[Mapping of QTL associated with rice cooking quality and candidate gene analysis].

Excavating the quantitative trait locus (QTL) associated with rice cooking quality, analyzing candidate genes, and improving cooking quality-associated traits of rice varieties by genetic breeding can effectively improve the taste of rice. In this study, we used the indica rice HZ, the japonica rice Nekken2 and 120 recombinant inbred lines (RILs) populations constructed from them as experimental materials to measure the gelatinization temperature (GT), gel consistency (GC) and amylose content (AC) of rice at the maturity stage. We combined the high-density genetic map for QTL mapping. A total of 26 QTLs associated with rice cooking quality (1 QTL associated with GT, 13 QTLs associated with GC, and 12 QTLs associated with AC) were detected, among which the highest likelihood of odd (LOD) value reached 30.24. The expression levels of candidate genes in the localization interval were analyzed by quantitative real-time polymerase chain reaction (qRT-PCR), and it was found that the expression levels of six genes were significantly different from that in parents. It was speculated that the high expression of LOC_Os04g20270 and LOC_Os11g40100 may greatly increase the GC of rice, while the high expression of LOC_Os01g04920 and LOC_Os02g17500 and the low expression of LOC_Os03g02650 and LOC_Os05g25840 may reduce the AC. The results lay a molecular foundation for the cultivation of new high-quality rice varieties, and provide important genetic resources for revealing the molecular regulation mechanism of rice cooking quality.

Insights into RAG Evolution from the Identification of "Missing Link" Family A RAGL Transposons.

A series of "molecular domestication" events are thought to have converted an invertebrate RAG-like (RAGL) transposase into the RAG1-RAG2 (RAG) recombinase, a critical enzyme for adaptive immunity in jawed vertebrates. The timing and order of these events are not well understood, in part because of a dearth of information regarding the invertebrate RAGL-A transposon family. In contrast to the abundant and divergent RAGL-B transposon family, RAGL-A most closely resembles RAG and is represented by a single orphan RAG1-like (RAG1L) gene in the genome of the hemichordate Ptychodera flava (PflRAG1L-A). Here, we provide evidence for the existence of complete RAGL-A transposons in the genomes of P. flava and several echinoderms. The predicted RAG1L-A and RAG2L-A proteins encoded by these transposons intermingle sequence features of jawed vertebrate RAG and RAGL-B transposases, leading to a prediction of DNA binding, catalytic, and transposition activities that are a hybrid of RAG and RAGL-B. Similarly, the terminal inverted repeats (TIRs) of the RAGL-A transposons combine features of both RAGL-B transposon TIRs and RAG recombination signal sequences. Unlike all previously described RAG2L proteins, RAG2L-A proteins contain an acidic hinge region, which we demonstrate is capable of efficiently inhibiting RAG-mediated transposition. Our findings provide evidence for a critical intermediate in RAG evolution and argue that certain adaptations thought to be specific to jawed vertebrates (e.g. the RAG2 acidic hinge) actually arose in invertebrates, thereby focusing attention on other adaptations as the pivotal steps in the completion of RAG domestication in jawed vertebrates.

Functional requirement of terminal inverted repeats for efficient ProtoRAG activity reveals the early evolution of V(D)J recombination.

The discovery of ProtoRAG in amphioxus indicated that vertebrate RAG recombinases originated from an ancient transposon. However, the sequences of ProtoRAG terminal inverted repeats (TIRs) were obviously dissimilar to the consensus sequence of mouse 12/23RSS and recombination mediated by ProtoRAG or RAG made them incompatible with each other. Thus, it is difficult to determine whether or how 12/23RSS persisted in the vertebrate RAG system that evolved from the TIRs of ancient RAG transposons. Here, we found that the activity of ProtoRAG is highly dependent on its asymmetric 5'TIR and 3'TIR, which are composed of conserved TR1 and TR5 elements and a partially conserved TRsp element of 27/31 bp to separate them. Similar to the requirements for the recombination signal sequences (RSSs) of RAG recombinase, the first CAC in TR1, the three dinucleotides in TR5 and the specific length of the partially conserved TRsp are important for the efficient recombination activity of ProtoRAG. In addition, the homologous sequences flanking the signal sequences facilitate ProtoRAG- but not RAG-mediated recombination. In addition to the diverged TIRs, two differentiated functional domains in BbRAG1L were defined to coordinate with the divergence between TIRs and RSSs. One of these is the CTT* domain, which facilitates the specific TIR recognition of the BbRAGL complex, and the other is NBD*, which is responsible for DNA binding and the protein stabilization of the BbRAGL complex. Thus, our findings reveal that the functional requirement for ProtoRAG TIRs is similar to that for RSS in RAG-mediated recombination, which not only supports the common origin of ProtoRAG TIRs and RSSs from the asymmetric TIRs of ancient RAG transposons, but also reveals the development of RAG and RAG-like machineries during chordate evolution.

BCS thermal vacuum of fermionic superfluids and its perturbation theory.

The thermal field theory is applied to fermionic superfluids by doubling the degrees of freedom of the BCS theory. We construct the two-mode states and the corresponding Bogoliubov transformation to obtain the BCS thermal vacuum. The expectation values with respect to the BCS thermal vacuum produce the statistical average of the thermodynamic quantities. The BCS thermal vacuum allows a quantum-mechanical perturbation theory with the BCS theory serving as the unperturbed state. We evaluate the leading-order corrections to the order parameter and other physical quantities from the perturbation theory. A direct evaluation of the pairing correlation as a function of temperature shows the pseudogap phenomenon, where the pairing persists when the order parameter vanishes, emerges from the perturbation theory. The correspondence between the thermal vacuum and purification of the density matrix allows a unitary transformation, and we found the geometric phase associated with the transformation in the parameter space.

Universal Stabilization of a Parametrically Coupled Qubit.

We autonomously stabilize arbitrary states of a qubit through parametric modulation of the coupling between a fixed frequency qubit and resonator. The coupling modulation is achieved with a tunable coupling design, in which the qubit and the resonator are connected in parallel to a superconducting quantum interference device. This allows for quasistatic tuning of the qubit-cavity coupling strength from 12 MHz to more than 300 MHz. Additionally, the coupling can be dynamically modulated, allowing for single-photon exchange in 6 ns. Qubit coherence times exceeding 20 µs are maintained over the majority of the range of tuning, limited primarily by the Purcell effect. The parametric stabilization technique realized using the tunable coupler involves engineering the qubit bath through a combination of photon nonconserving sideband interactions realized by flux modulation, and direct qubit Rabi driving. We demonstrate that the qubit can be stabilized to arbitrary states on the Bloch sphere with a worst-case fidelity exceeding 80%.

Ultrafast optical switching in quantum dot-metallic nanoparticle hybrid systems.

We study ultrafast excitonic population inversion resulting from the interaction of a semiconductor quantum dot (SQD) with localized surface plasmons. The plasmonic enhanced fields are generated when a metallic nanoparticle (MNP) is subject to a nonlinear chirped few-cycle pulse train. By numerically solving the time-dependent Bloch equations beyond the rotating-wave approximation, we show that the complete population inversion can be achieved for small interparticle distance and the dynamic in population inversion exhibits a steplike transition between absorption and amplifying. This phenomenon can be exploited as an all-optical ultrafast switching device. Moreover, the final state of population inversion is shown to be modified significantly with the interparticle distances, which is not only robust against the variation of probe pulse parameters but also suggests a straightforward method for measuring the interparticle distances via probing the final populations.