Phylogenetic relationships of Drosophila melanogaster species group deduced from spacer regions of histone gene H2A-H2B

Nucleotide sequences of the spacer region of the histone gene H2A-H2B from 36 species of Drosophila melanogaster species group were determined. The phylogenetic trees were reconstructed with maximum parsimony, maximum likelihood, and Bayesian methods by u

Phylogenetic relationships of Cyprinidae (Teleostei : Cypriniformes) inferred from the partial S6K1 gene sequences and implication of indel sites in intron 1

The family Cyprinidae is widely distributed in East Asia, and has the important phylogenetic significance in the fish evolution. In this study, the 5' end partial sequences (containing exon 1, exon 2 and indel 1) of S6K1 gene were obtained from 30 representative species in Cyprinidae and outgroup using PCR amplification and sequencing. The phylogenetic relationships of Cyprinidae were reconstructed with neighbor joining (NJ), maximum parsimony (MP), maximum likelihood (ML), and Bayesian methods. Myxocyprinus asiaticus (Catostomidae) was assigned to the outgroup taxon. Similar phylogenetic relationships within the family Cyprinidae were achieved with the four analyses. Leuciscini and Barbini were monophyletic lineages respectively with the high nodal supports. Leuciscini comprises Hypophthalmichthyinae, Xenocyprinae, Cultrinae, Gobioninae, Acheilognathinae and East Asian species of Leuciscinae and Danioninae. Monophyly of East Asian clade was supported with high nodal support. Barbini comprises Schizothoracinae, Barbinae, Cyprininae and Labeoninae. The monophyletic lineage consisting of Danio rerio, D. myersi, and Rasbora trilineata was basal in the tree. In addition, the large fragment indels in intron 1 were analyzed to improve the understanding of Cyprinidae relationships. The results showed that the large fragment indels were correlated with the relations among species. Some conserved regions in intron 1 were thought to be involved in the functional regulation. However, no correlation was found between sequence variations and species characteristic size.

Improved surface morphology of stacked 1.3 mu m InAs/GaAs quantum dot active regions by introducing annealing processes

The authors report a simple but effective way to improve the surface morphology of stacked 1.3 mu m InAs/GaAs quantum dot (QD) active regions grown by metal-organic chemical vapor deposition (MOCVD), in which GaAs middle spacer and top separate confining heterostructure (SCH) layers are deposited at a low temperature of 560 degrees C to suppress postgrowth annealing effect that can blueshift emission wavelength of QDs. By introducing annealing processes just after depositing the GaAs spacer layers, the authors demonstrate that the surface morphology of the top GaAs SCH layer can be dramatically improved. For a model structure of five-layer QDs, the surface roughness with the introduced annealing processes (IAPs) is reduced to about 1.3 nm (5x5 mu m(2) area), much less than 4.2 nm without the IAPs. Furthermore, photoluminescence measurements show that inserting the annealing steps does not induce any changes in emission wavelength. This dramatic improvement in surface morphology results from the improved GaAs spacer surfaces due to the IAPs. The technique reported here has important implications for realizing stacked 1.3 mu m InAs/GaAs QD lasers based on MOCVD.

Phylogeography of the Northern Atlantic species Chondrus crispus (Gigartinales, Rhodophyta) inferred from nuclear rDNA internal transcribed spacer sequences

Eighteen isolates of the red algae Chondrus crispus were collected from Northern Atlantic sites, together with C. ocellatus, C. yendoi and C. pinnulatus from the North Pacific. The nuclear rDNA internal transcribed spacer (ITS) was sequenced and compared, spanning both the ITS regions and the 5.8S rRNA gene. Percentage of nucleotide variation for C. crispus ranged from 0.3% to 4.0%. Phylogenetic analyses were performed using maximum parsimony (MP), neighbor-joining (NJ) and minimum evolution methods. They showed that two main clades existed within the C. crispus samples examined and that suggested C. crispus had a single Atlantic origin. The clustering however did not follow the geographic origin. We hypothesized that the current distribution of C. crispus populations might be a result of three main factors: temperature boundaries, paleoclimate and paleoceanography. ITS data exhibited abundant molecular information not only for phylogeographical investigation but also for systematics studies.

There are two 5 '-flanking regions of bkt encoding beta-carotene ketolase in Haematococcus pluvialis

The unicellular green alga Haematococcus pluvialis accumulates a commercially valuable astaxanthin, with levels reaching up to 4% dry weight under environmental stress. In recent years, much effort has been devoted to understanding the molecular mechanisms regulating astaxanthin biosynthetic pathways. Beta-carotene ketolase (bkt), with control being exhibited at the transcription level, plays an important role in astaxanthin biosynthesis by H. pluvialis. Here we demonstrate the presence of two separate 5'-flanking regions [1.5 kilobase (kb) and 2 kb] of bkt (bkt1 and bkt2) that possess regulatory elements similar to those of known stress-responsive genes in plants. Results of 5'-deletion constructs and transient beta-galactosidase expression assays demonstrate that there may be positive regulatory elements governing expression in the shorter promoter at -1060/-900 from the 1.5 kb 5' region, and in the longer promoter at -1838/-1219 and at -1046/ -734 from the 2 kb 5' region relative to each homologous ATG start codon. Furthermore, our present studies reveal that the first intron (+371/+497) downstream from the 1.5 kb 5' untranslated region of bkt1 may function as a negative regulatory element to regulate its own promoter.

The complete mitochondrial genome of the mantid shrimp Oratosquilla oratoria (Crustacea: Malacostraca: Stomatopoda): Novel non-coding regions features and phylogenetic implications of the Stomatopoda

The complete mitochondrial (mt) genome sequence of Oratosquilla oratoria (Crustacea: Malacostraca: Stomatopoda) was determined; a circular molecule of 15,783 bp in length. The gene content and arrangement are consistent with the pancrustacean ground pattern. The mt control region of O. oratoria is characterized by no GA-block near the 3' end and different position of [TA(A)]n-blocks compared with other reported Stomatopoda species. The sequence of the second hairpin structure is relative conserved which suggests this region may be a synapomorphic character for the Stomatopoda. In addition, a relative large intergenic spacer (101 bp) with higher A + T content than that in control region was identified between the tRNA(Glu) and tRNA(Phe) genes. Phylogenetic analyses based on the current dataset of complete mt genomes strongly support the Stomatopoda is closely related to Euphausiacea. They in turn cluster with Penaeoidea and Caridea clades while other decapods form a separate group, which rejects the monophyly of Decapoda. This challenges the suitability of Stomatopoda as an outgroup of Decapoda in phylogenetic analyses. The basal position of Stomatopoda within Eumalacostraca according to the morphological characters is also questioned. (C) 2010 Elsevier Inc. All rights reserved.

Phylogenetic origins of the Himalayan endemic Dolomiaea, Diplazoptilon and Xanthopappus (Asteraceae : Cardueae) based on three DNA regions

Background and Aims It is an enduring question as to the mechanisms leading to the high diversity and the processes producing endemics with unusual morphologies in the Himalayan alpine region. In the present study, the phylogenetic relationships and origins of three such endemic genera were analysed, Dolomiaea, Diplazoptilon and Xanthopappus, all in the tribe Cardueae of Asteraceae.Methods The nuclear rDNA internal transcribed spacer (ITS) and plastid trnL-F and psbA-trnH regions of these three genera were sequenced. The same regions for other related genera in Cardueae were also sequenced or downloaded from GenBank. Phylogenetic trees were constructed from individual and combined data sets of the three types of sequences using maximum parsimony, maximum likelihood and Bayesian analyses.Key Results The phylogenetic tree obtained allowed earlier hypotheses concerning the relationships of these three endemic genera based on gross morphology to be rejected. Frolovia and Saussurea costus were deeply nested within Dolomiaea, and the strong statistical support for the Dolomiaea-Frolovia clade suggested that circumscription of Dolomiaea should be more broadly redefined. Diplazoptilon was resolved as sister to Himalaiella, and these two together are sister to Lipschitziella. The clade comprising these three genera is sister to Jurinea, and together these four genera are sister to the Dolomiaea-Frolovia clade. Xanthopappus, previously hypothesized to be closely related to Carduus, was found to be nested within a well-supported but not fully resolved Onopordum group with Alfredia, Ancathia, Lamyropappus, Olgaea, Synurus and Syreitschikovia, rather than the Cardinis group. The crude dating based on ITS sequence divergence revealed that the divergence time of Dolomiaea-Frolovia from its sister group probably occurred 13.6-12.2 million years ago (Ma), and the divergence times of the other two genera, Xanthopappus and Diplazoptilon, from their close relatives around 5.7-4.7 Ma and 2.0-1.6 Ma, respectively.Conclusions The findings provide an improved understanding of the intergeneric relationships in Cardueae. The crude calibration of lineages indicates that the uplifts of the Qiinghai -Tibetan Plateau since the Miocene might have served as a continuous stimulus for the production of these morphologically aberrant endemic elements of the Himalayan flora.

Nd65Al10Fe25-xCox (x=0,5,10) bulk metallic glasses with wide supercooled liquid regions

Bulk metallic glasses of Nd65Al10Fe25-xCox (x=0,5,10) have been prepared in the form of 3 mm diam rods. Results of differential scanning calrimetry, dynamic mechanical thermal analysis (DMTA), and x-ray diffraction are presented for these alloys. It is shown that the glass transition and crystallization have been observed by DMTA. The reduced glass transition temperature of these glasses, defined as the ratio between the glass transition temperature T-g and the melting temperature T-l is in the range from 0.55 to 0.62. All these glasses have a large supercooled liquid region (SLR), ranging from 80 to 130 K. The high value of reduced glass transition temperature and wide SLR agree with their good glass formation ability.

On The Cyclic Bending Behaviour Of A Hard Coating On A Ductile Substrate With Periodic Surface Hardened Regions

A cyclic bending experiment is designed to investigate the interface fracture behaviour of a hard chromium coating on a ductile substrate with periodic surface hardened regions. The unique deflection pattern of the vertical cracks after they run through the coating and impinge at the interface is revealed experimentally. A simple double-layer elastic beam model is adopted to investigate the interfacial shear stresses analytically. A FE model is employed to compute the stresses of the tri-phase structure under a single round of bending, and to investigate the effect of the loading conditions on the deflection pattern of the vertical cracks at the interface. (C) 2008 Elsevier Ltd. All rights reserved.

The degree of predictability of earthquakes in several regions of China: statistical analysis of historical data

The stress release model, a stochastic version of the elastic-rebound theory, is applied to the historical earthquake data from three strong earthquake-prone regions of China, including North China, Southwest China, and the Taiwan seismic regions. The results show that the seismicity along a plate boundary (Taiwan) is more active than in intraplate regions (North and Southwest China). The degree of predictability or regularity of seismic events in these seismic regions, based on both the Akaike information criterion (AIC) and fitted sensitivity parameters, follows the order Taiwan, Southwest China, and North China, which is further identified by numerical simulations. (c) 2004 Elsevier Ltd. All rights reserved.

Energy conversions and storage caused by an unsteady poloidal flow in active solar regions

In this paper we discuss coupling processes between a magnetic field and an unsteady plasma motion, and analyze the features of energy storage and conversions in active region. It is pointed out that the static force-free field is insufficient for a discussion of storage processes, and also the pure unsteady plasma rotation is not a perfect approach. In order to analyze the energy storage, we must consider the addition of poloidal plasma motion. The paper shows that because the unsteady poloidal flow is added and coupling occurs between the magnetic field and both the toroidal and the poloidal plasma flows, an unsteady process is maintained which changes the force-free factor with time. Hence, the energy in the lower levels can be transferred to the upper levels, and a considerable energy can be stored in the active region. Finally, another storage process is given which is due to the pure poloidal flow. The article shows that even if there is no twisted magnetic line of force, the energy in the lower levels may still be transferred to the upper levels and stored there.

Explorations of electric-current system in solar active regions .1. Empirical inferences of the current flows

In this paper we explore techniques to identify sources of electric current systems and their channels of flow in solar active regions. Measured photospheric vector magnetic fields (VMF) together with high-resolution white-light and H filtergrams provide the data base to derive the current systems in the photosphere and chromosphere. Simple mathematical constructions of fields and currents are also adopted to understand these data. As an example, the techniques are then applied to infer current systems in AR 2372 in early April 1980. The main results are: (i) In unipolar sunspots the current density may reach values of 103 CGSE, and the Lorentz force on it can accelerate the Evershed flow, (ii) Spots exhibiting significant spiral pattrn in the penumbral filaments are the sources of vertical major currents at the photospheric surface, (iii) Magnetic neutral lines where the transverse field was strongly sheared were channels along which strong current system flows, (iv) The inferred current systems produced oppositely-flowing currents in the area of the delta configuration that was the site of flaring in AR 2372.

The dynamical process of a coronal transient associated with an eruptive prominence .2. Analytical solutions in finite regions

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Simulated pathogenic conformational switch regions matched well with the biochemical findings

Pathogenic conformational conversion is a general causation of many disease, such as transmissible spon- giform encephalopathy (TSE) caused by misfolding of prion, sickle cell anemia, and etc. In such structural changes, misfolding occurs in regions important for the stability of native structure firstly. This destabi- lizes the normal conformation and leads to subsequent errors in folding pathway. Sites involved in the first stage can be deemed switch regions of the protein, and are vital for conformational conversion. Namely it could be a switch of disease at residue level. Here we report an algorithm that can identify such sites computationally with an accuracy of 93%, by calculating the probability of the native structure of a short segment jumping to a mistake one. Knowledge of such switch sites could be used to target clinical therapy, study physiological and pathologic mechanism of protein, and etc.