enzyme that cleaves precursor tRNA transcripts to give mature 5' ends. RNase P in eubacteria has a large, catalytic RNA subunit and a small protein subunit that are required for precursor tRNA cleavage in vivo. Although the eukaryotic holoenzymes have similar, large RNA subunits, previous work in a number of systems has suggested that the eukaryotic enzymes require a greater protein content. We have purified the Saccharomyces cerevisiae nuclear RNase P to apparent homogeneity, allowing the first comprehensive analysis of an unexpectedly complex subunit composition. Peptide sequencing by ion trap mass spectrometry identifies nine proteins that copurify with the nuclear RNase P RNA subunit, totaling 20-fold more protein than in the bacterial enzyme. All of these proteins are encoded by genes essential for RNase P activity and for cell viability. Previous genetic studies suggested that four proteins might be subunits of both RNase P and RNase MRP, the related rRNA processing enzyme. We demonstrate that all four of these proteins, Pop1p, Pop3p, Pop4p, and Rpp1p, are integral subunits of RNase P. In addition, four of the five newly identified protein subunits, Pop5p, Pop6p, Pop7p, and Pop8p, also appear to be shared between RNase P and RNase MRP. Only one polypeptide, Rpr2p, is unique to the RNase P holoenzyme by genetic depletion and immunoprecipitation studies. The large increase in the number of protein subunits over eubacterial RNase P is consistent with an increase in functional complexity in eukaryotes. The degree of structural similarity between nuclear RNase P and RNase MRP suggests that some aspects of their functions in pre-tRNA and pre-rRNA processing pathways might overlap or be coordinated.

Amino Acid Sequence↗
PubMed2002

Athila4 of Arabidopsis and Calypso of soybean define a lineage of endogenous plant retroviruses.

The Athila retroelements of Arabidopsis thaliana encode a putative envelope gene, suggesting that they are infectious retroviruses. Because most insertions are highly degenerate, we undertook a comprehensive analysis of the A. thaliana genome sequence to discern their conserved features. One family (Athila4) was identified whose members are largely intact and share >94% nucleotide identity. As a basis for comparison, related elements (the Calypso elements) were characterized from soybean. Consensus Calypso and Athila4 elements are 12-14 kb in length and have long terminal repeats of 1.3-1.8 kb. Gag and Pol are encoded on a single open reading frame (ORF) of 1801 (Calypso) and 1911 (Athila4) amino acids. Following the Gag-Pol ORF are noncoding regions of ~0.7 and 2 kb, which, respectively, flank the env-like gene. The env-like ORF begins with a putative splice acceptor site and encodes a protein with a predicted central transmembrane domain, similar to retroviral env genes. RNA of Athila elements was detected in an A. thaliana strain with decreased DNA methylation (ddm1). Additionally, a PCR survey identified related reverse transcriptases in diverse angiosperm genomes. Their ubiquitous nature and the potential for horizontal transfer by infection implicates these endogenous retroviruses as important vehicles for plant genome evolution.

Amino Acid Sequence↗
PubMed2006

Tissue-specific expression and regulation of sexually dimorphic genes in mice.

We report a comprehensive analysis of gene expression differences between sexes in multiple somatic tissues of 334 mice derived from an intercross between inbred mouse strains C57BL/6J and C3H/HeJ. The analysis of a large number of individuals provided the power to detect relatively small differences in expression between sexes, and the use of an intercross allowed analysis of the genetic control of sexually dimorphic gene expression. Microarray analysis of 23,574 transcripts revealed that the extent of sexual dimorphism in gene expression was much greater than previously recognized. Thus, thousands of genes showed sexual dimorphism in liver, adipose, and muscle, and hundreds of genes were sexually dimorphic in brain. These genes exhibited highly tissue-specific patterns of expression and were enriched for distinct pathways represented in the Gene Ontology database. They also showed evidence of chromosomal enrichment, not only on the sex chromosomes, but also on several autosomes. Genetic analyses provided evidence of the global regulation of subsets of the sexually dimorphic genes, as the transcript levels of a large number of these genes were controlled by several expression quantitative trait loci (eQTL) hotspots that exhibited tissue-specific control. Moreover, many tissue-specific transcription factor binding sites were found to be enriched in the sexually dimorphic genes.

Animals↗
PubMed2006

Common fragile sites are conserved features of human and mouse chromosomes and relate to large active genes.

Common fragile sites (CFSs) are seen as chromosomal gaps and breaks brought about by inhibition of replication, and it is thought that they cluster with tumor breakpoints. This study presents a comprehensive analysis using conventional and molecular cytogenetic mapping of CFSs and their expression frequencies in two mouse strains, BALB/c and C57BL/6, and in human probands. Here we show that induced mouse CFSs relate to sites of spontaneous gaps and breaks and that CFS expression levels in chromosome bands are conserved between the two mouse strains and between syntenic mouse and human DNA segments. Furthermore, four additional mouse CFSs were found to be homologous to human CFSs on the molecular cytogenetic level (Fra2D-FRA2G, Fra4C2-FRA9E, Fra6A3.1-FRA7G, and Fra6B1-FRA7H), increasing the number of such CFSs already described in the literature to eight. Contrary to previous reports, DNA helix flexibility is not increased in the 15 human and eight mouse CFSs molecularly defined so far, compared to large nonfragile control regions. Our findings suggest that the mechanisms that provoke instability at CFSs are evolutionarily conserved. The role that large transcriptionally active genes may play in CFS expression is discussed.

Animals↗
PubMed2006

Mapping of the juxtacentromeric heterochromatin-euchromatin frontier of human chromosome 21.

Euchromatin and heterochromatin are functional compartments of the genome. However, little is known about the structure and the precise location of the heterochromatin-euchromatin boundaries in higher eukaryotes. Constitutive heterochromatin in centromeric regions is associated with (1) specific histone methylation patterns, (2) high levels of DNA methylation, (3) low recombination frequency, and (4) the repression of transcription. All of this contrasts with the permissive structure of euchromatin found along chromosome arms. On the sequence level, the transition between these two domains consists most often of patchworks of segmental duplications. We present here a comprehensive analysis of gene expression, DNA methylation in CpG islands, distribution of histone isoforms, and recombination activity for the juxtacentromeric (or pericentromeric) region of the long arm of human chromosome 21. We demonstrate that most HapMap data are reliable within this region. We show that high linkage disequilibrium between pairs of SNPs extends 719-737 kb from the centromeric alpha-satellite. In the same region we find a peak of histone isoforms H3K9Me3 and H3K27Me (715-822 kb distal to the alpha-satellite). In normal somatic cells, CpG islands proximal to this peak are highly methylated, whereas distal CpG islands are not or very little methylated. This methylation profile undergoes dramatic changes in cancer cells and during spermatogenesis. As a consequence, transcription from heterochromatic genes is activated in the testis, and aberrant gene activation can occur during neoplastic transformation. Our data indicate that the frontier between the juxtacentromeric heterochromatic domain and euchromatic domain of the long arm of chromosome 21 is marked by a heterochromatic peak located approximately 750 kb distal to the alpha-satellite.

Chromatin Immunoprecipitation↗
PubMed2003

Informatics for unveiling hidden genome signatures.

With the increasing amount of available genome sequences, novel tools are needed for comprehensive analysis of species-specific sequence characteristics for a wide variety of genomes. We used an unsupervised neural network algorithm, a self-organizing map (SOM), to analyze di-, tri-, and tetranucleotide frequencies in a wide variety of prokaryotic and eukaryotic genomes. The SOM, which can cluster complex data efficiently, was shown to be an excellent tool for analyzing global characteristics of genome sequences and for revealing key combinations of oligonucleotides representing individual genomes. From analysis of 1- and 10-kb genomic sequences derived from 65 bacteria (a total of 170 Mb) and from 6 eukaryotes (460 Mb), clear species-specific separations of major portions of the sequences were obtained with the di-, tri-, and tetranucleotide SOMs. The unsupervised algorithm could recognize, in most 10-kb sequences, the species-specific characteristics (key combinations of oligonucleotide frequencies) that are signature features of each genome. We were able to classify DNA sequences within one and between many species into subgroups that corresponded generally to biological categories. Because the classification power is very high, the SOM is an efficient and fundamental bioinformatic strategy for extracting a wide range of genomic information from a vast amount of sequences.

Animals↗
PubMed2002

Using a gene-switch transgenic approach to dissect distinct roles of MAP kinases in heart failure.

We have demonstrated that Cre-loxP-mediated gene-switch transgenesis is an effective approach to achieve targeted and temporally regulated gene manipulation in the heart. Using this approach, we have established animal models with targeted activation of different MAPK pathways. From these animal models, we identified distinct features of cardiac pathology associated with individual MAPK branches (summarized in Fig. 8). Specifically, Ras activation appears to promote cardiac hypertrophy, whereas p38 and JNK activation does not. Whereas Ras activation leads to depressed diastolic function associated with suppressed calcium transients and SR calcium uptake, p38 activity seems to modulate cellular contractility without affecting intracellular calcium cycling. Although all three models displayed extensive remodeling in the myocardium, the extent and the composition of interstitial fibrosis are different among them, with Ras- and p38-activated hearts promoting collagen-based fibrosis, and JNK activation leading to induction in fibronectin-based reticular fiber. In addition, JNK activation leads to loss of Cx43 expression and abnormal cell-cell communication. Therefore, ERK, p38, and JNK are three distinct intracellular signaling pathways that contribute to different aspects of cardiac pathology during heart failure. Combining sophisticated genetic manipulation with comprehensive analysis at physiological, molecular, and genomic levels, the transgenic animals established in these studies should serve as valuable model systems to identify and dissect the underlying mechanisms for different aspects of cardiac pathology such as hypertrophy, contractile dysfunction, and abnormal cell-cell communication. The insights learned from these investigations may help to develop novel therapeutic approaches to confront this devastating disease.

Animals↗
PubMed2001

Anomalous electron mobility in a coaxial Hall discharge plasma.

A comprehensive analysis of measurements supporting the presence of anomalous cross-field electron mobility in Hall plasma accelerators is presented. Nonintrusive laser-induced fluorescence measurements of neutral xenon and ionized xenon velocities, and various electrostatic probe diagnostic measurements are used to locally determine the effective electron Hall parameter inside the accelerator channel. These values are then compared to the classical (collision-driven) Hall parameters expected for a quiescent magnetized plasma. The results indicate that in the vicinity of the anode, where there are fewer plasma instabilities, the electron-transport mechanism is likely elastic collisions with the background neutral xenon. However, we find that in the vicinity of the discharge channel exit, where the magnetic field is the strongest and where there are intense fluctuations in the plasma properties, the inferred Hall parameter departs from the classical value, and is close to the Bohm value of (omega(ce)tau)(eff) approximately 16. These results are used to support a simple model for the Hall parameter that is based on the scalar addition of the electron collision frequencies (elastic collision induced plus fluctuation induced), as proposed by Boeuf and Garrigues [J. Appl. Phys. 84, 3541 (1998)]. The results also draw attention to the possible role of fluctuations in enhancing electron transport in regions where the electrons are highly magnetized.

Journal Article↗
PubMed2001

Effects of nonionizing prepulses in high-intensity laser-solid interactions.

We present theoretical and experimental evidence that nonionizing prepulses with intensities as low as 10(8)-10(9) W/cm(2) can substantially alter high intensity laser-solid interactions. We show that prepulse-heating and vaporization of the target can lead to a preformed plasma once the vapor is ionized by the rising edge of the high-intensity pulse. Our results indicate that peak prepulse intensity is not the only important parameter to consider in determining preformed plasma thresholds, and that a more comprehensive analysis of the prepulse duration and the target material is required.

Journal Article↗
PubMed2002

Nonlinear dynamics of periodically focused intense particle beams.

We extend a previous study [R. Pakter and F. B. Rizzato, Phys. Rev. Lett. 87, 044801 (2001)] and investigate the nonlinear dynamics of periodically focused intense particle beams. We show that (i) the scenario as the focusing field increases is not the existence of a single threshold above which stable matched (equilibrium) solutions are absent, as believed so far, but the existence of successive regions of stability interrupted by gaps where periodic solutions are either unstable or simply do not exist; (ii) the beam can be focused to tighter radii using stable matched solutions found for focusing field strengths greater than the previous threshold. A comprehensive analysis is carried out as a function of the relevant parameters of the system. Self-consistent simulations validate the findings. The gaps are of crucial importance because they must be avoided if the goal is beam confinement with matched solutions; we develop an analytical model to determine the gap structure, which agrees well with computer simulations.

Journal Article↗
PubMed2002

Exact results for hydrogen recombination on dust grain surfaces.

The recombination of hydrogen in the interstellar medium, taking place on surfaces of microscopic dust grains, is an essential process in the evolution of chemical complexity in interstellar clouds. Molecular hydrogen plays an important role in absorbing the heat that emerges during gravitational collapse, thus enabling the formation of structure in the universe. The H2 formation process has been studied theoretically, and in recent years also by laboratory experiments. The experimental results were analyzed using a rate equation model. The parameters of the surface that are relevant to H2 formation were obtained and used in order to calculate the recombination rate under interstellar conditions. However, it turned out that, due to the microscopic size of the dust grains and the low density of H atoms, the rate equations may not always apply. A master equation approach that provides a good description of the H2 formation process was proposed. It takes into account both the discrete nature of the H atoms and the fluctuations in the number of atoms on a grain. In this paper we present a comprehensive analysis of the H2 formation process, under steady state conditions, using an exact solution of the master equation. This solution provides an exact result for the hydrogen recombination rate and its dependence on the flux, the surface temperature, and the grain size. The results are compared with those obtained from the rate equations. The relevant length scales in the problem are identified and the parameter space is divided into two domains. One domain, characterized by first order kinetics, exhibits high efficiency of H2 formation. In the other domain, characterized by second order kinetics, the efficiency of H2 formation is low. In each of these domains we identify the range of parameters in which, due to the small size of the grains, the rate equations do not account correctly for the recombination rate and the master equation is needed.

Journal Article↗
PubMed2005

Parametric light bullets supported by quasi-phase-matched quadratically nonlinear crystals.

We present a comprehensive analysis of the dynamics of three-dimensional spatiotemporal nonspinning and spinning solitons in quasi-phased-matched (QPM) gratings. By employing an averaging approach based on perturbation theory, we show that the soliton's stability is strongly affected by the QPM-induced third-order nonlinearity (which is always of a mixed type, with opposite signs in front of the corresponding self-phase and cross-phase modulation terms). We study the dependence of the stability of the spatiotemporal soliton (STS) on its energy, spin, the wave-vector mismatch between the fundamental and second harmonics, and the relative strength of the intrinsic quadratic and QPM-induced cubic nonlinearities. In particular, all the spinning solitons are unstable against fragmentation, while zero-spin STS's have their stability regions on the system's parameter space.

Journal Article↗
PubMed2005

Propagation and relaxation of tension in stiff polymers.

We present a unified theory for the longitudinal dynamic response of a stiff polymer in solution to various external perturbations (mechanical excitations, hydrodynamic flows, electrical fields, temperature quenches, etc.) that can be represented as sudden changes of ambient/boundary conditions. The theory relies on a comprehensive analysis of the nonequilibrium propagation and relaxation of backbone stresses in a wormlike chain. We recover and substantially extend previous results based on heuristic arguments. New experimental implications are pointed out.

Journal Article↗
PubMed1989

Multiphasic uptake of potassium by corn roots: no linear component.

Concentration-dependence data (LV Kochian, WJ Lucas Plant Physiol 1982 70: 1723-1731; [1983] 73: 208-215; [1985] 429-436; LV Kochian, J Xin-zhi, WJ Lucas [1985], 79: 771-776) for potassium uptake by corn roots have been claimed to be resolvable into a saturable and a linear component representing two separate uptake mechanisms. A comprehensive analysis shows, however, that the data are not compatible with this concept. They can, in contrast, be precisely represented by multiphasic isotherms, in agreement with many findings for uptake of potassium and other solutes. Solute uptake in plants is proposed to be mediated by multistate entities having carrier-like properties at low external solute concentrations and channel-like properties at high concentrations.

Journal Article↗
PubMed2004

Silencing in Arabidopsis T-DNA transformants: the predominant role of a gene-specific RNA sensing mechanism versus position effects.

Pronounced variability of transgene expression and transgene silencing are commonly observed among independent plant lines transformed with the same construct. Single-copy T-DNA lines harboring reporter genes of various kind and number under the control of a strong promoter were established in Arabidopsis thaliana for a comprehensive analysis of transgene expression. Characterization of 132 independent transgenic lines revealed no case of silencing as a result of site of T-DNA integration. Below a certain number of identical transgenes in the genome, gene copy number and expression were positively correlated. Expression was high, stable over all generations analyzed, and of a comparable level among independent lines harboring the same copy number of a particular transgene. Conversely, RNA silencing was triggered if the transcript level of a transgene surpassed a gene-specific threshold. Transcript level-mediated silencing effectively accounts for the pronounced transgene expression variability seen among transformants. It is proposed that the RNA sensing mechanism described is a genome surveillance system that eliminates RNA corresponding to excessively transcribed genes, including transgenes, and so plays an important role in genome defense.

Arabidopsis↗