A Conceptual Framework for Mapping Quantitative Trait Loci Regulating Ontogenetic Allometry

Although ontogenetic changes in body shape and its associated allometry has been studied for over a century, essentially nothing is known about their underlying genetic and developmental mechanisms. One of the reasons for this ignorance is the unavailability of a conceptual framework to formulate the experimental design for data collection and statistical models for data analyses. We developed a framework model for unraveling the genetic machinery for ontogenetic changes of allometry. The model incorporates the mathematical aspects of ontogenetic growth and allometry into a maximum likelihood framework for quantitative trait locus (QTL) mapping. As a quantitative platform, the model allows for the testing of a number of biologically meaningful hypotheses to explore the pleiotropic basis of the QTL that regulate ontogeny and allometry. Simulation studies and real data analysis of a live example in soybean have been performed to investigate the statistical behavior of the model and validate its practical utilization. The statistical model proposed will help to study the genetic architecture of complex phenotypes and, therefore, gain better insights into the mechanistic regulation for developmental patterns and processes in organisms

Performance Evaluation of MDO Architectures within a Variable Complexity Problem

Though quite a number of multidisciplinary design optimization (MDO) architectures have been proposed for the optimal design of large-scale multidisciplinary systems, how their performance changes with the complexity of MDO problem varied is not well studied. In order to solve this problem, this paper presents a variable complexity problem which allows people to obtain a MDO problem with arbitrary complexity by specifying its changeable parameters, such as the number of disciplines and the numbers of design variables. Then four investigations are performed to evaluate how the performance of different MDO architectures changes with the number of disciplines, global variables, local variables, and coupling variables varied, respectively. Finally, the results supply guidance for the selection of MDO architectures in solving practical engineering problems with different complexity

Vortex Impeller-Based Aeration of Groundwater

Iron oxidation and removal from groundwater is a necessary and costly process in drinking water production. In most cases, iron removal is done via aeration, succeeded by precipitation. Most systems for aeration are based on increasing the interfacial area via injecting air in the system or spraying. Both methods have disadvantages, like clogging and formation of aerosols. In this study, a new vortex-based flow-through reactor consisting of a cylindrical tank with an impeller located at the bottom was studied regarding its aeration and iron oxidation capabilities in groundwater. During the aeration experiments, the flow rate, impeller rotation and aerated volume were varied. A nondimensional constant α was proposed to relate the system’s physical characteristics and its aeration capabilities, expressed in dissolved oxygen and system volumetric mass transfer coefficient (KLa). Three distinct operational regimes were defined: formation, complete and bubble regime. These regimes showed very specific characteristics regarding the air–water interface structure and the area to volume ratio, resulting in different aeration capabilities and iron oxidation efficiency values. The system presented KLa values similar to commercially available aeration systems, especially inside the bubble regime. By using dimensionless coefficients, the presented analysis provided the basis for the design of continuous impeller aeration and oxidation systems of arbitrary size

Spontaneous rotational symmetry breaking in KTaO3_3 interface superconductors

Strongly correlated electrons could display intriguing spontaneous broken symmetries in the ground state. Understanding these symmetry breaking states is fundamental to elucidate the various exotic quantum phases in condensed matter physics. Here, we report an experimental observation of spontaneous rotational symmetry breaking of the superconductivity at the interface of YAlO$_3$/KTaO$_3$ (111) with a superconducting transition temperature of 1.86 K. Both the magnetoresistance and upper critical field in an in-plane field manifest striking twofold symmetric oscillations deep inside the superconducting state, whereas the anisotropy vanishes in the normal state, demonstrating that it is an intrinsic property of the superconducting phase. We attribute this behavior to the mixed-parity superconducting state, which is an admixture of $s$-wave and $p$-wave pairing components induced by strong spin-orbit coupling. Our work demonstrates an unconventional nature of the pairing interaction in the KTaO$_3$ interface superconductor, and provides a new platform to clarify a delicate interplay of electron correlation and spin-orbit coupling.Comment: 7 pages, 4 figure

Bos taurus genome assembly

We present here the assembly of the bovine genome. The assembly method combines the BAC plus WGS local assembly used for the rat and sea urchin with the whole genome shotgun (WGS) only assembly used for many other animal genomes including the rhesus macaque. The assembly process consisted of multiple phases: First, BACs were assembled with BAC generated sequence, then subsequently in combination with the individual overlapping WGS reads. Different assembly parameters were tested to separately optimize the performance for each BAC assembly of the BAC and WGS reads. In parallel, a second assembly was produced using only the WGS sequences and a global whole genome assembly method. The two assemblies were combined to create a more complete genome representation that retained the high quality BAC-based local assembly information, but with gaps between BACs filled in with the WGS-only assembly. Finally, the entire assembly was placed on chromosomes using the available map information. Over 90% of the assembly is now placed on chromosomes. The estimated genome size is 2.87 Gb which represents a high degree of completeness, with 95% of the available EST sequences found in assembled contigs. The quality of the assembly was evaluated by comparison to 73 finished BACs, where the draft assembly covers between 92.5 and 100% (average 98.5%) of the finished BACs. The assembly contigs and scaffolds align linearly to the finished BACs, suggesting that misassemblies are rare. Genotyping and genetic mapping of 17,482 SNPs revealed that more than 99.2% were correctly positioned within the Btau_4.0 assembly, confirming the accuracy of the assembly. The biological analysis of this bovine genome assembly is being published, and the sequence data is available to support future bovine research

A Statistical Model for Estimating Maternal-Zygotic Interactions and Parent-of-Origin Effects of QTLs for Seed Development

Proper development of a seed requires coordinated exchanges of signals among the three components that develop side by side in the seed. One of these is the maternal integument that encloses the other two zygotic components, i.e., the diploid embryo and its nurturing annex, the triploid endosperm. Although the formation of the embryo and endosperm contains the contributions of both maternal and paternal parents, maternally and paternally derived alleles may be expressed differently, leading to a so-called parent-of-origin or imprinting effect. Currently, the nature of how genes from the maternal and zygotic genomes interact to affect seed development remains largely unknown. Here, we present a novel statistical model for estimating the main and interaction effects of quantitative trait loci (QTLs) that are derived from different genomes and further testing the imprinting effects of these QTLs on seed development. The experimental design used is based on reciprocal backcrosses toward both parents, so that the inheritance of parent-specific alleles could be traced. The computing model and algorithm were implemented with the maximum likelihood approach. The new strategy presented was applied to study the mode of inheritance for QTLs that control endoreduplication traits in maize endosperm. Monte Carlo simulation studies were performed to investigate the statistical properties of the new model with the data simulated under different imprinting degrees. The false positive rate of imprinting QTL discovery by the model was examined by analyzing the simulated data that contain no imprinting QTL. The reciprocal design and a series of analytical and testing strategies proposed provide a standard procedure for genomic mapping of QTLs involved in the genetic control of complex seed development traits in flowering plants