Laboratory phenomics predicts field performance and identifies superior indica haplotypes for early seedling vigour in dry direct-seeded rice

Seedling vigour is an important agronomic trait and is gaining attention in Asian rice (Oryza sativa) as cultivation practices shift from transplanting to forms of direct seeding. To understand the genetic control of rice seedling vigour in dry direct seeded (aerobic) conditions we measured multiple seedling traits in 684 accessions from the 3000 Rice Genomes (3K-RG) population in both the laboratory and field at three planting depths. Our data show that phenotyping of mesocotyl length in laboratory conditions is a good predictor of field performance. By performing a genome wide association study, we found that the main QTL for mesocotyl length, percentage seedling emergence and shoot biomass are co-located on the short arm of chromosome 7. We show that haplotypes in the indica subgroup from this region can be used to predict the seedling vigour of 3K-RG accessions. The selected accessions may serve as potential donors in genomics-assisted breeding programs

The birds of the Loyalty Islands (New Caledonia): census, ecological and biogeographical issues

The avifauna of the Loyalty Islands comprises 62 species, including 14 breeding or erratic seabirds, 5 migratory birds, 7 herons, ducks and rails, 4 birds of prey, 28 indigenous land breeders (belonging to 33 subspecies) and 2 species introduced from the Grande Terre (main island of New Caledonia). Six species are endemic: 3 on the Grande Terre and in the Loyalty Islands (New Caledonian Friarbird Philemon diemenensis, Green-backed White-eye Zosterops xanthochrous, Striated Starling Aplonis striatus) and 3 only found in the Loyalty Islands (Ouvea Parakeet Eunymphicus uvaeensis, Large Lifou White-eye Zosterops inornatus and Small Lifou White-eye Z. minutus). Eunymphicus is an endemic genus of New Caledonia. Eight subspecies are endemic to both the Grande Terre and the Loyalty Islands and 11 are exclusive of the Loyalty Islands. Of the 24 taxa whose geographical origin could be identified, 58% are identical or similar to those on the Grande Terre, 105 km away, and 42% have affinities with birds in Vanuatu, twice as far away (225 km). The paths of cyclones could explain the specific influence of Vanuatu. The correlation between the islands’land area and the number of species that have successfully settled is very close (r = 0.97) and confirms this biogeographical standard. The land breeding species frequencies vary, with rare localized species limited to some islands (Bluefaced Parrotfinch Erythrura trichroa, Ouvea Parakeet), or possibly extinct (Island Thrush Turdus poliocephalus) and others whose frequency varies widely from place to place (Fan-tailed Cuckoo Cacomantis flabelliformis, Gerygone Gerygone flavolateralis, Silvereye Zosterops lateralis), while others show high (Red-bellied Fruit-Dove Ptilinopus greyii), average (Melanesian Flycatcher Myiagra caledonica, Sacred Kingfischer Todiramphus sanctus) or low (Emerald Dove Chalcophaps indica) frequencies that remain comparable between these islands. The species ecology has been determined with some species associated with wide forests, e.g. the Ouvea Parakeet, while others are typical of the open settings. The threats onto this avifauna are mainly linked to habitat destruction and the impact of introduced species. A specific effort should be made to ensure the protection of populations of that species for which there is the greatest concern, i.e. the Ouvea ParakeetL'avifaune des Loyauté comprend 62 espèces, dont 14 marines nicheuses ou erratiques, 5 migratrices, 7 hérons, canards et râles, 4 rapaces/chouette, 28 oiseaux terrestres nicheurs indigènes (appartenant à 33 sous-espèces) et 2 espèces introduites de Grande Terre. Six espèces sont endémiques à l'archipel néo-calédonien: 3 présentes à la fois en Grande Terre et aux Loyauté: Polochion moine Philemon diemenensis, Zostérops à dos vert Zosterops xanthochrous, Stourne des Loyauté Aplanis striatus et 3 pour les seules Loyauté: Perruche d'Ouvéa Eunymphicus uvaeensis, Zostérops de Lifou Zosterops inornatus et Zostérops minute Z. minutus. Eunymphicus est un genre endémique de Nouvelle-Calédonie. Huit sous-espèces sont endémiques à la fois de Grande Terre et des Loyauté et 11 sont exclusives des Loyauté. Sur 24 taxons dont l'origine géographique peut être établie, 58 % sont identiques ou proches de ceux de Grande Terre distante de 105 km, et 42 % ont des affinités avec des oiseaux du Vanuatu, deux fois plus éloigné (225 km). La trajectoire des cyclones pourrait expliquer cette influence ni-vanuatu particulière. La corrélation entre la surface des îles et le nombre d'espèces qui y ont réussi leur implantation est très étroite (r = 0,97) et vérifie bien cette règle de la biogéographie. La fréquence des espèces terrestres nicheuses est variable, avec des espèces rares et localisées, limitées à certaines îles (Diamant de Kittlitz Erythrura trichroa, Perruche d'Ouvéa) et qui ont peut-être disparu (Merle des Iles Turdus poliocephalus), d'autres dont la fréquence est très inégalement répartie (Coucou à éventail Cacomantis flabelliformis, Gérygone Gerygone flavolateralis, Zostérops à dos noir Zosterops lateralis), d'autres enfin aux fréquences élevées (Ptilope de Grey Ptilinopus greyii), moyennes (Monarque Myiagra caledonica, Martin-chasseur Todiramphus sanctus) ou faibles (Colombine turvert Chalcophaps indica), mais comparables entre les îles. L'écologie des espèces a pu être précisée avec des espèces inféodées aux grandes forêts, parmi lesquelles la Perruche d'Ouvéa, et des espèces typiques des milieux ouverts. Les menaces pesant sur cette avifaune sont essentiellement liées aux destructions d'habitat et à l'impact des espèces introduites. Un effort particulier doit être consenti pour sécuriser les populations de l'espèce dont le statut est le plus préoccupant: la Perruche d'Ouvéa

Radiosurgery for brainstem metastases with and without whole brain radiotherapy: clinical series and literature review

Objective The objective of this study was to investigate outcomes for patients with brainstem metastases treated with stereotactic radiosurgery (SRS). Methods Patients with brainstem metastases treated with SRS between April 2006 and June 2012 were identified from a prospective database. Patient and treatment-related factors were recorded. Kaplan-Meier analysis was used to calculate survival and freedom from local and distant brain progression. Univariate and multivariate Cox regression was used to identify factors important for overall survival. Results In total, 44 patients received SRS for 48 brainstem metastases of whom 33 (75 %) also received whole brain radiotherapy (WBRT): 23 patients (52 %) WBRT prior to SRS, 6 (13.6 %) WBRT concurrently with SRS and 4 (9.0 %) WBRT after SRS. Eight patients received a second course ofWBRTat further progression. Median target volume was 1.33 cc (range 0.04–12.17) and median prescribed marginal dose was 15 Gy (range 10–22). There were four cases of local failure, and 6-month and 1-year freedom from local failure was 84.6 and 76.9 %, respectively. Median overall survival (OS) was 5.4 months. There were four cases of radionecrosis, 2 (4.8 %) of which were symptomatic. The absence of external beam brain radiotherapy (predominantly WBRT) showed a trend towards improved OS on univariate analysis. Neither local nor distant brain failure significantly impacted OS. Conclusion This retrospective series of patients treated with SRS for brainstem metastases, largely in combination with at least one course of WBRT, demonstrates that this approach is safe and results in good local control. In this cohort, no variables significantly impacted OS, including intracranial control

Optical properties and spatial distribution of MgII absorbers from SDSS image stacking

We present a statistical analysis of the photometric properties and spatial distribution of more than 2,800 MgII absorbers with 0.37<z<1 and rest equivalent width W_0(\lambda2796)>0.8\AA detected in SDSS quasar spectra. Using an improved image stacking technique, we measure the cross-correlation between MgII gas and light (in the g, r, i and z-bands) from 10 to 200 kpc and infer the light-weighted impact parameter distribution of MgII absorbers. Such a quantity is well described by a power-law with an index that strongly depends on W_0, ranging from ~-1 for W_0~ 1.5\AA. At redshift 0.37<z<0.55, we find the average luminosity enclosed within 100 kpc around MgII absorbers to be M_g=-20.65+-0.11 mag, which is ~0.5 L_g*. The global luminosity-weighted colors are typical of present-day intermediate type galaxies. However, while the light of weaker absorbers originates mostly from red passive galaxies, stronger systems display the colors of blue star-forming galaxies. Based on these observations, we argue that the origin of strong MgII absorber systems might be better explained by models of metal-enriched gas outflows from star-forming/bursting galaxies. Our analysis does not show any redshift dependence for both impact parameter and rest-frame colors up to z=1. However, we do observe a brightening of the absorbers related light at high redshift (~50% from z~0.4 to 1). We argue that MgII absorbers are a phenomenon typical of a given evolutionary phase that more massive galaxies experience earlier than less massive ones, in a downsizing fashion. (abridged)Comment: ApJ in press, 28 pages, 16 figures, using emulateapj. Only typo corrections wrt the original submission (v1

Hall effect in the accumulation layers on the surface of organic semiconductors

We have observed the Hall effect in the field-induced accumulation layer on the surface of small-molecule organic semiconductor. The Hall mobility mu_H increases with decreasing temperature in both the intrinsic (high-temperature) and trap-dominated (low-temperature) conduction regimes. In the intrinsic regime, the density of mobile field-induced charge carriers extracted from the Hall measurements, n_H, coincides with the density n calculated using the gate-channel capacitance, and becomes smaller than n in the trap-dominated regime. The Hall data are consistent with the diffusive band-like motion of field-induced charge carriers between the trapping events.Comment: 11 page

Transrectal Prostate Biopsy and Fiducial Marker Placement in a Standart 1.5T Magnetic Resonance Imaging Scanner

Cataloged from PDF version of article.Purpose: We investigated the accuracy and feasibility of a system that provides transrectal needle access to the prostate concurrent with 1.5 Tesla MRI which previously has not been possible. Materials and Methods: In 5 patients with previously diagnosed prostate cancer, MRI guided intraprostatic placement of gold fiducial markers (4 procedures) and/or prostate biopsy (3 procedures) was performed using local anesthesia. Results: Mean procedure duration was 76 minutes and all patients tolerated the intervention well. Procedure related adverse events included self-limited hematuria and hematochezia following 3 of 8 procedures (all resolved in less than 1 week). Mean needle placement accuracy was 1.9 mm for the fiducial marker placement studies and 1.8 mm for the biopsy procedures. Mean fiducial marker placement accuracy was 4.8 mm and the mean fiducial marker placement accuracy transverse to the needle direction was 2.6 mm. All patients who underwent the procedure were able to complete their course of radiotherapy without delay or complication. Conclusions: While studies of clinical usefulness are warranted, transrectal 1.5 T MRI guided prostate biopsy and fiducial marker placement is feasible using this system, providing new opportunities for image guided diagnostic and therapeutic prostate interventions

Diverting phenylpropanoid pathway flux from sinapine to produce industrially useful 4-vinyl derivatives of hydroxycinnamic acids in Brassicaceous oilseeds

Sinapine (sinapoylcholine) is an antinutritive phenolic compound that can account for up to 2% of seed weight in brassicaceous oilseed crops and reduces the suitability of their protein-rich seed meal for use as animal feed. Sinapine biosynthesis draws on hydroxycinnamic acid precursors produced by the phenylpropanoid pathway. The 4-vinyl derivatives of several hydroxycinnamic acids have industrial applications. For example, 4-vinyl phenol (4-hydroxystyrene) is a building block for a range of synthetic polymers applied in resins, inks, elastomers, and coatings. Here we have expressed a modified bacterial phenolic acid decarboxylase (PAD) in developing seed of Camelina sativa to redirect phenylpropanoid pathway flux from sinapine biosynthesis to the production of 4-vinyl phenols. PAD expression led to a ∼95% reduction in sinapine content in seeds of both glasshouse and field grown C. sativa and to an accumulation of 4-vinyl derivatives of hydroxycinnamic acids, primarily as glycosides. The most prevalent aglycone was 4-vinyl phenol, but 4-vinyl guaiacol, 6-hydroxy-4-vinyl guaiacol and 4-vinylsyringol (Canolol) were also detected. The molar quantity of 4-vinyl phenol glycosides was more than twice that of sinapine in wild type seeds. PAD expression was not associated with an adverse effect on seed yield, harvest index, seed morphology, storage oil content or germination in either glasshouse or field experiments. Our data show that expression of PAD in brassicaceous oilseeds can supress sinapine accumulation, diverting phenylpropanoid pathway flux into 4-vinyl phenol derivatives, thereby also providing a non-petrochemical source of this class of industrial chemicals

Elements Related to Heterogeneity of Antibody-Dependent Cell Cytotoxicity in Patients Under Trastuzumab Therapy for Primary Operable Breast Cancer Overexpressing Her2

Preliminary results from a pilot trial on trastuzumab's mechanism of action against operable breast tumors overexpressing Her2 suggested a role for antibody-dependent cell cytotoxicity (ADCC). To examine factors affecting ADCC intensity and variability, we extended this study to the phenotypic and functional analysis of circulating mononuclear cells in 18 patients. ADCC was induced by trastuzumab therapy in 15 of 18 patients (83%). Inability to develop ADCC in three patients did not depend on inadequate levels of trastuzumab because further increase in its concentration in vitro was ineffective. Rather, susceptibility to develop ADCC was fairly predicted by test with trastuzumab before therapy and was correlated to the number of lymphocytes coexpressing CD16 and CD56. Phenotypic analysis at the end of ADCC evaluating down-regulation of CD16, and up-regulation of CD69 and CD107a, confirmed that natural killer (NK) cells and CD56+ T cells were involved in productive engagement of trastuzumab. Also, the killing efficiency of CD16+ lymphocytes was influenced by 158 V/F polymorphism of FcγRIII (CD16), whereas variations of CD247 on NK cells were consistent with trends between ADCC before and after therapy. Complete pathologic response was observed in one patient showing ADCC of outstanding intensity, whereas four cases of partial response showed intermediate ADCC; none of the three patients unable to mount ADCC had significant tumor regression. These data indicate that quantity and lytic efficiency of CD16+ lymphocytes are major factors for ADCC induction by trastuzumab, and confirm that breast cancer responses to short-term trastuzumab monotherapy may depend on involvement of the ADCC mechanism. [Cancer Res 2007;67(24):11991–9

Block of death-receptor apoptosis protects mouse cytomegalovirus from macrophages and is a determinant of virulence in immunodeficient hosts.

The inhibition of death-receptor apoptosis is a conserved viral function. The murine cytomegalovirus (MCMV) gene M36 is a sequence and functional homologue of the human cytomegalovirus gene UL36, and it encodes an inhibitor of apoptosis that binds to caspase-8, blocks downstream signaling and thus contributes to viral fitness in macrophages and in vivo. Here we show a direct link between the inability of mutants lacking the M36 gene (ΔM36) to inhibit apoptosis, poor viral growth in macrophage cell cultures and viral in vivo fitness and virulence. ΔM36 grew poorly in RAG1 knockout mice and in RAG/IL-2-receptor common gamma chain double knockout mice (RAGγC(-/-)), but the depletion of macrophages in either mouse strain rescued the growth of ΔM36 to almost wild-type levels. This was consistent with the observation that activated macrophages were sufficient to impair ΔM36 growth in vitro. Namely, spiking fibroblast cell cultures with activated macrophages had a suppressive effect on ΔM36 growth, which could be reverted by z-VAD-fmk, a chemical apoptosis inhibitor. TNFα from activated macrophages synergized with IFNγ in target cells to inhibit ΔM36 growth. Hence, our data show that poor ΔM36 growth in macrophages does not reflect a defect in tropism, but rather a defect in the suppression of antiviral mediators secreted by macrophages. To the best of our knowledge, this shows for the first time an immune evasion mechanism that protects MCMV selectively from the antiviral activity of macrophages, and thus critically contributes to viral pathogenicity in the immunocompromised host devoid of the adaptive immune system