Genomic preselection with genotyping-bysequencing increases performance of commercial oil palm hybrid crosses

Background: There is great potential for the genetic improvement of oil palm yield. Traditional progeny tests allow accurate selection but limit the number of individuals evaluated. Genomic selection (GS) could overcome this constraint. We estimated the accuracy of GS prediction of seven oil yield components using A × B hybrid progeny tests with almost 500 crosses for training and 200 crosses for independent validation. Genotyping-by-sequencing (GBS) yielded +5000 single nucleotide polymorphisms (SNPs) on the parents of the crosses. The genomic best linear unbiased prediction method gave genomic predictions using the SNPs of the training and validation sets and the phenotypes of the training crosses. The practical impact was illustrated by quantifying the additional bunch production of the crosses selected in the validation experiment if genomic preselection had been applied in the parental populations before progeny tests. Results: We found that prediction accuracies for cross values plateaued at 500 to 2000 SNPs, with high (0.73) or low (0.28) values depending on traits. Similar results were obtained when parental breeding values were predicted. GS was able to capture genetic differences within parental families, requiring at least 2000 SNPs with less than 5% missing data, imputed using pedigrees. Genomic preselection could have increased the selected hybrids bunch production by more than 10%. Conclusions: Finally, preselection for yield components using GBS is the first possible application of GS in oil palm. This will increase selection intensity, thus improving the performance of commercial hybrids. Further research is required to increase the benefits from GS, which should revolutionize oil palm breeding. (Résumé d'auteur

CAESAR source finder: recent developments and testing

A new era in radioastronomy will begin with the upcoming large-scale surveys planned at the Australian Square Kilometre Array Pathfinder (ASKAP). ASKAP started its Early Science program in October 2017 and several target fields were observed during the array commissioning phase. The SCORPIO field was the first observed in the Galactic Plane in Band 1 (792-1032 MHz) using 15 commissioned antennas. The achieved sensitivity and large field of view already allow to discover new sources and survey thousands of existing ones with improved precision with respect to previous surveys. Data analysis is currently ongoing to deliver the first source catalogue. Given the increased scale of the data, source extraction and characterization, even in this Early Science phase, have to be carried out in a mostly automated way. This process presents significant challenges due to the presence of extended objects and diffuse emission close to the Galactic Plane. In this context we have extended and optimized a novel source finding tool, named CAESAR , to allow extraction of both compact and extended sources from radio maps. A number of developments have been done driven by the analysis of the SCORPIO map and in view of the future ASKAP Galactic Plane survey. The main goals are the improvement of algorithm performances and scalability as well as of software maintainability and usability within the radio community. In this paper we present the current status of CAESAR and report a first systematic characterization of its performance for both compact and extended sources using simulated maps. Future prospects are discussed in light of the obtained results.Comment: 15 pages, 10 figure

An exercise in transformational programming: Backtracking and Branch-and-Bound

We present a formal derivation of program schemes that are usually called Backtracking programs and Branch-and-Bound programs. The derivation consists of a series of transformation steps, specifically algebraic manipulations, on the initial specification until the desired programs are obtained. The well-known notions of linear recursion and tail recursion are extended, for structures, to elementwise linear recursion and elementwise tail recursion; and a transformation between them is derived too

Algorithms and Hardware Co-Design of HEVC Intra Encoders

Digital video is becoming extremely important nowadays and its importance has greatly increased in the last two decades. Due to the rapid development of information and communication technologies, the demand for Ultra-High Definition (UHD) video applications is becoming stronger. However, the most prevalent video compression standard H.264/AVC released in 2003 is inefficient when it comes to UHD videos. The increasing desire for superior compression efficiency to H.264/AVC leads to the standardization of High Efficiency Video Coding (HEVC). Compared with the H.264/AVC standard, HEVC offers a double compression ratio at the same level of video quality or substantial improvement of video quality at the same video bitrate. Yet, HE-VC/H.265 possesses superior compression efficiency, its complexity is several times more than H.264/AVC, impeding its high throughput implementation. Currently, most of the researchers have focused merely on algorithm level adaptations of HEVC/H.265 standard to reduce computational intensity without considering the hardware feasibility. What’s more, the exploration of efficient hardware architecture design is not exhaustive. Only a few research works have been conducted to explore efficient hardware architectures of HEVC/H.265 standard. In this dissertation, we investigate efficient algorithm adaptations and hardware architecture design of HEVC intra encoders. We also explore the deep learning approach in mode prediction. From the algorithm point of view, we propose three efficient hardware-oriented algorithm adaptations, including mode reduction, fast coding unit (CU) cost estimation, and group-based CABAC (context-adaptive binary arithmetic coding) rate estimation. Mode reduction aims to reduce mode candidates of each prediction unit (PU) in the rate-distortion optimization (RDO) process, which is both computation-intensive and time-consuming. Fast CU cost estimation is applied to reduce the complexity in rate-distortion (RD) calculation of each CU. Group-based CABAC rate estimation is proposed to parallelize syntax elements processing to greatly improve rate estimation throughput. From the hardware design perspective, a fully parallel hardware architecture of HEVC intra encoder is developed to sustain UHD video compression at 4K@30fps. The fully parallel architecture introduces four prediction engines (PE) and each PE performs the full cycle of mode prediction, transform, quantization, inverse quantization, inverse transform, reconstruction, rate-distortion estimation independently. PU blocks with different PU sizes will be processed by the different prediction engines (PE) simultaneously. Also, an efficient hardware implementation of a group-based CABAC rate estimator is incorporated into the proposed HEVC intra encoder for accurate and high-throughput rate estimation. To take advantage of the deep learning approach, we also propose a fully connected layer based neural network (FCLNN) mode preselection scheme to reduce the number of RDO modes of luma prediction blocks. All angular prediction modes are classified into 7 prediction groups. Each group contains 3-5 prediction modes that exhibit a similar prediction angle. A rough angle detection algorithm is designed to determine the prediction direction of the current block, then a small scale FCLNN is exploited to refine the mode prediction

Mistranslation can promote the exploration of alternative evolutionary trajectories in enzyme evolution

Darwinian evolution preferentially follows mutational pathways whose individual steps increase fitness. Alternative pathways with mutational steps that do not increase fitness are less accessible. Here, we show that mistranslation, the erroneous incorporation of amino acids into nascent proteins, can increase the accessibility of such alternative pathways and, ultimately, of high fitness genotypes. We subject populations of the beta-lactamase TEM-1 to directed evolution in Escherichia coli under both low- and high-mistranslation rates, selecting for high activity on the antibiotic cefotaxime. Under low mistranslation rates, different evolving TEM-1 populations ascend the same high cefotaxime-resistance peak, which requires three canonical DNA mutations. In contrast, under high mistranslation rates they ascend three different high cefotaxime-resistance genotypes, which leads to higher genotypic diversity among populations. We experimentally reconstruct the adaptive DNA mutations and the potential evolutionary paths to these high cefotaxime-resistance genotypes. This reconstruction shows that some of the DNA mutations do not change fitness under low mistranslation, but cause a significant increase in fitness under high-mistranslation, which helps increase the accessibility of different high cefotaxime-resistance genotypes. In addition, these mutations form a network of pairwise epistatic interactions that leads to mutually exclusive evolutionary trajectories towards different high cefotaxime-resistance genotypes. Our observations demonstrate that protein mistranslation and the phenotypic mutations it causes can alter the evolutionary exploration of fitness landscapes and reduce the predictability of evolution

A Systematic Evaluation of Methods to Separate X- and Y- Bearing Sperm

This project was initiated to determine if was possible to enrich either X- or Y- bearing sperm, and hence to preselect the sex of a child. Two of the possible reasons why couple might want to select the sex of a child are firstly because of a family history of an X-linked recessive genetic disorder, which usually only affect sons, and secondly families who have had several children of one sex. For this study, men with three or more children of the same sex were recruited following the publication of an article in The West Australian newspaper. The percentage of X- and Y- bearing sperm within the semen samples of men with three or more children of the same sex was determined using dual colour fluorescence in situ hybridisation (FISH). The aim of the investigation was to determine if these men had an altered ratio of X- to Y- bearing sperm, which would explain why these men had a predominance of children of one sex. Comprehensive analyses were also carried out on the semen samples. The reliability of the dual colour FISH technique was established using a number of standard metaphase spreads; from male and female subjects and an individual with Klinefelters syndrome. It was determined that dual colour FISH was a suitable technique for determining the percentage of X- or Y- bearing sperm within a sample. The semen samples were processed using one of two protocols. Samples from men with three or more daughters were treated using Human serum albumin columns, with the intention of increasing the percentage of Y-bearing sperm within the final fraction. It has been suggested that this method enriches the Y- bearing sperm from a sample due to the differential motility exhibited by the X- and Y- bearing sperm, although this characteristic has not been proven. Samples from men with three or more sons were processed using 8-layer ISolate® discontinuous gradients, with, the aim of enhancing the amount of X- bearing sperm within the final fraction. This method is based on the formation of the discontinuous gradients because Percoll has not been approved for the production of sperm fractions for human insemination. It has been suggested that the X- and Y- bearing sperm can be enriched using such gradients either as a result of differences in their velocity of sedimentation or due to a greater nett negative charge on the surface of X- bearing sperm. However, neither of these theories have been validated. As it has also been proposed that the survival rate of X- bearing sperm is slightly longer than that for Y- bearing sperm, this was also investigated. In summary no statistically significant enrichment of X- or Y- bearing sperm was observed following the treatment of the semen samples with either the ISolate® discontinuous gradient or the Human serum albumin column protocols. Nor was there any enrichment in X- bearing sperm due to their suggested greater survival time

Construction and functional validation of combinatorial designed ankyrin repeat protein (DARPin) libraries for phage display

Designed ankyrin repeat protein (DARPin) is one of the most advanced alternative scaffold proteins. In this study, a combinatorial DARPin library for phage display was constructed. Firstly, a binary DARPin phage display library (termed BiLiBST) was constructed containing variating tyrosine and serine residues. Five PelB signal sequence mutants were then analyzed to find the one with the best display levels for BiLiBST. These variants were found in earlier study on anti-GFP DARPin display using modified signal sequence, but it was not known if the increased display levels were a generic behavior irrespective of displaying either fixed DARPin protein or library DARPin. The capability of each PelB variant to display BiLiBST was determined by anti-DARPin immunoassay, and the phage stocks titers were normalized by total phage immunoassay. All tested PelB variants exhibited statistically significant improvement in display of the BiLiBST compared to the parental PelB and few variants had even twofold higher display efficiency than DsbA, which has previously been the standard for filamentous phage display of DARPins. The BiLiBST library was displayed with DN5 signal sequence and preselected for open reading frames by panning two rounds against anti-DARPin Fabs. The DARPin libraries were effectively purified from frameshifts as the frequency of frameshift decreased from 50 % to 13 %. The main DARPin library construction was performed by assembly PCR using purified BiLiBST as template and its validity was confirmed by selecting against the GST-tagged protein N from SARS-COV-2 for three rounds. Successful enrichment of binders was confirmed by phage immunoreactivity assay with signal to background ratios up to 11-fold. This is a solid foundation for further molecular diversification and library construction