Research progress in the effects of terahertz waves on biomacromolecules.

With the rapid development of terahertz technologies, basic research and applications of terahertz waves in biomedicine have attracted increasing attention. The rotation and vibrational energy levels of biomacromolecules fall in the energy range of terahertz waves; thus, terahertz waves might interact with biomacromolecules. Therefore, terahertz waves have been widely applied to explore features of the terahertz spectrum of biomacromolecules. However, the effects of terahertz waves on biomacromolecules are largely unexplored. Although some progress has been reported, there are still numerous technical barriers to clarifying the relation between terahertz waves and biomacromolecules and to realizing the accurate regulation of biological macromolecules by terahertz waves. Therefore, further investigations should be conducted in the future. In this paper, we reviewed terahertz waves and their biomedical research advantages, applications of terahertz waves on biomacromolecules and the effects of terahertz waves on biomacromolecules. These findings will provide novel ideas and methods for the research and application of terahertz waves in the biomedical field.

Convergent horizontal gene transfer and cross-talk of mobile nucleic acids in parasitic plants.

Horizontal gene transfer (HGT), the movement and genomic integration of DNA across species boundaries, is commonly associated with bacteria and other microorganisms, but functional HGT (fHGT) is increasingly being recognized in heterotrophic parasitic plants that obtain their nutrients and water from their host plants through direct haustorial feeding. Here, in the holoparasitic stem parasite Cuscuta, we identify 108 transcribed and probably functional HGT events in Cuscuta campestris and related species, plus 42 additional regions with host-derived transposon, pseudogene and non-coding sequences. Surprisingly, 18 Cuscuta fHGTs were acquired from the same gene families by independent HGT events in Orobanchaceae parasites, and the majority are highly expressed in the haustorial feeding structures in both lineages. Convergent retention and expression of HGT sequences suggests an adaptive role for specific additional genes in parasite biology. Between 16 and 20 of the transcribed HGT events are inferred as ancestral in Cuscuta based on transcriptome sequences from species across the phylogenetic range of the genus, implicating fHGT in the successful radiation of Cuscuta parasites. Genome sequencing of C. campestris supports transfer of genomic DNA-rather than retroprocessed RNA-as the mechanism of fHGT. Many of the C. campestris genes horizontally acquired are also frequent sources of 24-nucleotide small RNAs that are typically associated with RNA-directed DNA methylation. One HGT encoding a leucine-rich repeat protein kinase overlaps with a microRNA that has been shown to regulate host gene expression, suggesting that HGT-derived parasite small RNAs may function in the parasite-host interaction. This study enriches our understanding of HGT by describing a parasite-host system with unprecedented gene exchange that points to convergent evolution of HGT events and the functional importance of horizontally transferred coding and non-coding sequences.

Evidence for cell-free nucleic acids as continuously arising endogenous DNA mutagens.

There is extensive literature to show that nucleic acids can be taken up by cells under experimental conditions and that foetal DNA can be detected in maternal tissues. The uptaken DNA can integrate into host cell genomes and can be transcribed and translated into proteins. They can also cause chromosomal damage and karyotype alterations. Cell-free nucleic acids (cfNAs)-based non-invasive DNA diagnostic techniques are being extensively researched in the field of cancer with the potential to advance new prognostic parameters and direct treatment decisions. However, whether extracellular cfNAs that are released into circulation from dying cells as a consequence of normal physiology have any functional significance has not been explored. A recent study has demonstrated that circulating cfNAs have the ability to cause DNA damage and mutagenesis by illegitimately integrating into healthy cells of the body, thereby acting as mobile genetic elements. Fluorescently-labeled cfNAs isolated from sera of cancer patients and healthy volunteers were shown to be readily taken up by host cells followed by activation of a DNA-damage-repair-response which led their large scale integration into the host cell genomes. The latter caused dsDNA breaks and apoptosis in cells in vitro and in those of vital organs when injected intravenously into mice. Cell-free chromatin was consistently more active than cell-free DNA, while cfNAs derived from cancer patients were significantly more active than those from healthy volunteers. This study suggests that circulating extracellular cfNAs act as physiological continuously arising DNA mutagens with implications for ageing, cancer and a host of other degenerative human pathologies.

Campomanesia adamantium (Cambess.) O. Berg seed desiccation: influence on vigor and nucleic acids.

The aim of this study was to evaluate the sensitivity of Campomanesia adamantium seeds to desiccation by drying in activated silica gel (fast) and under laboratory conditions (slow). To assess the sensitivity of the seeds to desiccation, we used drying with silica gel and drying under laboratory conditions (25 °C), in order to obtain seeds with moisture content of 45, 35, 30, 25, 20, 15, 10 and 5%. The physiological potential of the seeds after desiccation was evaluated by measuring primary root protrusion, percentage of normal seedlings, germination seed index, seedling length, total seedling dry mass, electrical conductivity and DNA and RNA integrities. The C. adamantium seeds were sensitive to desiccation and to a reduction in moisture content to 21.1% or less by desiccation using silica gel, and to 17.2% or less by desiccation under laboratory conditions; impairment of the physiological potential of the seeds was observed at these low moisture content levels. The integrity of the seed genomic DNA was not affected after drying seeds in the two methods. However, drying in silica gel to 4.5% moisture content and drying under laboratory conditions to 5.4% moisture content resulted in the loss of seed RNA integrity.

Seven novel probe systems for real-time PCR provide absolute single-base discrimination, higher signaling, and generic components.

We have developed novel probe systems for real-time PCR that provide higher specificity, greater sensitivity, and lower cost relative to dual-labeled probes. The seven DNA Detection Switch (DDS)-probe systems reported here employ two interacting polynucleotide components: a fluorescently labeled probe and a quencher antiprobe. High-fidelity detection is achieved with three DDS designs: two internal probes (internal DDS and Flip probes) and a primer probe (ZIPR probe), wherein each probe is combined with a carefully engineered, slightly mismatched, error-checking antiprobe. The antiprobe blocks off-target detection over a wide range of temperatures and facilitates multiplexing. Other designs (Universal probe, Half-Universal probe, and MacMan probe) use generic components that enable low-cost detection. Finally, single-molecule G-Force probes employ guanine-mediated fluorescent quenching by forming a hairpin between adjacent C-rich and G-rich sequences. Examples provided show how these probe technologies discriminate drug-resistant Mycobacterium tuberculosis mutants, Escherichia coli O157:H7, oncogenic EGFR deletion mutations, hepatitis B virus, influenza A/B strains, and single-nucleotide polymorphisms in the human VKORC1 gene.

Sensing temperature.

Temperature is an omnipresent physical variable reflecting the rotational, vibrational and translational motion of matter, what Richard Feynman called the "jiggling" of atoms. Temperature varies across space and time, and this variation has dramatic effects on the physiology of living cells. It changes the rate and nature of chemical reactions, and it alters the configuration of the atoms that make up nucleic acids, proteins, lipids and other biomolecules, significantly affecting their activity. While life may have started in a "warm little pond", as Charles Darwin mused, the organisms that surround us today have only made it this far by devising sophisticated systems for sensing and responding to variations in temperature, and by using these systems in ways that allow them to persist and thrive in the face of thermal fluctuation.

Circulating and synovial antibody profiling of juvenile arthritis patients by nucleic acid programmable protein arrays.

INTRODUCTION: Juvenile idiopathic arthritis (JIA) is a heterogeneous disease characterized by chronic joint inflammation of unknown cause in children. JIA is an autoimmune disease and small numbers of autoantibodies have been reported in JIA patients. The identification of antibody markers could improve the existing clinical management of patients. METHODS: A pilot study was performed on the application of a high-throughput platform, the nucleic acid programmable protein array (NAPPA), to assess the levels of antibodies present in the systemic circulation and synovial joint of a small cohort of juvenile arthritis patients. Plasma and synovial fluid from 10 JIA patients was screened for antibodies against 768 proteins on NAPPAs. RESULTS: Quantitative reproducibility of NAPPAs was demonstrated with > 0.95 intra-array and inter-array correlations. A strong correlation was also observed for the levels of antibodies between plasma and synovial fluid across the study cohort (r = 0.96). Differences in the levels of 18 antibodies were revealed between sample types across all patients. Patients were segregated into two clinical subtypes with distinct antibody signatures by unsupervised hierarchical cluster analysis. CONCLUSION: The NAPPAs provide a high-throughput quantitatively reproducible platform to screen for disease-specific autoantibodies at the proteome level on a microscope slide. The strong correlation between the circulating antibody levels and those of the inflamed joint represents a novel finding and provides confidence to use plasma for discovery of autoantibodies in JIA, thus circumventing the challenges associated with joint aspiration. We expect that autoantibody profiling of JIA patients on NAPPAs could yield antibody markers that can act as criteria to stratify patients, predict outcomes and understand disease etiology at the molecular level.

[Regulation of innate immune responses by nucleic acid analogues].

The activation of innate immune responses by nucleic acids is critical to host responses against pathogens, such as viruses; however, nucleic acids can also trigger the development and/or exacerbation of pathogenic responses such as autoimmunity. We previously demonstrated that the selective activation of nucleic acid-sensing cytosolic and Toll-like receptors is contingent on the promiscuous sensing of nucleic acids by high-mobility group box proteins (HMGBs). Basides these findings, we also found that nonimmunogenic nucleotide with high-affinity HMGB binding, termed ISM ODN, functions as suppressing agent for nucleic acid-activated innate immune responses. In this review, we aim to summerize this novel feature of HMGB proteins in nucleic acid-mediated innate immune responses. In addition, we will discuss the inhibitory effect of nonimmunogenic oligodeoxynucleotides (ni-ODNs) targeting HMGB proteins.

Human CD14dim monocytes patrol and sense nucleic acids and viruses via TLR7 and TLR8 receptors.

Monocytes are effectors of the inflammatory response to microbes. Human CD14(+) monocytes specialize in phagocytosis and production of reactive oxygen species and secrete inflammatory cytokines in response to a broad range of microbial cues. Here, we have characterized the functions of human monocytes that lack CD14 (CD14(dim)) and express CD16. CD14(dim) monocytes were genetically distinct from natural killer cells. Gene expression analyses indicated similarities with murine patrolling Gr1(dim) monocytes, and they patrolled the endothelium of blood vessels after adoptive transfer, in a lymphocyte function-associated antigen-1-dependent manner. CD14(dim) monocytes were weak phagocytes and did not produce ROS or cytokines in response to cell-surface Toll-like receptors. Instead, they selectively produced TNF-α, IL-1ß, and CCL3 in response to viruses and immune complexes containing nucleic acids, via a proinflammatory TLR7-TLR 8-MyD88-MEK pathway. Thus, CD14(dim) cells are bona fide monocytes involved in the innate local surveillance of tissues and the pathogenesis of autoimmune diseases.

Darwinian chemistry: towards the synthesis of a simple cell.

The total synthesis of a simple cell is in many ways the ultimate challenge in synthetic biology. Outlined eight years ago in a visionary article by Szostak et al. (J. W. Szostak, D. P. Bartel and P. L. Luisi, Nature, 2001, 409, 387), the chances of success seemed remote. However, recent progress in nucleic acid chemistry, directed evolution and membrane biophysics have brought the prospect of a simple synthetic cell with life-like properties such as growth, division, heredity and evolution within reach. Success in this area will not only revolutionize our understanding of abiogenesis but provide a fertile test-bed for models of prebiotic chemistry and early evolution. Last but not least, a robust "living" protocell may provide a versatile and safe chassis for embedding synthetic devices and systems.

[Medicinal chemistry targeting nucleosides and nucleic acids based on fine synthetic chemistry].

Nucleosides and nucleotides are one of the most important elements for cells by the fact that they are components of DNAs and RNAs. In addition, they play important roles in most fundamental cellular metabolic pathways such as energy donors, second messengers, and cofactors for various enzymes. Therefore, there exists a rich source in drug discovery targeting nucleosides and nucleotides. In order to utilize nucleosides and nucleic acids on the drug development, it is very important to develop reactions and methods, by which the highly coordinating and labile nucleoside intermediates can be used. With these in mind, we have been working on synthetic nucleoside and nucleic acid chemistry. First, branched sugar nucleoside derivatives, which are potential antitumor agents, have been synthesized utilizing samarium diiodide (SmI(2)) mediated Reformatsky reaction or aldol reaction. 3'-beta-Carbamoylmethylcytidine (CAMC) was found to exhibit potent cytotoxicity against various human tumor cell lines. Synthetic methodology of the caprazamycins, which are promising antibacterial nucleoside natural products, was also developed by the strategy including beta-selective ribosylation without using a neighboring group participation. Our synthetic route provided a range of key analogues with partial structures to define the pharmacophore. Simplification of the caprazamycins was further pursued to develop diketopiperazine analogs. Medicinal chemistry of oligodeoxynucleotides has been conducted. Thus, novel triazole-linked dumbbell oligodeoxynucleotides and modular bent oligodeoxynucleotides were synthesized. They exhibit excellent binding affinity to NF-kappaB or HMGB1 A-box protein, which are important therapeutic targets. Therefore, the results obtained conclusively demonstrated these oligodeoxynucleotides could be proposed as powerful decoy molecules.

Nucleic acid recognition receptors in autoimmunity.

Recent studies in mouse models of systemic autoimmune diseases have drawn attention to the involvement of Toll-like receptors (TLRs) in the generation of autoreactive immune responses. The endosomally localized TLRs7 and 9 are activated by autoimmune complexes containing self DNA and RNA in B lymphocytes and dendritic cells. These endogenous TLR ligands act as autoadjuvants providing a stimulatory signal together with the autoantigen and thus contribute to break peripheral tolerance against self antigens in systemic lupus erythematosus (SLE), for example. In vivo studies in SLE mouse models demonstrate an essential role for TLR7 in the generation of RNA-containing antinuclear antibodies and deposition of pathogenic immune complexes in the kidney. TLR9, however, appears to have immunostimulatory as well as regulatory functions in SLE mouse models. Type I Interferon, which is produced by plasmacytoid dendritic cells in response to autoimmune complexes containing RNA and DNA recognized by TLR7 and 9 acts as a potent amplifier of the autoimmune response. TLR-independent recognition of self nucleic acids by cytosolic RNA and DNA sensors may also play a role in the generation of autoimmune responses. Defects in protective mechanisms, which normally prevent immunostimulation by self nucleic acids in healthy individuals, promote the development of autoimmune diseases. For example, defects in nucleases that clear nucleic acids derived from apoptotic material, changes in the level and localization of TLR expression, defects in negative regulators of TLR signaling, or changes in the posttranscriptional modification of mammalian DNA and RNA may contribute to autoreactive responses. A better understanding of the exact function of different nucleic acid recognition receptors in the development of systemic autoimmunity will allow targeting of these innate immune receptors for the therapy of patients with systemic autoimmune diseases.

Web services at the European bioinformatics institute.

We present a new version of the European Bioinformatics Institute Web Services, a complete suite of SOAP-based web tools for structural and functional analysis, with new and improved applications. New functionality has been added to most of the services already available, and an improved version of the underlying framework has allowed us to include more applications. Information on the EBI Web Services, tutorials and clients can be found at http://www.ebi.ac.uk/Tools/webservices.

Extracellular nucleic acids.

Extracellular nucleic acids are found in different biological fluids in the organism and in the environment: DNA is a ubiquitous component of the organic matter pool in the soil and in all marine and freshwater habitats. Data from recent studies strongly suggest that extracellular DNA and RNA play important biological roles in microbial communities and in higher organisms. DNA is an important component of bacterial biofilms and is involved in horizontal gene transfer. In recent years, the circulating extracellular nucleic acids were shown to be associated with some diseases. Attempts are being made to develop noninvasive methods of early tumor diagnostics based on analysis of circulating DNA and RNA. Recent observations demonstrated the possibility of nucleic acids exchange between eukaryotic cells and extracellular space suggesting their participation in so far unidentified biological processes.