The isolation and amplification of full length cDNA of oleosins from oil palm (Elaeis guineensis Jacq.)

This study focused on the isolation and amplification of the cDNA clone of oleosin from oil palm. The oil palm cDNA library constructed from the kernel tissues 10 weeks after anthesis (WAA) produced a clone of pO1A containing partial 563 bp sequence of oleosin. The polymerase chain reaction for the rapid amplification of cDNA ends (RACE-PCR) was performed to obtain full length cDNA of oleosin from the RNA transcripts using forward gene-specific primers that is, primer Oleo 3. The product was then cloned into pCR 4 TOPO vector and subjected to sequencing using M13 forward and reverse primers. The end-to-end PCR method was performed to amplify the complete cDNA sequence of oleosin and it produce a 750 bp PCR product. The BLAST results showed that the cDNA from oil palm kernel isolated exhibited high similarities with low molecular weight isoforms of oleosin cDNA from crops like rice,maize and barley

Poly[dimethylammonium aquadi-μ-oxalato-europate(III) trihydrate]

In the crystal structure of the polymeric title compound, (C2H8N)[Eu(C2O4)2(H2O)]·3H2O, the independent oxalate that lies on a general position chelates to two Eu atoms, as do the other two oxalates that lie on different centres of inversion, the bridging mode of the oxalates giving rise to a three-dimensional anionic network. The water-coordinated Eu atom exists in a tricapped trigonal–prismatic geometry. The cations and solvent water mol­ecules occupy the cavities of the network and are involved in hydrogen bonding with each other and with the network.published_or_final_versio

On the data compression and transmission aspects of panoramic video

This paper proposes efficient data compression and transmission techniques for panoramic video. Panoramic videos have been used as a means for representing dynamic scenes or paths along a static environment. They allow the user to change viewpoints interactively at a point in time or space. High-resolution panoramic videos, while desirable, consume a significant amount of storage and bandwidth for transmission, and make real-time decoding very compute-intensive. A high performance MPEG-like compression algorithm, which takes into account the random access requirements and the redundancies of the panoramic video, is presented. The transmission aspects of panoramic video over cable network, LAN and Internet are also briefly discussed.published_or_final_versio

The switching dynamics of the bacterial flagellar motor

Many swimming bacteria are propelled by flagellar motors that stochastically switch between the clockwise and counterclockwise rotation direction. While the switching dynamics are one of the most important characteristics of flagellar motors, the mechanisms that control switching are poorly understood. We present a statistical-mechanical model of the flagellar rotary motor, which consists of a number of stator proteins that drive the rotation of a ring of rotor proteins, which in turn drives the rotation of a flagellar filament. At the heart of our model is the assumption that the rotor protein complex can exist in two conformational states corresponding to the two respective rotation directions, and that switching between these states depends on interactions with the stator proteins. This naturally couples the switching dynamics to the rotation dynamics, making the switch sensitive to torque and speed. Another key element of our model is that after a switching event, it takes time for the load to build up, due to polymorphic transitions of the filament. Our model predicts that this slow relaxation dynamics of the filament, in combination with the load dependence of the switching frequency, leads to a characteristic switching time, in agreement with recent observations.Comment: 7 pages, 6 figures, RevTeX

Quantifying single nucleotide variant detection sensitivity in exome sequencing

BACKGROUND: The targeted capture and sequencing of genomic regions has rapidly demonstrated its utility in genetic studies. Inherent in this technology is considerable heterogeneity of target coverage and this is expected to systematically impact our sensitivity to detect genuine polymorphisms. To fully interpret the polymorphisms identified in a genetic study it is often essential to both detect polymorphisms and to understand where and with what probability real polymorphisms may have been missed. RESULTS: Using down-sampling of 30 deeply sequenced exomes and a set of gold-standard single nucleotide variant (SNV) genotype calls for each sample, we developed an empirical model relating the read depth at a polymorphic site to the probability of calling the correct genotype at that site. We find that measured sensitivity in SNV detection is substantially worse than that predicted from the naive expectation of sampling from a binomial. This calibrated model allows us to produce single nucleotide resolution SNV sensitivity estimates which can be merged to give summary sensitivity measures for any arbitrary partition of the target sequences (nucleotide, exon, gene, pathway, exome). These metrics are directly comparable between platforms and can be combined between samples to give “power estimates” for an entire study. We estimate a local read depth of 13X is required to detect the alleles and genotype of a heterozygous SNV 95% of the time, but only 3X for a homozygous SNV. At a mean on-target read depth of 20X, commonly used for rare disease exome sequencing studies, we predict 5–15% of heterozygous and 1–4% of homozygous SNVs in the targeted regions will be missed. CONCLUSIONS: Non-reference alleles in the heterozygote state have a high chance of being missed when commonly applied read coverage thresholds are used despite the widely held assumption that there is good polymorphism detection at these coverage levels. Such alleles are likely to be of functional importance in population based studies of rare diseases, somatic mutations in cancer and explaining the “missing heritability” of quantitative traits

Teleimpedance Control of a Synergy-Driven Anthropomorphic Hand

In this paper, a novel synergy driven teleimpedance controller for the Pisa–IIT SoftHand is presented. Towards the development of an efficient, robust, and low-cost hand prothesis, the Pisa–IIT SoftHand is built on the motor control principle of synergies, through which the immense complexity of the hand is simplified into distinct motor patterns. As the SoftHand grasps, it follows a synergistic path with built-in flexibility to allow grasping of objects of various shapes using only a single motor. In this work, the hand grasping motion is regulated with an impedance controller which incorporates the user’s postural and stiffness synergy profiles in realtime. In addition, a disturbance observer is realized which estimates the grasping contact force. The estimated force is then fedback to the user via a vibration motor. Grasp robustness and transparency improvements were evaluated on two healthy subjects while grasping different objects. Implementation of the proposed teleimpedance controller led to the execution of stable grasps by controlling the grasping forces, via modulation of hand compliance. In addition, utilization of the vibrotactile feedback resulted in reduced physical load on the user. While these results need to be validated with amputees, they provide evidence that a low-cost, robust hand employing hardwarebased synergies is a viable alternative to traditional myoelectric prostheses

Design Considerations for Massively Parallel Sequencing Studies of Complex Human Disease

Massively Parallel Sequencing (MPS) allows sequencing of entire exomes and genomes to now be done at reasonable cost, and its utility for identifying genes responsible for rare Mendelian disorders has been demonstrated. However, for a complex disease, study designs need to accommodate substantial degrees of locus, allelic, and phenotypic heterogeneity, as well as complex relationships between genotype and phenotype. Such considerations include careful selection of samples for sequencing and a well-developed strategy for identifying the few “true” disease susceptibility genes from among the many irrelevant genes that will be found to harbor rare variants. To examine these issues we have performed simulation-based analyses in order to compare several strategies for MPS sequencing in complex disease. Factors examined include genetic architecture, sample size, number and relationship of individuals selected for sequencing, and a variety of filters based on variant type, multiple observations of genes and concordance of genetic variants within pedigrees. A two-stage design was assumed where genes from the MPS analysis of high-risk families are evaluated in a secondary screening phase of a larger set of probands with more modest family histories. Designs were evaluated using a cost function that assumes the cost of sequencing the whole exome is 400 times that of sequencing a single candidate gene. Results indicate that while requiring variants to be identified in multiple pedigrees and/or in multiple individuals in the same pedigree are effective strategies for reducing false positives, there is a danger of over-filtering so that most true susceptibility genes are missed. In most cases, sequencing more than two individuals per pedigree results in reduced power without any benefit in terms of reduced overall cost. Further, our results suggest that although no single strategy is optimal, simulations can provide important guidelines for study design

Live birth following double-factor pre-implantation genetic diagnosis for both reciprocal translocation and alpha-thalassaemia

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Statistical Guidance for Experimental Design and Data Analysis of Mutation Detection in Rare Monogenic Mendelian Diseases by Exome Sequencing

Recently, whole-genome sequencing, especially exome sequencing, has successfully led to the identification of causal mutations for rare monogenic Mendelian diseases. However, it is unclear whether this approach can be generalized and effectively applied to other Mendelian diseases with high locus heterogeneity. Moreover, the current exome sequencing approach has limitations such as false positive and false negative rates of mutation detection due to sequencing errors and other artifacts, but the impact of these limitations on experimental design has not been systematically analyzed. To address these questions, we present a statistical modeling framework to calculate the power, the probability of identifying truly disease-causing genes, under various inheritance models and experimental conditions, providing guidance for both proper experimental design and data analysis. Based on our model, we found that the exome sequencing approach is well-powered for mutation detection in recessive, but not dominant, Mendelian diseases with high locus heterogeneity. A disease gene responsible for as low as 5% of the disease population can be readily identified by sequencing just 200 unrelated patients. Based on these results, for identifying rare Mendelian disease genes, we propose that a viable approach is to combine, sequence, and analyze patients with the same disease together, leveraging the statistical framework presented in this work