Parallel and Convergent Evolution of the Dim-Light Vision Gene RH1 in Bats (Order: Chiroptera)

Rhodopsin, encoded by the gene Rhodopsin (RH1), is extremely sensitive to light, and is responsible for dim-light vision. Bats are nocturnal mammals that inhabit poor light environments. Megabats (Old-World fruit bats) generally have well-developed eyes, while microbats (insectivorous bats) have developed echolocation and in general their eyes were degraded, however, dramatic differences in the eyes, and their reliance on vision, exist in this group. In this study, we examined the rod opsin gene (RH1), and compared its evolution to that of two cone opsin genes (SWS1 and M/LWS). While phylogenetic reconstruction with the cone opsin genes SWS1 and M/LWS generated a species tree in accord with expectations, the RH1 gene tree united Pteropodidae (Old-World fruit bats) and Yangochiroptera, with very high bootstrap values, suggesting the possibility of convergent evolution. The hypothesis of convergent evolution was further supported when nonsynonymous sites or amino acid sequences were used to construct phylogenies. Reconstructed RH1 sequences at internal nodes of the bat species phylogeny showed that: (1) Old-World fruit bats share an amino acid change (S270G) with the tomb bat; (2) Miniopterus share two amino acid changes (V104I, M183L) with Rhinolophoidea; (3) the amino acid replacement I123V occurred independently on four branches, and the replacements L99M, L266V and I286V occurred each on two branches. The multiple parallel amino acid replacements that occurred in the evolution of bat RH1 suggest the possibility of multiple convergences of their ecological specialization (i.e., various photic environments) during adaptation for the nocturnal lifestyle, and suggest that further attention is needed on the study of the ecology and behavior of bats.

Rapid and parallel chromosomal number reductions in muntjac deer inferred from mitochondrial DNA phylogeny

Muntjac deer (Muntiacinae, Cervidae) are of great interest in evolutionary studies because of their dramatic chromosome variations and recent discoveries of several new species. In this paper, we analyze the evolution of karyotypes of muntjac deer in the context of a phylogeny which is based on 1,844-bp mitochondrial DNA sequences of seven generally recognized species in the muntjac subfamily. The phylogenetic results support the hypothesis that karyotypic evolution in muntjac deer has proceeded via reduction in diploid number. However, the reduction in number is not always linear, i.e., not strictly following the order: 46-->14/13-->8/9-->6/7. For example, Muntiacus muntjak (2n = 6/7) shares a common ancestor with Muntiacus feae (2n = 13/14), which indicates that its karyotype was derived in parallel with M. feae's from an ancestral karyotype of 2n greater than or equal to 13/14. The newly discovered giant muntjac (Muntiacus vuquangensis) may represent another pa;allel reduction lineage from the ancestral 2n = 46 karyotype. Our phylogenetic results indicate that the giant muntjac is relatively closer to Muntiacus reevesi than to other muntjacs and may be placed in the genus Muntiacus. Analyses of sequence divergence reveal that the rate of change in chromosome number in muntjac deer is one of the fastest in vertebrates. Within the muntjac subfamily, the fastest evolutionary rate is found in the Fea's lineage, in which two species with different karyotypes diverged in around 0.5 Myr.

BarraCUDA - a fast short read sequence aligner using graphics processing units.

BACKGROUND: With the maturation of next-generation DNA sequencing (NGS) technologies, the throughput of DNA sequencing reads has soared to over 600 gigabases from a single instrument run. General purpose computing on graphics processing units (GPGPU), extracts the computing power from hundreds of parallel stream processors within graphics processing cores and provides a cost-effective and energy efficient alternative to traditional high-performance computing (HPC) clusters. In this article, we describe the implementation of BarraCUDA, a GPGPU sequence alignment software that is based on BWA, to accelerate the alignment of sequencing reads generated by these instruments to a reference DNA sequence. FINDINGS: Using the NVIDIA Compute Unified Device Architecture (CUDA) software development environment, we ported the most computational-intensive alignment component of BWA to GPU to take advantage of the massive parallelism. As a result, BarraCUDA offers a magnitude of performance boost in alignment throughput when compared to a CPU core while delivering the same level of alignment fidelity. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the alignment throughput. CONCLUSIONS: BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the alignment of millions of sequencing reads generated by NGS 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 from http://seqbarracuda.sf.net.

Parallel implementation of Multilevel BDDC

In application of the Balancing Domain Decomposition by Constraints (BDDC) to a case with many substructures, solving the coarse problem exactly becomes the bottleneck which spoils scalability of the solver. However, it is straightforward for BDDC to substitute the exact solution of the coarse problem by another step of BDDC method with subdomains playing the role of elements. In this way, the algorithm of three-level BDDC method is obtained. If this approach is applied recursively, multilevel BDDC method is derived. We present a detailed description of a recently developed parallel implementation of this algorithm. The implementation is applied to an engineering problem of linear elasticity and a benchmark problem of Stokes flow in a cavity. Results by the multilevel approach are compared to those by the standard (two-level) BDDC method.

Comparative studies on parallel and antiparallel duplex and triplex DNA

Parallel strand models for base sequences d(A)(10). d(T)(10), d(AT)(5) . d(TA)(5), d(G(5)C(5)). d(C(5)G(5)), d(GC)(5) . d(CG)(5) and d(CTATAGGGAT). d(GATATCCCTA), where reverse Watson-Crick A-T pairing with two H-bonds and reverse Watson-Crick G-C pairing with one H-bond or with two H-bonds were adopted, and three models of d(T)(14). d(A)(14). d(T)(14) triple helix with different strand orientations were built up by molecular architecture and energy minimization. Comparisons of parallel duplex models with their corresponding B-DNA models and comparisons among the three triple helices showed: (i) conformational energies of parallel AT duplex models were a little lower, while for GC duplex models they were about 8% higher than that of their corresponding B-DNA models; (ii) the energy differences between parallel and B-type duplex models and among the three triple helices arose mainly from base stacking energies, especially for GC base pairing; (iii) the parallel duplexes with one H-bond G-C pairs were less stable than those with two H-bonds G-C pairs. The present paper includes a brief discussion about the effect of base stacking and base sequences on DNA conformations. (C) 1997 Academic Press Limited.

Dual-mode thin film bulk acoustic wave resonators for parallel sensing of temperature and mass loading.

Thin film bulk acoustic wave resonator (FBAR) devices supporting simultaneously multiple resonance modes have been designed for gravimetric sensing. The mechanism for dual-mode generation within a single device has been discussed, and theoretical calculations based on finite element analysis allowed the fabrication of FBARs whose resonance modes have opposite reactions to temperature changes; one of the modes exhibiting a positive frequency shift for a rise of temperature whilst the other mode exhibits a negative shift. Both modes exhibit negative frequency shift for a mass load and hence by monitoring simultaneously both modes it is possible to distinguish whether a change in the resonance frequency is due to a mass load or temperature variation (or a combination of both), avoiding false positive/negative responses in gravimetric sensing without the need of additional reference devices or complex electronics.

Dual-mode thin film bulk acoustic wave resonators for parallel sensing of temperature and mass loading

Thin film bulk acoustic wave resonator (FBAR) devices supporting simultaneously multiple resonance modes have been designed for gravimetric sensing. The mechanism for dual-mode generation within a single device has been discussed, and theoretical calculations based on finite element analysis allowed the fabrication of FBARs whose resonance modes have opposite reactions to temperature changes; one of the modes exhibiting a positive frequency shift for a rise of temperature whilst the other mode exhibits a negative shift. Both modes exhibit negative frequency shift for a mass load and hence by monitoring simultaneously both modes it is possible to distinguish whether a change in the resonance frequency is due to a mass load or temperature variation (or a combination of both), avoiding false positive/negative responses in gravimetric sensing without the need of additional reference devices or complex electronics. © 2012 Elsevier B.V.

Superconducting fault current limiter design using parallel-connected YBCO thin films

Superconducting Fault Current Limiters (SFCLs) are able to reduce fault currents to an acceptable value, reducing potential mechanical and thermal damage to power system apparatus and allowing more flexibility in power system design and operation. The device can also help avoid replacing circuit breakers whose capacity has been exceeded. Due to limitations in current YBCO thin film manufacturing processes, it is not easy to obtain one large thin film that satisfies the specifications for high voltage and large current applications. The combination of standardized thin films has merit to reduce costs and maintain device quality, and it is necessary to connect these thin films in different series and parallel configurations in order to meet these specifications. In this paper, the design of a resistive type SFCL using parallel-connected YBCO thin films is discussed, including the role of a parallel resistor and the influence of individual thin film characteristics, based on both theory and experimental results. © 2009 IEEE.

Channel-hopping model predictive control

In Multiplexed MPC, the control variables of a MIMO plant are moved asynchronously, following a pre-planned periodic sequence. The advantage of Multiplexed MPC lies in its reduced computational complexity, leading to faster response to disturbances, which may result in improved performance, despite finding sub-optimal solution to the original problem. This paper extends the original Multiplexed MPC in a way such that the control inputs are no longer restricted to a pre-planned periodic sequence. Instead, the most appropriate control input channel would be optimised and selected to counter the disturbances, hence the name 'Channel-Hopping'. In addition, the proposed algorithm is suitable for execution on modern computing platforms such as FPGA or GPU, exploits multi-core, parallel and pipeline computing techniques. The algorithm for the proposed Channel-hopping MPC (CH-MPC) will be described and its stability established. Illustrative examples are given to demonstrate the behaviour of the proposed Channel-Hopping MPC algorithm. © 2011 IFAC.