A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency.

BACKGROUND: Tobacco (Nicotiana tabacum) is an important plant model system that has played a key role in the early development of molecular plant biology. The tobacco genome is large and its characterisation challenging because it is an allotetraploid, likely arising from hybridisation between diploid N. sylvestris and N. tomentosiformis ancestors. A draft assembly was recently published for N. tabacum, but because of the aforementioned genome complexities it was of limited utility due to a high level of fragmentation. RESULTS: Here we report an improved tobacco genome assembly, which, aided by the application of optical mapping, achieves an N50 size of 2.17 Mb and enables anchoring of 64% of the genome to pseudomolecules; a significant increase from the previous value of 19%. We use this assembly to identify two homeologous genes that explain the differentiation of the burley tobacco market class, with potential for greater understanding of Nitrogen Utilization Efficiency and Nitrogen Use Efficiency in plants; an important trait for future sustainability of agricultural production. CONCLUSIONS: Development of an improved genome assembly for N. tabacum enables what we believe to be the first successful map-based gene discovery for the species, and demonstrates the value of an improved assembly for future research in this model and commercially-important species.

Learning the hard way: the importance of accurate data.

AIM: The outcome of surgery for colorectal cancer in each unit in the UK is collated by the National Bowel Cancer Audit Project (NBOCAP). In 2008-2009 our unit had a raw 30-day postoperative mortality close to the national average, but when it was nationally adjusted it appeared to be an outlier. The purpose of this study was to identify reasons for this disparity. METHOD: All records were obtained for patients undergoing surgery for colorectal cancer over the 2 years. Data submitted to NBOCAP to determine adjusted rates were compared with actual data. RESULTS: There were major discordances between submitted and actual data for American Society of Anesthesiology grades and timing of surgery. This explained why the unit appeared to be an outlier. CONCLUSION: There is increasing emphasis on outcome of health service delivery, which has important implications. Submission of correct data is essential if objective comparison is to be made on which to base decisions on service delivery among units and within health regions.

Variability for Resistance to Phytophthora nicotianae Within a Collection of Nicotiana rustica Accessions.

Black shank, caused by Phytophthora nicotianae, is one of the most important diseases affecting tobacco (Nicotiana tabacum) production worldwide. Many current tobacco cultivars possess immunity to race 0 of this pathogen conferred by introgressed dominant genetic factors. Novel alleles conditioning resistance to alternative races are desired. The objective of this research was to evaluate variability for black shank resistance within a collection of N. rustica germplasm using both soilborne disease nurseries and controlled race-specific (race 0 and race 1) inoculations. Nearly all of the 86 accessions studied exhibited very high resistance to race 0, and many displayed levels of race 1 resistance greater than that exhibited by the resistant flue-cured tobacco check, 'K 346'. Materials found to be highly resistant to race 0 and race 1 in growth-chamber experiments also had the best survivability in field disease nurseries. N. rustica accessions TR 6, TR 12, TR 16, TR 21, TR 20, TR 48, TR 54, TR 57, and TR 69 could be sources of novel alleles with large effects on black shank resistance, and could have value for burley and flue-cured tobacco breeding.

Fedratinib hydrochloride to treat intermediate-2 or high-risk primary or secondary myelofibrosis.

Fedratinib hydrochloride is a selective Janus kinase 2 (JAK2) inhibitor approved by the U.S. Food and Drug Administration (FDA) in August 2019 for intermediate- 2 or high-risk primary or secondary myelofibrosis. The approval of this novel oral agent was based on the phase II and III JAKARTA-2 and JAKARTA trials, which both showed significant reduction in splenomegaly and myelofibrosis symptom burden. The most common adverse effects associated with fedratinib include anemia, gastrointestinal symptoms and elevation in liver transaminases. Early clinical trial data was concerning for an increased incidence of Wernicke's encephalopathy (WE), which led the FDA to place a clinical hold on further drug development. However, upon further investigation it was determined that there was no clear evidence that fedratinib causes WE, and the clinical hold was lifted in 2017. This inclusive review provides insight into the pharmacology, safety and efficacy, and future direction of fedratinib use in myeloproliferative neoplasms.

Mitochondrial regulation of store-operated calcium signaling in T lymphocytes.

Mitochondria act as potent buffers of intracellular Ca2+ in many cells, but a more active role in modulating the generation of Ca2+ signals is not well established. We have investigated the ability of mitochondria to modulate store-operated or "capacitative" Ca2+ entry in Jurkat leukemic T cells and human T lymphocytes using fluorescence imaging techniques. Depletion of the ER Ca2+ store with thapsigargin (TG) activates Ca2+ release-activated Ca2+ (CRAC) channels in T cells, and the ensuing influx of Ca2+ loads a TG-insensitive intracellular store that by several criteria appears to be mitochondria. Loading of this store is prevented by carbonyl cyanide m-chlorophenylhydrazone or by antimycin A1 + oligomycin, agents that are known to inhibit mitochondrial Ca2+ import by dissipating the mitochondrial membrane potential. Conversely, intracellular Na+ depletion, which inhibits Na+-dependent Ca2+ export from mitochondria, enhances store loading. In addition, we find that rhod-2 labels mitochondria in T cells, and it reports changes in Ca2+ levels that are consistent with its localization in the TG-insensitive store. Ca2+ uptake by the mitochondrial store is sensitive (threshold is <400 nM cytosolic Ca2+), rapid (detectable within 8 s), and does not readily saturate. The rate of mitochondrial Ca2+ uptake is sensitive to extracellular [Ca2+], indicating that mitochondria sense Ca2+ gradients near CRAC channels. Remarkably, mitochondrial uncouplers or Na+ depletion prevent the ability of T cells to maintain a high rate of capacitative Ca2+ entry over prolonged periods of >10 min. Under these conditions, the rate of Ca2+ influx in single cells undergoes abrupt transitions from a high influx to a low influx state. These results demonstrate that mitochondria not only buffer the Ca2+ that enters T cells via store-operated Ca2+ channels, but also play an active role in modulating the rate of capacitative Ca2+ entry.

Characterization of T cell mutants with defects in capacitative calcium entry: genetic evidence for the physiological roles of CRAC channels.

Prolonged Ca2+ influx is an essential signal for the activation of T lymphocytes by antigen. This influx is thought to occur through highly selective Ca2+ release-activated Ca2+ (CRAC) channels that are activated by the depletion of intracellular Ca2+ stores. We have isolated mutants of the Jurkat human T cell line NZdipA to explore the molecular mechanisms that underlie capacitative Ca2+ entry and to allow a genetic test of the functions of CRAC channels in T cells. Five mutant cell lines (CJ-1 through CJ-5) were selected based on their failure to express a lethal diphtheria toxin A chain gene and a lacZ reporter gene driven by NF-AT, a Ca(2+)- and protein kinase C-dependent transcription factor. The rate of Ca2+ influx evoked by thapsigargin was reduced to varying degrees in the mutant cells whereas the dependence of NF-AT/lacZ gene transcription on [Ca2+]i was unaltered, suggesting that the transcriptional defect in these cells is caused by a reduced level of capacitative Ca2+ entry. We examined several factors that determine the rate of Ca2+ entry, including CRAC channel activity, K(+)-channel activity, and Ca2+ clearance mechanisms. The only parameter found to be dramatically altered in most of the mutant lines was the amplitude of the Ca2+ current (ICRAC), which ranged from 1 to 41% of that seen in parental control cells. In each case, the severity of the ICRAC defect was closely correlated with deficits in Ca2+ influx rate and Ca(2-)-dependent gene transcription. Behavior of the mutant cells provides genetic evidence for several roles of ICRAC in T cells. First, mitogenic doses of ionomycin appear to elevate [Ca2+]i primarily by activating CRAC channels. Second, ICRAC promotes the refilling of empty Ca2+ stores. Finally, CRAC channels are solely responsible for the Ca2+ influx that underlies antigen-mediated T cell activation. These mutant cell lines may provide a useful system for isolating, expressing, and exploring the functions of genes involved in capacitative Ca2+ entry.

Cretaceous extinctions: evidence for wildfires and search for meteoritic material.

Clay samples from three Cretaceous-Tertiary boundary sites contain 0.36 to 0.58 percent graphitic carbon, mainly as fluffy aggregates of 0.1 to 0.5 micrometers-apparently a worldwide layer of soot. It may have been produced by wildfires triggered by a giant meteorite. This carbon, corresponding to a global abundance of 0.021 +/- 0.006 gram per square centimeter, could have greatly enhanced the darkening and cooling of the earth by rock dust, which has been suggested as a cause of the extinctions. The surprisingly large amount of soot (10 percent of the present biomass of the earth) implies either that much of the earth's vegetation burned down or that substantial amounts of fossil fuels were ignited also. The particle-size distribution of the soot is similar to that assumed for the smoke cloud of "nuclear winter," but the global distribution is more uniform and the amounts are much greater, suggesting that soot production by large wildfires is about 10 times more efficient that has been assumed for a nuclear winter. Thus cooling would be more pervasive and lasting. No trace of meteoritic noble gases and no meteoritic spinel were found in these carbon fractions. Accordingly, limits can be set on the mass fraction of the meteorite that escaped degassing (

Subset-specific expression of potassium channels in developing murine T lymphocytes.

Ion channels were studied in four major subsets of developing murine thymocytes by using patch-clamp recording and cell-surface staining techniques. The expression of three types of voltage-gated potassium channels in thymocytes varies consistently with the cell's developmental state and functional class as defined by cell-surface markers. One class of potassium channel (type n) predominates in immature thymocyte subsets as well as in mature-phenotype CD4+CD8- thymocytes (precursors to helper T lymphocytes), and the average surface density of this channel type correlates with the extent of cell proliferation. Two additional types of potassium channels (types n' and l) are found in the mature CD4-CD8+ thymocyte subset that contains precursors to cytotoxic and suppressor T cells. The subset-specific expression of type n' and l potassium channels suggests their use as additional cell-surface markers with which to identify precursors to the cytotoxic suppressor T cell lineage.

Primordial noble gases in chondrites: the abundance pattern was established in the solar nebula.

Ordinary chondrites, like carbonaceous chondrites, contain primordial noble gases mainly in a minor phase comprising

Barium isotopes in allende meteorite: evidence against an extinct superheavy element.

Carbon and chromite fractions from the Allende meteorite that contain isotopically anomalous xenon-131 to xenon-136 (carbonaceous chondrite fission or CCF xenon) at up to 5 x 10(11) atoms per gram show no detectable isotopic anomalies in barium-130 to barium-138. This rules out the possibility that the CCF xenon was formed by in situ fission of an extinct superheavy element. Apparently the CCF xenon and its carbonaceous carrier are relics from stellar nucleosynthesis.

Samarium-146 in the early solar system: evidence from neodymium in the allende meteorite.

A carbon-chromite fraction from the Allende C3V chondrite shows strikingly large isotopic enrichments of neodymium-142 (0.47 percent) and neodymium- 143 (36 percent). Both apparently formed by alpha decay of samarium-146 and samarium-147 (half-lives 1.03 x 10(8) and 1.06 x 10(11) years), but the isotopic enrichment was greatly magnified by recoil of residual nuclei into a carbon film surrounding the samarium-bearing grains. These data provide an improved estimate of the original abundance of extinct samarium-146 in the early solar system [(146)Sm/(144)Sm = (4.5 +/- 0.5) x 10(-3)], higher than predicted by some models of pprocess nucleosynthesis. It may be possible to use this isotopic pair as a chronometer of the early solar system.

Argon-40-argon-39 dating of apollo sample 15555.

An age of 3.33+/-0.05x10(9) years was obtained for Apollo 15 sample 15555 by argon40-argon-39 dating. The age of rock 15555, a basalt from the rim of Hadley Rille, establishes an upper limit to the age of the rille. The basalt flows filling the Hadley Rille section of the Imbrium basin postdate the formation of the basin-as measured by the Apollo 14 samples of the Fra Mauro formation-by at least 500x10(6) years. Therefore, the mare basalts cannot be simple impact melts but rather must result from some igneous activity on the moon.

Carbynes: carriers of primordial noble gases in meteorites.

Five carbynes (triply bonded allotropes of carbon) have been found by electron diffraction in the Allende and Murchison carbonaceous chondrites: carbon VI, VIII, X, XI, and (tentatively) XII. From the isotopic composition of the associated noble-gas components, it appears that the carbynes in Allende (C3V chondrite) are local condensates from the solar nebula, whereas at least two carbynes in Murchison (C2 chondrite) are of exotic, presolar origin. They may be dust grains that condensed in stellar envelopes and trapped isotopically anomalous matter from stellar nucleosynthesis.

Carbynes in meteorites: detection, low-temperature origin, and implications for interstellar molecules.

Carbon from the Allende meteorite is not graphite but carbyne (triply bonded elemental carbon), inasmuch as on heating to 250 degrees to 330 degrees C it releases mainly triply bonded fragments: -(C identical withC)(n),- with n = 1 to 5, and -(C identical withC)(n)-CN, with n = 1 to 3. Although carbynes have been known to form only by condensation of carbon vapor above 2600 K or by explosive shock of > 600 kilobars, it is found that they also form metastably by the reaction 2CO --> CO(2) + C (solid) at 300 degrees to 400 degrees C in the presence of a chromite catalyst. Such low-temperature formation by surface catalysis may be the dominant source of carbynes on the earth and in meteorites, and a major source of interstellar carbynes and cyanopolyacetylenes.

Interstellar carbon in meteorites.

The Murchison and Allende chondrites contain up to 5 parts per million carbon that is enriched in carbon-13 by up to + 1100 per mil (the ratio of carbon-12 to carbon-13 is approximately 42, compared to 88 to 93 for terrestrial carbon). This "heavy" carbon is associated with neon-22 and with anomalous krypton and xenon showing the signature of the s-process (neutron capture on a slow time scale). It apparently represents interstellar grains ejected from late-type stars. A second anomalous xenon component ("CCFXe") is associated with a distinctive, light carbon (depleted in carbon-13 by 38 per mil), which, however, falls within the terrestrial range and hence may be of either local or exotic origin.

Plutonium-244: confirmation as an extinct radioactivity.

The mass spectrum of xenon from spontaneous fission in a laboratory sample of plutonium-244 is precisely what meteoriticists predicted it would be; this discovery completes a web of proof that this nuclide is a bona fide extinct radioactivity of galactic origin, that r-process nucleosynthesis was ongoing in the galaxy at the time of the birth of the sun, and that the early meteoritic abundances of plutonium-244, heretofore tentative, can be utilized with confidence in models for the chronology of galactic nucleosynthesis. The search for an explanation for anomalous fission-like xenon in carbonaceous chondrites can now be narrowed.

Iodine-129/xenon-129 age of magnetite from the orgueil meteorite.

Magnetite from the Orgueil C1 chondrite is only 2.0 +/- 2.4 million years older by the iodine-xenon method than the next oldest meteorite, the Karoonda C4 chondrite. This age ties the primitive C1 chondrites to the extensive iodine-xenon chronology of normal chrondrites. If Karoonda and Orgueil magnetite formed from similar material, then the age difference is an upper limit to the formation time of these meteorites-and by customary extension, the solar system. Condensation, chondrule formation, accretion, and metamorphism of the Karoonda parent body all seem to have been completed within a few million years.

Isotopic analysis of rare gases from stepwise heating of lunar fines and rocks.

Highlights of a first effort in sorting out rare gases in lunar material are solar wind rare gases in abundance; variable (20)Ne/(22)Ne but constant (21)Ne/ (22)Ne ratios in fractions of the trapped neon; cosmogenic rare gases similar to those found in meteorites, except for copious (131)Xe in one rock but not in another; at Tranquillity Base a rock 4.1 x 10(9) years old which reached the surface 35 to 65 million years ago, amid soil whose particles have typically been within a meter of the surface for 10(9) years or more.

Autologous tissue immediate breast reconstruction: desired but oncologically safe?

BACKGROUND: There has been a dramatic increase in the incidence of immediate breast reconstruction after mastectomy for breast cancer over the past few decades and autologous tissue flaps are being used with increasing frequency. Concern has been expressed that these complex procedures may lead to a delay in the delivery of adjuvant therapy, which in turn may adversely affect recurrence and survival rates. Several publications have looked into the effect of immediate reconstruction on the timing of delivery of adjuvant therapy, but all types of immediate breast reconstruction (IBR) tend to be examined as a homogenous group. AIM: The aim of this review was to search current literature and look specifically at the effect of autologous tissue reconstructions on adjuvant therapy, and identify possible causes of delay. DISCUSSION: From the data analysed, it appears that there may be a delay in the delivery of adjuvant therapy associated with autologous tissue IBR, especially transverse rectus abdominis muscle (TRAM) flaps. The studies available, however, examine small numbers of patients, which makes proving statistical significance difficult. Moreover, there also appears to be no consensus on what constitutes a delay in the delivery of adjuvant therapy. From 3% to 72% of autologous tissue IBR patients seem to receive their adjuvant treatment with a delay, according to the guidelines of the respective centres. Moreover, the period of time until chemotherapy appears generally increased from 13% to 36% compared with mastectomy alone patients. The most common reasons for delay are wound and flap complications. CONCLUSION: At the moment, despite the increasing popularity of autologous IBR, these procedures have not proved their oncological safety. Further studies looking at the effect of IBR, especially TRAM flap reconstruction, are needed.

Evaluation of Tobacco Germplasm for Seedling Resistance to Stem Rot and Target Spot Caused by Thanatephorus cucumeris.

Stem rot and target spot of tobacco, caused by Rhizoctonia solani and its teleomorph Thanatephorus cucumeris, respectively, can cause serious problems in production of tobacco (Nicotiana tabacum) seedlings. Previous screens for genetic resistance in tobacco have been limited. The objective of this study was to evaluate 97 genotypes composing several classes of tobacco and related Nicotiana spp. for seedling resistance to stem rot and target spot. Significant differences in disease incidence initially were observed among the genotypes for both stem rot and target spot; however, resistance to target spot was not observed when disease pressure was high. Partial resistance to stem rot was observed in several genotypes in repeated tests. These accessions may be useful as a source of resistance to R. solani in future breeding efforts.