Keeping it cool: Soil sample cold pack storage and DNA shipment up to 1 month does not impact metabarcoding results

A grant from the One-University Open Access Fund at the University of Kansas was used to defray the author's publication fees in this Open Access journal. The Open Access Fund, administered by librarians from the KU, KU Law, and KUMC libraries, is made possible by contributions from the offices of KU Provost, KU Vice Chancellor for Research & Graduate Studies, and KUMC Vice Chancellor for Research. For more information about the Open Access Fund, please see http://library.kumc.edu/authors-fund.xml.With the advances of sequencing tools, the fields of environmental microbiology and soil ecology have been transformed. Today, the unculturable majority of soil microbes can be sequenced. Although these tools give us tremendous power and open many doors to answer important questions, we must understand how sample processing may impact our results and interpretations. Here, we test the impacts of four soil storage methods on downstream amplicon metabarcoding and qPCR analyses for fungi and bacteria. We further investigate the impact of thaw time on extracted DNA to determine a safe length of time during which this can occur with minimal impact on study results. Overall, we find that storage using standard cold packs with subsequent storage at −20°C is little different than immediate storage in liquid nitrogen, suggesting that the historical and current method is adequate. We further find evidence that storage at room temperature or with aid of RNAlater can lead to changes in community composition and in the case of RNAlater, lower gene copies. We therefore advise against these storage methods for metabarcoding analyses. Finally, we show that over 1 month, DNA extract thaw time does not impact diversity or qPCR metrics. We hope that this work will help researchers working with soil bacteria and fungi make informed decisions about soil storage and transport to ensure repeatability and accuracy of results and interpretations.National Science Foundation (DEB- 1738041, OIA 1656006)National Geographic Society (WW-036ER-17

Mixing among light scalar mesons and L=1 q\bar{q} scalar mesons

Following the re-establishment of the \sigma(600) and the \kappa(900), the light scalar mesons a_0(980) and f_0(980) together with the \sigma(600) and the \kappa(900) are considered as the chiral scalar partner of pseudoscalar nonet in SU(3) chiral symmetry, and the high mass scalar mesons a_0(1450), K^*_0(1430), f_0(1370) and f_0(1710) turned out to be considered as the L=1 q\bar{q} scalar mesons. We assume that the high mass of the L=1 q\bar{q} scalar mesons is caused by the mixing with the light scalar mesons. For the structure of the light scalar mesons, we adopted the qq\bar{q}\bar{q} model in order to explain the "scalar meson puzzle". The inter-mixing between the light scalar nonet and the high mass L=1 q\bar{q} nonet and the intra-mixing among each nonet are analyzed by including the glueball into the high mass scalar nonet.Comment: 16 pages, 5 figure

Effects of Medium Shape, Fertilization Methods and Plant Density on the Growth of Pansy Grown in Medium Hardened by Heat Fusion Polyester Fiber without Polyethylene Pot

To develop bedding plant production system without polyethylene pots (PP), problems that may be encountered with compacted medium hardened by heat fusion polyester fiber were investigated. Effects of medium shape, fertilization methods and plant density on the growth of pansy in medium without PP were investigated. To improve water usage on compacted medium, a watering space (6×6×depth 3cm) was made on the upper part of the compacted medium (9×9×depth 9cm). In the early stages of the experiment the amount of water supplied per pot (weight after irrigation-weight before irrigation) of medium with water space was 10–25% greater than that of medium without a water space. However, from the mid to late stages of the experiment, the difference gradually declined. The amount of water supplied per pot was similar between with and without water space especially on cloudy or rainy days. The growth of pansies on medium without PP was remarkably greater with water space than without water space. On 10g/liter basal fertilizer treatment, pansies had severe symptoms of fertilizer damage. The growth of pansy on 10g/liter basal fertilizer was inhibited compared to that of 5g/liter basal fertilizer. Spacing treatment was conducted whenever plant density was half. Height of pansy grown with spacing treatment was significantly lower than that without spacing treatment. PP had no effects on growth when pansy was grown without spacing treatment. However, when pansy was grown with spacing treatment, pansy grown without PP had significantly greater growth than with PP. Algal growth on the medium increased with increasing irrigation rate or nutrient rate. Combination of spacing treatment and medium without PP decreased the rate of algal growth on medium.固化培地を利用したポリポットを用いないポットレス栽培において，潅水効率の上昇，施肥の簡易化，藻の発生抑制のため，培地の形状，施肥方法および栽植密度がパンジーの生育に及ぼす影響について検討した．9㎝角のポット型培地に6×6×深さ3㎝のくぼみ（ウォータースペース）を培地上部に作成すると，栽培前期の水供給量（灌水後の重量―灌水前の重量）が約10～25% に多くなった．しかし，栽培中期から後期にかけてはその違いは次第に小さくなり，特に曇雨天時には水供給量に差はみられなくなった．ウォータースペースの有無にかかわらず，ポリポットがあると生育に違いは認めらなかったが，ポットレス区ではウォータースペースによって生育が改善された．元肥量10ｇ/liter 区では生育初期に高濃度障害と思われる症状が見られ，5ｇ/liter 区より生育が抑制された．栽植密度を半分にしたスペーシングによって，草丈はかなり抑制された．スペーシングなしの場合にはポットの有無による差は小さかったが，ポットレス栽培の生育がスペーシング栽培でかなり改善された．ポットレス・スペーシング有・灌水量120ml区の生育が最も旺盛であった．養分量が多いほど灌水量が多いほど，藻の発生が大であったが，スペーシングとポットレスを組み合わせると藻の発生が改善された

Effects to Scalar Meson Decays of Strong Mixing between Low and High Mass Scalar Mesons

We analyze the mass spectroscopy of low and high mass scalar mesons and get the result that the coupling strengths of the mixing between low and high mass scalar mesons are very strong and the strengths of mixing for $I=1, 1/2$ scalar mesons and those of I=0 scalar mesons are almost same. Next, we analyze the decay widths and decay ratios of these mesons and get the results that the coupling constants $A'$ for $I=1, 1/2$ which represents the coupling of high mass scalar meson $N'$ -> two pseudoscalar mesons $PP$ are almost same as the coupling $A'$ for the I=0. On the other hand, the coupling constant $A$ for $I=1, I=1/2$ which represents the low mass scalar meson $N$ -> $PP$ are far from the coupling constant $A$ for I=0. We consider a resolution for this discrepancy. Coupling constant $A''$ for glueball $G$ -> $PP$ is smaller than the coupling $A'$. $\theta_P$ is $40^\circ \sim 50^\circ$.Comment: 15 pages, 6 figure

Effects of vessel traffic on relative abundance and behaviour of cetaceans : the case of the bottlenose dolphins in the Archipelago de La Maddalena, north-western Mediterranean sea

Acknowledgements This study was part of the Tursiops Project of the Dolphin Research Centre of Caprera, La Maddalena. Financial and logistical support was provided by the Centro Turistico Studentesco (CTS) and by the National Park of the Archipelago de La Maddalena. We thank the Natural Reserve of Bocche di Bonifacio for the support provided during data collection. The authors thank the numerous volunteers of the Caprera Dolphin Research Centre and especially Marco Ferraro, Mirko Ugo, Angela Pira and Maurizio Piras whose assistance during field observation and skills as a boat driver were invaluable.Peer reviewedPostprin

Tri-meson-mixing of π\pi-η\eta-η′\eta' and ρ\rho-ω\omega-ϕ\phi in the light-cone quark model

The radiative transition form factors of the pseudoscalar mesons {$\pi$, $\eta$, $\eta'$} and the vector mesons {$\rho$, $\omega$, $\phi$} are restudied with $\pi$-$\eta$-$\eta'$ and $\rho$-$\omega$-$\phi$ in tri-meson-mixing pattern, which is described by tri-mixing matrices in the light-cone constituent quark model. The experimental transition decay widths are better reproduced with tri-meson-mixing than previous results in a two-mixing-angle scenario of only two-meson $\eta$-$\eta'$ mixing and $\omega$-$\phi$ mixing.Comment: 8 pages, 6 figures, final version to appear in EPJ

Computational strategies for dissecting the high-dimensional complexity of adaptive immune repertoires

The adaptive immune system recognizes antigens via an immense array of antigen-binding antibodies and T-cell receptors, the immune repertoire. The interrogation of immune repertoires is of high relevance for understanding the adaptive immune response in disease and infection (e.g., autoimmunity, cancer, HIV). Adaptive immune receptor repertoire sequencing (AIRR-seq) has driven the quantitative and molecular-level profiling of immune repertoires thereby revealing the high-dimensional complexity of the immune receptor sequence landscape. Several methods for the computational and statistical analysis of large-scale AIRR-seq data have been developed to resolve immune repertoire complexity in order to understand the dynamics of adaptive immunity. Here, we review the current research on (i) diversity, (ii) clustering and network, (iii) phylogenetic and (iv) machine learning methods applied to dissect, quantify and compare the architecture, evolution, and specificity of immune repertoires. We summarize outstanding questions in computational immunology and propose future directions for systems immunology towards coupling AIRR-seq with the computational discovery of immunotherapeutics, vaccines, and immunodiagnostics.Comment: 27 pages, 2 figure