Minseok Seo

The genome landscape of indigenous African cattle

BackgroundThe history of African indigenous cattle and their adaptation to environmental and human selection pressure is at the root of their remarkable diversity. Characterization of this diversity is an essential step towards understanding the genomic basis of productivity and adaptation to survival under African farming systems.ResultsWe analyze patterns of African cattle genetic variation by sequencing 48 genomes from five indigenous populations and comparing them to the genomes of 53 commercial taurine breeds. We find the highest genetic diversity among African zebu and sanga cattle. Our search for genomic regions under selection reveals signatures of selection for environmental adaptive traits. In particular, we identify signatures of selection including genes and/or pathways controlling anemia and feeding behavior in the trypanotolerant N’Dama, coat color and horn development in Ankole, and heat tolerance and tick resistance across African cattle especially in zebu breeds.ConclusionsOur findings unravel at the genome-wide level, the unique adaptive diversity of African cattle while emphasizing the opportunities for sustainable improvement of livestock productivity on the continent.

Mixing of axino and goldstino, and axino mass

Abstract Axino, related to the SUSY transformation of axion, can mix with goldstino in principle. This case is realized when some superfields carrying nonvanishing Peccei–Quinn charges develop both scalar VEVs and F-terms. In this case, we present a proper definition of axion and axino. With this definition, we present the QCD axino mass in the most general framework, including nonminimal Kahler potential. The axino mass is known to have a hierarchical mass structure depending on accidental symmetries. With only one axino, if G A = 0 where G = K + ln | W | 2 , we obtain m a ˜ = m 3 / 2 . For G A ≠ 0 , the axino mass depends on the details of the Kahler potential. In the gauge mediation scenario, the gaugino mass is the dominant axino mass parameter. Therefore, we can take the theoretical QCD axino mass as a free parameter in the study of its cosmological effects, ranging from eV to multi-TeV scales, without a present knowledge on its ultraviolet completion.

Quark and lepton mixing angles with a dodeca-symmetry

The discrete symmetry D12 at the electroweak scale is used to fix the quark and lepton mixing angles. At the leading order, the Cabbibo angle θC is 15°, and the PMNS matrix is of a bi-dodeca-mixing form giving the Solar-neutrino angle θsol = 30°. Thus, there results the relation θsol + θC ≃ 45°. Out of discrete vacua, a certain vacuum is chosen for this assignment to be consistent with the dodeca-symmetry. A shift of θC from 15° to 13.14° might arise from a small breaking of the dodeca-symmetry. The spontaneous breaking leading to the required electroweak vacuum is made possible by realizing the electroweak dodeca-symmetry explicitly at a high energy scale. At the vacuum we chose Arg.Det.Mq is nonzero, and hence a solution of the strong CP problem invites a very light axion at a high energy scale. We also comment how the next level corrections can fit the mixing angles to the observed values. An example realizing this idea needs a symmetry SU(3)c × SU(2)L × U(1)Y × D12 × U(1)Γ × Z3 × Z2.

Communication with SIMP dark mesons via Z′ -portal

We consider a consistent extension of the SIMP models with dark mesons by including a dark U(1)D gauge symmetry. Dark matter density is determined by a thermal freeze-out of the 3→2 self-annihilation process, thanks to the Wess–Zumino–Witten term. In the presence of a gauge kinetic mixing between the dark photon and the SM hypercharge gauge boson, dark mesons can undergo a sufficient scattering off the Standard Model particles and keep in kinetic equilibrium until freeze-out in this SIMP scenario. Taking the SU(Nf)×SU(Nf)/SU(Nf) flavor symmetry under the SU(Nc) confining group, we show how much complementary the SIMP constraints on the parameters of the dark photon are for current experimental searches for dark photon.

Transcriptome profiling of differentially expressed genes in floral buds and flowers of male sterile and fertile lines in watermelon

BackgroundMale sterility is an important mechanism for the production of hybrid seeds in watermelon. Although fruit development has been studied extensively in watermelon, there are no reports on gene expression in floral organs. In this study, RNA-sequencing (RNA-seq) was performed in two near-isogenic watermelon lines (genic male sterile [GMS] line, DAH3615-MS and male fertile line, DAH3615) to identify the differentially expressed genes (DEGs) related to male sterility.ResultsDEG analysis showed that 1259 genes were significantly associated with male sterility at a FDR P-value of < 0.01. Most of these genes were only expressed in the male fertile line. In addition, 11 functional clusters were identified using DAVID functional classification analysis. Of detected genes in RNA-seq analysis, 19 were successfully validated by qRT-PCR.ConclusionsIn this study, we carried out a comprehensive floral transcriptome sequence comparison of a male fertile line and its near-isogenic male sterile line in watermelon. This analysis revealed essential genes responsible for stamen development, including pollen development and pollen tube elongation, and allowed their functional classification. These results provided new information on global mechanisms related to male sterility in watermelon.

CBFS: High Performance Feature Selection Algorithm Based on Feature Clearness

Background The goal of feature selection is to select useful features and simultaneously exclude garbage features from a given dataset for classification purposes. This is expected to bring reduction of processing time and improvement of classification accuracy. Methodology In this study, we devised a new feature selection algorithm (CBFS) based on clearness of features. Feature clearness expresses separability among classes in a feature. Highly clear features contribute towards obtaining high classification accuracy. CScore is a measure to score clearness of each feature and is based on clustered samples to centroid of classes in a feature. We also suggest combining CBFS and other algorithms to improve classification accuracy. Conclusions/Significance From the experiment we confirm that CBFS is more excellent than up-to-date feature selection algorithms including FeaLect. CBFS can be applied to microarray gene selection, text categorization, and image classification.

String theoretic QCD axions in the light of PLANCK and BICEP2

A bstractThe QCD axion solving the strong CP problem may originate from antisymmetric tensor gauge fields in compactified string theory, with a decay constant around the GUT scale. Such possibility appears to be ruled out now by the detection of tensor modes by BICEP2 and the PLANCK constraints on isocurvature density perturbations. A more interesting and still viable possibility is that the string theoretic QCD axion is charged under an anomalous U(1)A gauge symmetry. In such case, the axion decay constant can be much lower than the GUT scale if moduli are stabilized near the point of vanishing Fayet-Illiopoulos term, and U(1)A-charged matter fields get a vacuum value v ~ (mSUSYMPln)1/(n + 1) (n ≥ 0) induced by a tachyonic SUSY breaking mass mSUSY. We examine the symmetry breaking pattern of such models during the inflationary epoch with HI ≃ 1014 GeV, and identify the range of the QCD axion decay constant, as well as the corresponding relic axion abundance, consistent with known cosmological constraints. In addition to the case that the PQ symmetry is restored during inflation, i.e. v(tI) = 0, there are other viable scenarios, including that the PQ symmetry is broken during inflation with v(tI) ∼ (4πHIMPln)1/(n + 1) ~ 1016–1017 GeV due to the Hubble-induced D-term DA ~ 8π2HI2, while v(t0) ~ (mSUSYMPln)1/(n + 1) ~ 109–5 × 1013 GeV in the present universe, where v(t0) above 1012 GeV requires a fine-tuning of the axion misalignment angle. We also discuss the implications of our results for the size of SUSY breaking soft masses.

SINGLET SUPERFIELD EXTENSION OF THE MINIMAL SUPERSYMMETRIC STANDARD MODEL WITH PECCEI–QUINN SYMMETRY AND A LIGHT PSEUDOSCALAR HIGGS BOSON AT THE LHC

Motivated by the μ-problem and the axion solution to the strong CP-problem, we extend the MSSM with one more chiral singlet field Xew. The underlying PQ-symmetry allows only one more renormalizable term Xew Hu Hd in the superpotential. The spectrum of the Higgs system includes a light pseudoscalar aX (in addition to the standard CP-even Higgs boson), predominantly decaying to two photons: aX →γγ. Both Higgs bosons might be in the range accessible to current LHC experiments.Motivated by the mu-problem and the axion solution to the strong CP-problem, we extend the MSSM with one more chiral singlet field

HGTree: database of horizontally transferred genes determined by tree reconciliation

X_e

Parametrization of the CKM matrix

. The underlying PQ-symmetry allows only one more term