BarraCUDA – a Fast Sequence Mapping Software using Graphics Processing Units

High-throughput DNA sequencing (HTS) instruments today are capable of generating millions of sequencing reads in a short period of time, and this represents a serious challenge to current bioinformatics pipeline in processing such an enormous amount of data in a fast and economical fashion. Modern graphics cards are powerful processing units that consist of hundreds of scalar processors in parallel in order to handle the rendering of high-definition graphics in real-time. It is this computational capability that we propose to harness in order to accelerate some of the time-consuming steps in analyzing data generated by the HTS instruments. We have developed BarraCUDA, a novel sequence mapping software that utilizes the parallelism of NVIDIA CUDA graphics cards to map sequencing reads to a particular location on a reference genome. While delivering a similar mapping fidelity as other mainstream programs , BarraCUDA is a magnitude faster in mapping throughput compared to its CPU counterparts. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the mapping throughput. BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the mapping of millions of sequencing reads generated by HTS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology. BarraCUDA is currently available at http://seqbarracuda.sf.net

Effects of microcystin-RR on the antioxidant system of Bacillus subtilis

Microcystins are a kind of cyclic hepatotoxins produced by many cyanobacterial species. Many works have been done concerning, the toxic effects of microcystins on animals and plants. However, the reports about their effects on microbial cells are very limited. In the present paper, Bacillus subtilis (B. subtilis) was used to determine the dose- and time-effect of microcystin-RR, and the results showed that the activity of antioxidant enzymes including superoxide dismutase (SOD) and catalase (CAT) was significantly increased to that of control, when exposed to 5 or 10 mu g/ml microcystin-RR for 1 h. The contents of thiobarbituric acid-reactive sub-stances (TBARS) and glutathione (GSH) as well as glu-tathione reductase (GR) activity were obviously increased only when exposed to 10 mu g/ml microcystin-RR. For the time-effect of microcystin-RR on B. subtilis, the activities of antioxidant enzymes including SOD and CAT as well as GR activity and TBARS, GSH contents in B. subtilis were at first significantly increased, and then subsequently de-creased. These results suggested that microcystin-RR could induce the oxidative stress of B. subtilis for a short period. The antioxidant system protects B. subtilis from oxidative damage.

Range-wide Yangtze freshwater dolphin expedition: The last chance to see Baiji?

Background, Aim and Scope. There are two species of fresh water cetaceans surviving in the Yangtze River system in China: Baiji (Lipotes vexillifer) and Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis). As a result of the expansion of human activities on the river, their distribution ranges appear to be decreasing and in the case of the Baiji, are even being restricted to several sections. The Baiji is the world's most critically endangered cetacean species with a population estimated at only a few tens of individuals. The Yangtze finless porpoise is the world's only freshwater-adapted population of the species, and it has been estimated that only around 1,000 individuals remain in the river system. In order to prevent the extinction of Baiji and a sharp decline in the abundance of the porpoise, in situ conservation (i.e. in the river) and two ex situ conservation (i.e. in semi-natural reserves and in captivity) strategies were proposed and have been implemented since the early 1990s. In view of both the severely endangered status of the animals and the severely degraded conditions of their habitats, the feasibility and actual status of these two strategies are raised for discussion. Main Features. The threats faced by the cetaceans are mainly from the unfettered exploitation of the river's resources. In the past 20 years, five nature reserves have been established along the river. Imposing maximum prohibition of harmful and illegal fishing methods in the reserves might prolong the process of extinction of these cetaceans in the wild, but so far, the administrative measures taken in the reserves have not yet kept the abundance from sharply declining. As human use of the river and its resources is expected to intensify for many decades into the future, the ability of the river to continue to support these species is certainly undecided. Therefore, rescuing animals from the river and establishing viable breeding populations in semi-natural reserves, in which the environment is similar to the main stream of the river, and in captivity, has to be considered urgently as the short-term goal of ex situ strategies. Since the abundance of porpoises is higher than that of the Baiji, we have first established breeding populations of them in the semi-natural reserves and in captivity. But, considering the extremely low density of Baiji in the river, an immediate range-wide Yangtze Baiji survey is an urgent need for locating and capturing sufficient Baiji for successfully establishing a breeding population of them in semi-natural reserves. Results. Two semi-natural reserves (in Shishou, Hubei Province, and Tongling, Anhui Province) have been set up along the river in order to establish breeding populations of the Baiji and the porpoises. So far, several small groups of porpoises that were caught in the main stream of the river have successively been introduced into the semi-natural reserves. Under careful management, these animals in both of the semi-natural reserves not only survive, but can also reproduce naturally and successfully. At least one or three calves were born in each reserve each year. Additionally, a breeding group of porpoises is being established at the Baiji Dolphinarium at the Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan. There are presently four adults and one calf living in the Dolphinarium. The calf, born in July, 2005, is the first captive bred Yangtze Finless Porpoise in the world. In preparation for the range-wide Yangtze cetacean survey, a 9-day pilot expedition on the river near Wuhan was conducted in March, 2006, in order to develop methods for locating the Baiji. No Baiji were expected to be seen in such a short period but about 40 porpoise sightings were observed. Results of the pilot survey indicated that traditional visual and acoustical survey methods for cetaceans should be adapted to find the elusive Baiji in the river. Currently, the range-wide Yangtze cetacean survey is in preparation. The survey will cover over 1,700 km of the Yangtze River from Yichang to Shanghai, and is expected to provide detailed information on Baiji and porpoise numbers and distribution patterns in the river. Discussion. Although the short-term goal of ex situ conservation is to rescue cetaceans from the river and to establish viable breeding populations in semi-natural reserves and in captivity, the long-term goal of releasing the animals back into the river when the threats have decreased and the natural environment has been improved, should not be neglected. Moreover, the in situ conservation efforts in the natural reserves, and even in the entire Yangtze River system, including the lakes, should not be ignored or abandoned at any time. The activities contributing to the conservation of the Baiji and the porpoise in the wild have the incidental effect of benefiting the entire Yangtze ecosystem and other rare threatened species. The dynamics of the groups of porpoises in semi-natural reserves should be monitored continually, in order to guide the establishment of breeding groups of Baiji in these semi-natural reserves in the near future. Conclusions. Under the existing severely degraded conditions of the Yangtze system, the sharply fall populations of Baiji and porpoises will not be suspended in the foreseeable future. Therefore, ex situ conservation should be emphasized, and the severely threatened Baiji in the river should be removed and translocated to semi-natural reserves for establishing viable breeding populations. The successful program of capturing, translocating and maintaining finless porpoises in the Shishou semi-natural reserve has demonstrated its adequacy as an ex situ environment for cetaceans. Following the successful pilot survey in the river, the immediate range-wide Yangtze cetacean survey is proposed and is in preparation. The range-wide survey is expected to ensure that any remaining Baiji can be found reliably and captured successfully after the survey. Recommendations and Perspectives. During the range-wide survey, not only the Baiji but also the porpoise as well as their habitats should be investigated based on visual and acoustical methods that adapted to the river and the animals. Meanwhile, the current risk levels to the Baiji and porpoises should be evaluated at each area where Baiji or porpoises can be reliably sighted. Any capture efforts should be targeted on the most threatened areas, or where there is maximum risk of injury or death. The immediate track of the Baiji should be carried out once a Baiji is sighted during the range-wide survey in order to obtain the movement route of the animals, which is crucial information for the successful capture operation. Additionally, the need to establish new semi-natural reserves for the porpoises should be placed on the agenda of local and central governments in the near future.

Interfaces in InAs/GaSb Superlattices Grown by Molecular Beam Epitaxy

Short period InAs(4 ML)/GaSb(8 ML) superlattices (SLs) with InSb- and mixed-like (or Ga(1-x)In(x)As(1-)ySb(y)-like) interfaces (IFs) are grown by molecular-beam epitaxy (MBE) on (001) GaSb substrates at optimized growth temperature. Raman scattering reveals that two kinds of IFs can be formed by controlling shutter sequences. X-ray diffraction (XRD) and atomic force microscopy (AFM) demonstrate that SLs with mixed-like IFs are more sensitive to growth temperature than that with InSb-like IFs. The photoluminescence (PL) spectra of SLs with mixed-like IFs show a stronger intensity and narrower line width than with InSb-like IFs. It is concluded that InAs/GaSb SLs with mixed-like IFs have better crystalline and optical properties.

Investigation of GaAs/AlGaAs interfaces by reflectance-difference spectroscopy

The in-plane optical anisotropy of several GaAs/AlGaAs quantum well samples with different well widths has been measured at room temperature by reflectance-difference spectroscopy (RDS). The RDS line shapes are found to be similar in all the samples examined here, which dominantly consist of two peak-like signals corresponding to 1HH-->1E and 1LH-->1E transition. As the well width is decreased, or the 1 ML InAs layer is inserted at one interface, the intensity of the anisotropy increases quickly. Our detail analysis shows that the anisotropy mainly arises from the anisotropic interface roughness. The results demonstrate that the RDS technique is sensitive to the interface structures.

Role of different cap layers tuning the wavelength of self-assembled InAs/GaAs quantum dots

We have investigated the effect of different cap layers on the photoluminescence (PL) of self-assembled InAs/GaAs quantum dots (QDs). Based upon different cap layers, the wavelength of InAs QDs can be tuned to the range from 1.3 to 1.5 mum. An InAlAs and InGaAs combination layer can enlarge the energy separation between the ground and first excited radiative transition. GaAs/InAs short period superlattices (SLs) make the emission wavelength shift to 1.53 mum. The PL intensity of InAs QDs capped with GaAs/InAs SLs shows an anomalous increase with increasing temperature. We attribute this to the transfer of carriers between different QDs.

Self-assembled InAs quantum wires on InP(001)

Self-assembled InAs quantum wires (QWRs) embedded in In0.52Al0.48As, In0.53Ga0.47As, and (In0.52Al0.48As)(n)/(In0.53Ga0.47As)(m)-short-period-lattice matrices on InP(001) were fabricated with molecular beam epitaxy (MBE). These QWR lines are along [110], x 4 direction in the 2 x 4 reconstructed (001) surface as revealed with reflection high-energy electron diffraction (RHEED). Alignment of quantum wires in different layers in the InAs/spacer multilayer structures depends on the composition of spacer layers. (C) 2000 Elsevier Science B.V. All rights reserved.

Comparative Raman scattering studies of GaAs/AlxGa1-xAs and AlxGa1-xAs/AlAs superlattices

The room-temperature Raman scattering studies of longitudinal optic phonons in AlAs/AlxGa1-xAs and GaAs/AlxGa1-xAs short-period superlattices with different layer thicknesses were reported. The AlAs LO modes confined in AlAs layers and GaAs-like LO modes confined in AlxGa1-xAs layers were observed in AlAs/AlxGa1-xAs superlattices under off-resonance conditions. And the GaAs LO modes confined in GaAs layers and AlAs-like LO modes confined in AlxGa1-xAs layers were observed in GaAs/AlxGa1-xAs superlattices. In addition, the AlAs interface mode in AlAs/AlxGa1-xAs was also observed under near-resonance conditions. Based on the linear chain mode, the frequencies of confined LO modes measured by Raman scattering were unfolded according to q=m/(n+1)(2 pi/a(0)) by which the dispersion curves of AlAs-like and GaAs-like LO phonons in AlxGa1-xAs mixed crystal were obtained.

Optical properties of Ge self-organized quantum dots in Si

Small-size, high-density, and vertical-ordering Ge quantum dots are observed in strained Si/Ge short-period superlattices grown on Si(001) at low growth temperature by molecular-beam epitaxy. The photoluminescence (PL) peak position, the strong PL at room temperature, and the high exciton binding energy suggest an indirect-to-direct conversion of the Ge quantum dots. This conversion is in good agreement with the theoretical prediction. The characteristic of absorption directly indicates this conversion. The tunneling of carriers between these quantum dots is also observed. [S0163-1829(98)03515-2].

WANNIER LOCALIZATION IN GAAS/GAALAS SUPERLATTICES UNDER ELECTRIC-FIELD

We have studied the Wannier-Stark effect in GaAs/GaAlAs short-period superlattices under applied electric field perpendicular to the layers by room- and low-temperature photocurrent measurements. The changes in the transition intensities with biasing are well fitted to a theoretical calculation based on the finite Kronig-Penney model on which the potential of an applied electric field is superposed. With increasing electric field, the 0h peak grows to a maximum while the -1h and +1h peaks monotonousely decrease. By a comparison of the spectra measured at different temperatures, the two peaks in the room temperature photocurrent spectra at relatively low electric field (1.0 X 10(4) V/cm) are identified to be caused by the Wannier localization effect instead of saddle-point excitons.

RAMAN-SCATTERING BY LO PHONONS IN (GAAS)N1/(ALAS)N2 ULTRATHIN-LAYER SUPERLATTICES

Raman spectra of (GaAs)n1/(AlAs)n2 ultrathin-layer superlattices were measured at room temperature and under off-resonance conditions. The experimental results show that there are two effects in ultrathin-layer superlattices: the confinement effect of LO phonons and the alloy effect. It is found that the relative intensity of the disorder-activated TO mode can give a measure of the alloy effect. The Raman spectra of one-monolayer superlattices measured in various scattering configurations are very similar to those of the Al0.5Ga0.5As alloy, and thus the alloy effect is prominent. However, in the case of monolayer number n greater-than-or-equal-to 4, the confined effect is prominent, while the alloy effect is only shown as an interface effect.

PRESSURE-DEPENDENCE OF PHOTOLUMINESCENCE FROM ZNSE-TE-(CDSE)(1) (ZNSE)(3) SUPERLATTICE QUANTUM-WELLS

Pressure dependence of photoluminescence from ZnSe:Te-(CdSe)(1)(ZnSe)(3) short period superlattice quantum wells is reported. In addition to the exciton band from the superlattice layers, strong bands for localized excitons self-trapped al single Te (Te-1) atom, double Te atoms (Te-2) and Te clusters (Te-n, n greater than or equal to 3) as well as for the free excitons in isoelectronic Te incorporated ZnSe layers are observed. Significant differences in the pressure and temperature dependencies of the observed exciton transitions are presented and discussed.

Stable Temperature Characteristics of InAs/GaAs Quantum Dots at Long Wavelength Emission

The time-resolved photoluminescence and steady photoluminescence (TRPL and PL) spectra on self-assembled InAs/GaAs quantum dots (QDs) are investigated. By depositing GaAs/InAs short period superlattices (SLs), 1. 48 μtm emission is obtained at room temperature. Temperature dependent PL measurements show that the PL intensity of the emission is very steady. It decays only to half as the temperature increases from 15 K to room temperature, while at the same time, the intensity of the other emission decreases by a factor of 5 orders of magnitude. These two emissions are attributed to large-size QDs and short period superlattices (SLs), respectively. Large-size QDs are easier to capture and confine carriers,which benefits the lifetime of PL, and therefore makes the emission intensity insensitive to the temperature.

Investigation of GaAs/AlGaAs interfaces by reflectance-difference spectroscopy

The in-plane optical anisotropy of several GaAs/AlGaAs quantum well samples with different well widths has been measured at room temperature by reflectance-difference spectroscopy (RDS). The RDS line shapes are found to be similar in all the samples examined here, which dominantly consist of two peak-like signals corresponding to 1HH-->1E and 1LH-->1E transition. As the well width is decreased, or the 1 ML InAs layer is inserted at one interface, the intensity of the anisotropy increases quickly. Our detail analysis shows that the anisotropy mainly arises from the anisotropic interface roughness. The results demonstrate that the RDS technique is sensitive to the interface structures.

Self-assembled InAs quantum wires on InP(001)

Self-assembled InAs quantum wires (QWRs) embedded in In0.52Al0.48As In0.53Ga0.47As, and (In0.52Al0.48As)(2)/(In(0.53)Ga(0.47)AS)(2)-short-period-lattice matrixes on InP (001) were fabricated with molecular beam epitaxy (MBE). These QWR lines are along [110], x4 direction in the 2x4 reconstructed (001) surface as revealed with high energy electron diffraction (RHEED). Alignment of quantum wires in a multilayer structure depends on the composition of spacer layers.