Draft genome of Myxosarcina sp. strain GI1, a baeocytous cyanobacterium associated with the marine sponge Terpios hoshinota.

To date, genome sequences (complete or in draft form) from only six baeocytous cyanobacteria in four genera have been reported: Xenococcus, Chroococcidiopsis, Pleurocapsa, and Stanieria. To expand our knowledge on the diversity of baeocytous cyanobacteria, this study sequenced the genome of GI1, which is a Myxosarcina-like baeocytous cyanobacterium. GI1 is of interest not only because of its phylogenetic niche, but also because it is a cyanobiont isolated from the marine cyanobacteriosponge Terpios hoshinota, which has been shown to cause the death of corals.

Ecological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts.

Background: Comparative genomics provides insights into the diversification of bacterial species. Bacterial speciation usually takes place with lasting homologous recombination, which not only acts as a cohering force between diverging lineages but brings advantageous alleles favored by natural selection, and results in ecologically distinct species, e.g.

New bioactive chromanes from Litchi chinensis.

Seven new δ-tocotrienols, designated litchtocotrienols A-G (1-7), together with one glorious macrocyclic analogue, macrolitchtocotrienol A (8), and one new meroditerpene chromane, cyclolitchtocotrienol A (9), were isolated from the leaves of Litchi chinensis. Their structures were mainly determined by extensive spectroscopic analysis, and their biological activities were evaluated by cytotoxicity against human gastric adenocarcinoma cell lines (AGS, ATCC CRL-1739) and hepatoma carcinoma cell line (HepG2 2.2.

Adaptive divergence with gene flow in incipient speciation of Miscanthus floridulus/sinensis complex (Poaceae).

Young incipient species provide ideal materials for untangling the process of ecological speciation in the presence of gene flow. The Miscanthus floridulus/sinensis complex exhibits diverse phenotypic and ecological differences despite recent divergence (approximately 1.59 million years ago).

Long-lived quantum coherence and non-Markovianity of photosynthetic complexes.

Long-lived quantum coherence in photosynthetic pigment-protein complexes has recently been reported at physiological temperature. It has been pointed out that the discrete vibrational modes may be responsible for the long-lived coherence. Here, we propose an analytical non-Markovian model to explain the origin of the long-lived coherence in pigment-protein complexes.

OMACC: an Optical-Map-Assisted Contig Connector for improving de novo genome assembly.

Background: Genome sequencing and assembly are essential for revealing the secrets of life hidden in genomes. Because of repeats in most genomes, current programs collate sequencing data into a set of assembled sequences, called contigs, instead of a complete genome. Toward completing a genome, optical mapping is powerful in rendering the relative order of contigs on the genome, which is called scaffolding.

Effects of GC bias in next-generation-sequencing data on de novo genome assembly.

Next-generation-sequencing (NGS) has revolutionized the field of genome assembly because of its much higher data throughput and much lower cost compared with traditional Sanger sequencing. However, NGS poses new computational challenges to de novo genome assembly. Among the challenges, GC bias in NGS data is known to aggravate genome assembly.

Evolutionary rates of commonly used nuclear and organelle markers of Arabidopsis relatives (Brassicaceae).

Recovering the genetic divergence between species is one of the major interests in the evolutionary biology. It requires accurate estimation of the neutral substitution rates. Arabidopsis thaliana, the first whole-genome sequenced plant, and its out-crossing relatives provide an ideal model for examining the split between sister species.

Footprints of natural and artificial selection for photoperiod pathway genes in Oryza.

Asian rice, Oryza sativa, consists of two major subspecies, indica and japonica, which are physiologically differentiated and adapted to different latitudes. Genes for photoperiod sensitivity are likely targets of selection along latitude. We examined the footprints of natural and artificial selections for four major genes of the photoperiod pathway, namely PHYTOCHROME B (PhyB), HEADING DATE 1 (Hd1), HEADING DATE 3a (Hd3a), and EARLY HEADING DATE 1 (Ehd1), by investigation of the patterns of nucleotide polymorphisms in cultivated and wild rice.

Elastic properties of self-supported circular thin copper films calculated from equilibrium thermal vibration.

Thermomechanical vibration of ultrathin, self-supported copper films due to thermal fluctuations is studied via the molecular dynamics simulation at room temperature. The elastodynamic theory with pre-stress is adopted to extract the physical properties of the films by comparing with the molecular dynamics data. The edge-clamped circular films consist of several atomic layers of fcc copper with the [100] direction normal to the film surface.

Four-component pharmacophore model for endomorphins toward μ opioid receptor subtypes.

In the present work, a series of simulation tools were used to determine structure-activity relationships for the endomorphins (EMs) and derive μ-pharmacophore models for these peptides. Potential lowest energy conformations were determined in vacuo by systematically varying the torsional angles of the Tyr(1)-Pro(2) (ω(1)) and Pro(2)-Trp(3)/Phe(3) (ω(2)) as tuning parameters in AM1 calculations. These initial models were then exposed to aqueous conditions via molecular dynamics simulations.

Genetic population structure of the alpine species Rhododendron pseudochrysanthum sensu lato (Ericaceae) inferred from chloroplast and nuclear DNA.

Background: A complex of incipient species with different degrees of morphological or ecological differentiation provides an ideal model for studying species divergence. We examined the phylogeography and the evolutionary history of the Rhododendron pseudochrysanthum s. l.

The operations of quantum logic gates with pure and mixed initial states.

The implementations of quantum logic gates realized by the rovibrational states of a C(12)O(16) molecule in the X((1)Σ(+)) electronic ground state are investigated. Optimal laser fields are obtained by using the modified multitarget optimal theory (MTOCT) which combines the maxima of the cost functional and the fidelity for state and quantum process. The projection operator technique together with modified MTOCT is used to get optimal laser fields.

Conservation genetics and phylogeography of endangered and endemic shrub Tetraena mongolica (Zygophyllaceae) in Inner Mongolia, China.

Background: Tetraena mongolica (Zygophyllaceae), an endangered endemic species in western Inner Mongolia, China. For endemic species with a limited geographical range and declining populations, historical patterns of demography and hierarchical genetic structure are important for determining population structure, and also provide information for developing effective and sustainable management plans. In this study, we assess genetic variation, population structure, and phylogeography of T.

A molecular dynamics study on opioid activities of biphalin molecule.

Molecular dynamics simulations of the biphalin molecule, (Tyr-D-Ala-Gly-Phe-NH)(2), and the active tetrapeptide hydrazide, Tyr-D-Ala-Gly-Phe-NH-NH(2) were performed to investigate the cause of the increased μ and δ receptor binding affinities of the former over the latter. The simulation results demonstrate that the acylation of the two equal tetrapeptide fragments of biphalin produces the constrained hydrazide bridges [Formula: see text] and [Formula: see text], which in turn increase the opportunity of conformations for binding to μ or δ receptors. Meanwhile, the connection of the two active tetrapeptide fragments of biphalin also results in the constrained side chain torsion angle χ(2) at one of the two residues Phe.

Multilocus analysis of genetic divergence between outcrossing Arabidopsis species: evidence of genome-wide admixture.

• Outcrossing Arabidopsis species that diverged from their inbreeding relative Arabidopsis thaliana 5 million yr ago and display a biogeographical pattern of interspecific sympatry vs intraspecific allopatry provides an ideal model for studying impacts of gene introgression and polyploidization on species diversification. • Flow cytometry analyses detected ploidy polymorphisms of 2× and 4× in Arabidopsis lyrata ssp. kamchatica of Taiwan.

Population structure of Nouelia insignis (Asteraceae), an endangered species in southwestern China, based on chloroplast DNA sequences: recent demographic shrinking.

Nouelia insignis, an endangered species, is distributed in the Jinsha and Nanpan drainage areas in southwestern China. In this study, we examined the genetic diversity and population structure based on the sequences of the cpDNA rpL 16 intron. Low levels of genetic variation were detected within all populations of the endemic species.

Role of hydroxyl groups in the NH(x) (x = 1-3) adsorption on the TiO2 anatase (101) surface determined by a first-principles study.

A spin-polarized density functional theory calculation was carried out to study the adsorption of NH(x) species (x = 1-3) on a TiO2 anatase (101) surface with and without hydroxyl groups by using first-principles calculations. It was found that the present hydroxyl group has the effect of significantly enhancing the adsorption of monodentate adsorbates H2N-Ti(a) compared to that on a bare surface. The nature of the interaction between the adsorbate (NH(x)) and the hydroxylated or bare surface was analyzed by the Mulliken charge and density of states (DOS) calculations.

The nanoindentation of a copper substrate by single-walled carbon nanocone tips: a molecular dynamics study.

This study dealt with deep nanoindentation of a copper substrate with single-walled carbon nanocones (SWCNCs) as the proximal probe tip, using molecular dynamics (MD) simulations. As an important feature, during the indentation the end part of the SWCNC tip will suffer a narrowing effect due to the radial component of resistant compression from the substrate and then forms into a somewhat flat arrowhead-like shape. The effective cross-sectional area of the SWCNC tip inside the substrate that the resistant force is acting on therefore is reduced to lower the normal resistant force on the tip.

Structure-activity relationships of alphaS1-casomorphin using AM1 calculations and molecular dynamics simulations.

This paper investigates the structure-activity relationships of alphaS1-casomorphin (alphaS1-CM) using AM1 calculations and molecular dynamics (MD) simulations. Previous studies have shown that this peptide has remarkable opioid actions, and not only has a high affinity toward all three subtypes (kappa1-kappa3) of the kappa-opioid sites, but also inhibits the proliferation of the T47D human breast cancer cell line. The systematic conformer search performed by the AM1 calculations is based on the torsional angles of the Val2-Pro3 (omega2) and Phe4-Pro5 (omega4) amide bonds.

Structure-activity relationships of Leu-Enkephalin analog with (4-Carboxamido)phenylalanine substituted for tyrosine: a molecular dynamics study.

Motivated by recent experimental work on Leu-Enkephalin modification with (4-Carboxamido)phenylalanine (Cpa), we perform MD simulations to study the structure-activity relationships of the [Cpa(1), Leu(5)]-enkephalin (Cpa-LE) for better understandings of the binding affinity in delta-selective opioid ligands. Recently, Tyr(1) substituted into Cpa(1) form was experimentally found to be the first example of an amino acid that acts as a surrogate for Tyr(1) in opioid peptide ligands, which challenges a long-standing belief that a phenolic residue is required for high affinity binding. Our simulations show the Cpa-LE structure in aqueous solution revealed that the occurrence of single-bend packed state can be stabilized by an intramolecular hydrogen bond from Leu(5)-NH to Gly(2)-CO (5-->2).

Globally asymptotic stability of a class of neutral-type neural networks with delays.

Several stability conditions for a class of systems with retarded-type delays are presented in the literature. However, no results have yet been presented for neural networks with neutral-type delays. Accordingly, this correspondence investigates the globally asymptotic stability of a class of neutral-type neural networks with delays.

Generalized projective synchronization of chaotic systems with unknown dead-zone input: observer-based approach.

In this paper we investigate the synchronization problem of drive-response chaotic systems with a scalar coupling signal. By using the scalar transmitted signal from the drive chaotic system, an observer-based response chaotic system with dead-zone nonlinear input is designed. An output feedback control technique is derived to achieve generalized projective synchronization between the drive system and the response system.

Conformational stability and three-dimensional model of the delta-opioid pharmacophore for the extended antiparallel dimer structure of Met-enkephalin in water.

The conformational stability of the extended antiparallel dimer structure of Met-enkephalin in water was analyzed by examining the hydration structure of enkephalin using molecular dynamics simulations. The result shows that, despite of the hydrophicility of the terminal atoms in the pentapeptide, the main contributor for the stability of the dimer in water is the four intermolecular hydrogen bonds between the Gly(2) and Phe(4) groups. The three-dimensional model of the delta-opioid pharmacophore for this dimer structure was also established.

Electronic properties of capped, finite-length armchair carbon nanotubes in an electric field.

This study investigates the electronic properties of finite-length armchair carbon nanotubes in an electric field (E) using a single-pi-band tight-binding model. Three different tip configurations are considered, namely, open ends with hydrogen terminations (H-terminations), one end capped with half of C60 fullerene and the other end open with H-terminations, and both ends capped with half of C60 fullerene. In general, the electronic states and energy gaps of low-energy electronic structures are highly sensitive to changes in the direction and magnitude of the applied electric field and to the tip configuration.