Design of nucleic acid sequences for DNA computing based on a thermodynamic approach

We have developed an algorithm for designing multiple sequences of nucleic acids that have a uniform melting temperature between the sequence and its complement and that do not hybridize non-specifically with each other based on the minimum free energy (ΔG(min)). Sequences that satisfy these constraints can be utilized in computations, various engineering applications such as microarrays, and nano-fabrications. Our algorithm is a random generate-and-test algorithm: it generates a candidate sequence randomly and tests whether the sequence satisfies the constraints. The novelty of our algorithm is that the filtering method uses a greedy search to calculate ΔG(min). This effectively excludes inappropriate sequences before ΔG(min) is calculated, thereby reducing computation time drastically when compared with an algorithm without the filtering. Experimental results in silico showed the superiority of the greedy search over the traditional approach based on the hamming distance. In addition, experimental results in vitro demonstrated that the experimental free energy (ΔG(exp)) of 126 sequences correlated well with ΔG(min) (|R| = 0.90) than with the hamming distance (|R| = 0.80). These results validate the rationality of a thermodynamic approach. We implemented our algorithm in a graphic user interface-based program written in Java

Fairness in non-convex systems

In general, the set of users utilities is boundedbecause of the limitation of resources. There may existmany Pareto optimal points in the set of users utilities.For selecting a Pareto optimum point, a family of fairnesscriteria, that contains the max-min fairness and aparameterized family of fairness (by Mo andWalrand), hasbeen proposed and examined in some concrete networkingcontexts that result in specific convex utility sets. We newlyexamine general compact (closed and bounded) utility setswhich include the specific utility sets as special cases. Wefirst prove that each of the family of fairness criteria givesa unique fair (Pareto optimum) point if the utility set isconvex. We find, however, counter-examples where each ofthe family of fairness criteria gives multiple fair points ifthe utility set is not convex. We propose an extention of thefamily of fairness criteria such that each of them gives onlya unique fair point regardless of whether the utility set isconvex or not, to which we give proofs. By using a specificload balancing model, we illustrate the counter-examplesand how each criterion of our extended fair family givesa unique fair point

Selective phenol recovery via simultaneous hydrogenation/ dealkylation of isopropyl- and isopropenyl-phenols employing an H2 generator combined with tandem micro-reactor GC/MS

Abstract The pyrolysis of bisphenol A (BPA), an essential process ingredient used in industry and many everyday life products, helps produce low-industrial-demand chemicals such as isopropenyl- and isopropyl-phenols (IPP and iPrP). In this study, tandem micro-reactor gas chromatography/mass spectrometry combined with an H2 generator (H2-TR-GC/MS) was employed for the first time to investigate the selective recovery of phenol via simultaneous hydrogenation/dealkylation of IPP and iPrP. After investigating the iPrP dealkylation performances of several zeolites, we obtained full iPrP conversion with over 99% phenol selectivity using the Y-zeolite at 350 °C. In contrast, when applied to IPP, the zeolite acid centres caused IPP polymerisation and subsequent IPP-polymer cracking, resulting in many byproducts and reduced phenol selectivity. This challenge was overcome by the addition of 0.3 wt% Ni on the Y-zeolite (0.3Ni/Y), which enabled the hydrogenation of IPP into iPrP and subsequent dealkylation into phenol (full IPP conversion with 92% phenol selectivity). Moreover, the catalyst deactivation and product distribution over repetitive catalytic use were successfully monitored using the H2-TR-GC/MS system. We believe that the findings presented herein could allow the recovery of phenol-rich products from polymeric waste with BPA macro skeleton

トットリケン ニ オケル クロガケジグモ ノ ブンプ ハンイ

最近，鳥取県において生息が確認された外来性クモ，クロガケジグモ（ウシオグモ科）の鳥取県内における分布範囲を調査した。クロガケジグモはこれまで知られていた鳥取市に加え，倉吉市周辺から国道9号線沿いに琴浦町まで分布していることを確認した。鳥取市内では本種の生息範囲は千代川河口付近－湯所町－桂見－湖山町西に囲まれた範囲にまだ限定されているが，生息範囲内ではどこでも高密度である。倉吉市では1993年にすでに本種の営巣が確認されていることがわかった。生息範囲も県中部がもっとも広い。したがって鳥取県での最初の侵入は倉吉市で，鳥取市の集団もそこから拡大した可能性が高い。 The present range of distribution of an exotic spider Badumna insignis (Araneae: Desidae) in Tottori Prefecture, Honshu, Japan, where the species has recently settled, was surveyed. In addition to a part of the urban area of Tottori City, the spider was also found from Kurayoshi City and its vicinities along Route 9 west to Kotoura-cho. In Tottori City, the rage was limited to an area of ca. 5 km radius,indicating the species range is in the process of expanding. Density of the spiders is extraordinarily high (usually more than 20 per 10 m long of bridge balustrades, or guard rails along roads) everywhere in the area settled It was found that invasion of the spider in Kurayoshi City dates back to 193 at least

イニュウシュオナジショウジョウバエ ノ トットリケン カラ ノ カクニン フロク：トットリケンサン ショウジョウバエ

外来種オナジショウジョウバエの鳥取県における生息を確認するため、２００８年９月に鳥取市湖山の鳥取大構内の４カ所と鳥取市桂見の１カ所に合計９個のトラップを設置し、１６種２，０３０個体のショウジョウバエを採集した。オナジショウジョウバエは設置したすべてのトラップから合計１５５個体採集され、鳥取県における定着が確認された。鳥取県における過去のショウジョウバエ調査と島根県からの最初のオナジショウジョウバエの記録から、本種の鳥取県への侵入時期は１９９０年前後と推定される。採集された種のうち、Drosophila kuntzei カクレポシショウウジョウバエとDrosophila annulipes ダンダラショウジョウバエも鳥取県新記録である。文献調査と今回のデータに基づき、鳥取県のショウジョウバエとして５６種の記録を末尾に掲げる。　To confirm occurrence of Drosophila simulans, an exotic　species of Drosophilidae (Diptera) in　Japan, we collected drosophilid flies using nine bait (banana mixed with yeasts) traps in the campus of Tottori　University and Katsurami, Tottori City in September 2008. We found a total of 155 adults of Drosophila　simulans from all the traps among 2,030 flies of a total of 16 drosophilid species, and it confirmed settlement　of the species in Tottori Prefecture. It is estimated that the species invaded Tottori Prefecture around　1990, since no flies of this species had been found in the faunal surveys of Drosophila conducted in the 1980s in Tottori City and the species was discovered in 193 in Matsue City of Shimane Prefecture, which is adjacent to Tottori Prefecture. Drosophila (Sophophora) kuntzei and D. (S.) annulipes were also new to fauna of Tottori Prefecture. On the basis of literature survey and the present data, a list of 56 drosophilid species of Tottori Prefecture is presented

トットリケン ニ オケル ガイライセイ ハンシモク ニシュ ノ ブンプ

鳥取県に最近侵入したと考えられる外来性の半翅目昆虫2 種，アワダチソウグンバイとセイタカアワダチソウヒゲナガアブラムシの鳥取県内における分布を調べた。アワダチソウグンバイはセイタカアワダチソウの調査地点ではほとんどの場所で確認された．よって本種はすでに全県的に分布を拡大していると思われる。また，本県の東部から西部までの広範囲で，セイタカアワダチソウヒゲナガアブラムシの生息を鳥取県から初めて確認した。 / The lace bug, Corythucha marmorata iptera: Tingidae) is an exotic species of Tingidae which was recently introduced to Tottori Prefecture. Although the species utilizes an exotic plant, goldenrod Solidago altissima L. (Asteraceae) as a main host, it also attacks crops such as the sweet potato Ipomoea batatas (Convolvulaceae). Thus special attention is needed for the expansion of the species range. We surveyed present range of distribution of C. marmorata in Tottori Prefecture, by checking S. altissima growing roadside along main national roads. The species was widely found from various sites of Tottori Prefecture. During the survey, we also found colonies of an exotic aphid Uroleucon nigrotuberculatum (Hemiptera: Homoptera: Aphididae) which is also parasitic on S. altissima from various sites in the prefecture

Gene expression profiling of loss of TET2 and/or JAK2V617F mutant hematopoietic stem cells from mouse models of myeloproliferative neoplasms

AbstractMyeloproliferative neoplasms (MPNs) are clinically characterized by the chronic overproduction of differentiated peripheral blood cells and the gradual expansion of malignant intramedullary/extramedullary hematopoiesis. In MPNs mutations in JAK2 MPL or CALR are detected mutually exclusive in more than 90% of cases [1,2]. Mutations in them lead to the abnormal activation of JAK/STAT signaling and the autonomous growth of differentiated cells therefore they are considered as “driver” gene mutations. In addition to the above driver gene mutations mutations in epigenetic regulators such as TET2 DNMT3A ASXL1 EZH2 or IDH1/2 are detected in about 5%–30% of cases respectively [3]. Mutations in TET2 DNMT3A EZH2 or IDH1/2 commonly confer the increased self-renewal capacity on normal hematopoietic stem cells (HSCs) but they do not lead to the autonomous growth of differentiated cells and only exhibit subtle clinical phenotypes [4,6–8,5]. It was unclear how mutations in such epigenetic regulators influenced abnormal HSCs with driver gene mutations how they influenced the disease phenotype or whether a single driver gene mutation was sufficient for the initiation of human MPNs. Therefore we focused on JAK2V617F and loss of TET2—the former as a representative of driver gene mutations and the latter as a representative of mutations in epigenetic regulators—and examined the influence of single or double mutations on HSCs (Lineage−Sca-1+c-Kit+ cells (LSKs)) by functional analyses and microarray whole-genome expression analyses [9]. Gene expression profiling showed that the HSC fingerprint genes [10] was statistically equally enriched in TET2-knockdown-LSKs but negatively enriched in JAK2V617F–LSKs compared to that in wild-type-LSKs. Double-mutant-LSKs showed the same tendency as JAK2V617F–LSKs in terms of their HSC fingerprint genes but the expression of individual genes differed between the two groups. Among 245 HSC fingerprint genes 100 were more highly expressed in double-mutant-LSKs than in JAK2V617F–LSKs. These altered gene expressions might partly explain the mechanisms of initiation and progression of MPNs which was observed in the functional analyses [9]. Here we describe gene expression profiles deposited at the Gene Expression Omnibus (GEO) under the accession number GSE62302 including experimental methods and quality control analyses

Physical properties of the Dome Fuji deep ice core (review)

Recent results of physical analyses of the Dome Fuji ice core are summarized with special attention to new methods introduced in the present studies. Microphysical processes which affect the ice core records are reviewed to better understand the paleoclimatic and paleoenvironmental signals stored

Identification of 45 New Neutron-Rich Isotopes Produced by In-Flight Fission of a 238U Beam at 345 MeV/nucleon

A search for new isotopes using in-flight fission of a 345 MeV/nucleon 238U beam has been carried out at the RI Beam Factory at the RIKEN Nishina Center. Fission fragments were analyzed and identified by using the superconducting in-flight separator BigRIPS. We observed 45 new neutron-rich isotopes: 71Mn, 73,74Fe, 76Co, 79Ni, 81,82Cu, 84,85Zn, 87Ga, 90Ge, 95Se, 98Br, 101Kr, 103Rb, 106,107Sr, 108,109Y, 111,112Zr, 114,115Nb, 115,116,117Mo, 119,120Tc, 121,122,123,124Ru, 123,124,125,126Rh, 127,128Pd, 133Cd, 138Sn, 140Sb, 143Te, 145I, 148Xe, and 152Ba

Amino acid influx via LAT1 regulates iron demand and sensitivity to PPMX-T003 of aggressive natural killer cell leukemia

Yanagiya R., Miyatake Y., Watanabe N., et al. Amino acid influx via LAT1 regulates iron demand and sensitivity to PPMX-T003 of aggressive natural killer cell leukemia. Leukemia , (2024); 10.1038/s41375-024-02296-6.Aggressive natural killer cell leukemia (ANKL) is a rare hematological malignancy with a fulminant clinical course. Our previous study revealed that ANKL cells proliferate predominantly in the liver sinusoids and strongly depend on transferrin supplementation. In addition, we demonstrated that liver-resident ANKL cells are sensitive to PPMX-T003, an anti-human transferrin receptor 1 inhibitory antibody, whereas spleen-resident ANKL cells are resistant to transferrin receptor 1 inhibition. However, the microenvironmental factors that regulate the iron dependency of ANKL cells remain unclear. In this study, we first revealed that the anti-neoplastic effect of PPMX-T003 was characterized by DNA double-strand breaks in a DNA replication-dependent manner, similar to conventional cytotoxic agents. We also found that the influx of extracellular amino acids via LAT1 stimulated sensitivity to PPMX-T003. Taken together, we discovered that the amount of extracellular amino acid influx through LAT1 was the key environmental factor determining the iron dependency of ANKL cells via adjustment of their mTOR/Myc activity, which provides a good explanation for the different sensitivity to PPMX-T003 between liver- and spleen-resident ANKL cells, as the liver sinusoid contains abundant amino acids absorbed from the gut. (Figure presented.