Primary analysis of repeat elements of the Asian seabass (Lates calcarifer) transcriptome and genome

As part of our Asian seabass genome project, we are generating an inventory of repeat elements in the genome and transcriptome. The karyotype showed a diploid number of 2n = 24 chromosomes with a variable number of B-chromosomes. The transcriptome and genome of Asian seabass were searched for repetitive elements with experimental and bioinformatics tools. Six different types of repeats constituting 8–14% of the genome were characterized. Repetitive elements were clustered in the pericentromeric heterochromatin of all chromosomes, but some of them were preferentially accumulated in pretelomeric and pericentromeric regions of several chromosomes pairs and have chromosomes specific arrangement. From the dispersed class of fish-specific non-LTR retrotransposon elements Rex1 and MAUI-like repeats were analyzed. They were wide-spread both in the genome and transcriptome, accumulated on the pericentromeric and peritelomeric areas of all chromosomes. Every analyzed repeat was represented in the Asian seabass transcriptome, some showed differential expression between the gonads. The other group of repeats analyzed belongs to the rRNA multigene family. FISH signal for 5S rDNA was located on a single pair of chromosomes, whereas that for 18S rDNA was found on two pairs. A BAC-derived contig containing rDNA was sequenced and assembled into a scaffold containing incomplete fragments of 18S rDNA. Their assembly and chromosomal position revealed that this part of Asian seabass genome is extremely rich in repeats containing evolutionarily conserved and novel sequences. In summary, transcriptome assemblies and cDNA data are suitable for the identification of repetitive DNA from unknown genomes and for comparative investigation of conserved elements between teleosts and other vertebrates

Nutrigenomic and nutritional analyses reveal the effects of pelleted feeds on Asian Seabass (Lates calcarifer)

As nutrition-related expenses constitute the majority of the costs for aquaculture farms, it is essential for them to use feeds that provide an ideal combination of nutrients for the species of choice. In this study, the relative effect of consuming three different pelleted feeds (B, C and D) in comparison to frozen baitfish (A; control) were compared on juvenile Asian seabass (77.3 ± 22.4g) that were selected for increased growth rate over two generations. Our objectives were: 1) to evaluate the effects of different pelleted feeds based on overall physiological changes and nutritional quality of fillets; 2) improve our understanding of the underlying mechanisms with transcriptomic analysis; 3) if possible, identify the feed type that supports the growth of these fishes without substantially reducing the nutritional quality of fillet. The growth performance, fatty acid composition of fillet, hepatic histology and transcriptome of the fishes (Groups A-D) were analyzed. The majority of fatty acids of the fillets, except γ-linolenic acid (GLA, C18:3n6), correlated significantly with the respective diets. Asian seabass fed Feed C showed highest specific growth rate (SGR) and feed conversion efficiency (FCE) with closest histology and transcriptomic profile to control, but their fillet contained the highest n6/n3 ratio. When the liver-based transcriptomes were analyzed, a complex set of differentially expressed genes were detected between groups fed pelleted feeds and controls as well as among the pellet-fed groups themselves. Significant enrichment of genes with growth-related function tallied with the morphological data measured. When compared with control (Group A), ‘Biosynthesis of unsaturated fatty acids’ and ‘Steroid biosynthesis’ pathways were significantly enriched in pellet-fed groups. Reduced goblet cell numbers were observed in the gut of pellet-fed fish compared to controls and fads6 was found to be a suitable candidate gene to separate wild-caught Asian seabass, from pellet-fed ones. These results provide insights for researchers on the various effects of feeds on the biochemistry and global gene expression of the fish and potentially for seabass farms to make more informed feed choices

Five-year impact of different multi-year mass drug administration strategies on childhood Schistosoma mansoni-associated morbidity:A combined analysis from the schistosomiasis consortium for operational research and evaluation cohort studies in the Lake Victoria Regions of Kenya and Tanzania

The WHO recommends mass treatment with praziquantel as the primary approach for; Schistosoma mansoni; -related morbidity control in endemic populations. The Schistosomiasis Consortium for Operational Research and Evaluation implemented multi-country, cluster-randomized trials to compare effectiveness of community-wide and school-based treatment (SBT) regimens on prevalence and intensity of schistosomiasis. To assess the impact of two different treatment schedules on; S. mansoni; -associated morbidity in children, cohort studies were nested within the randomized trials conducted in villages in Kenya and Tanzania having baseline prevalence ≥ 25%. Children aged 7-8 years were enrolled at baseline and followed to ages 11-12 years. Infection intensity and odds of infection were reduced both in villages receiving four years of annual community-wide treatment (CWT) and those who received biennial SBT over 4 years. These regimens were also associated with reduced odds of undernutrition and reduced odds of portal vein dilation at follow-up. However, neither hemoglobin levels nor the prevalence of the rare abnormal pattern C liver scores on ultrasound improved. For the combined cohorts, growth stunting worsened in the areas receiving biennial SBT, and maximal oxygen uptake as estimated by fitness testing scores declined under both regimens. After adjusting for imbalance in starting prevalence between study arms, children in villages receiving annual CWT had significantly greater decreases in infection prevalence and intensity than those villages receiving biennial SBT. Although health-related quality-of-life scores improved in both study arms, children in the CWT villages gained significantly more. We conclude that programs using annual CWT are likely to achieve better overall; S. mansoni; morbidity control than those implementing only biennial SBT

Elaboration and characterisation of novel low-cost adsorbents from grass-derived sulphonated lignin

AbstractThis study investigated the use of water-soluble sulphonated lignin (SL) extracted from grass, which has not been used before as a precursor of activated carbon (AC). Chemical activation of SL with three dehydrating salts (ZnCl2, KCl, Fe2(SO4)3·xH2O) at various salt concentrations (10%, 20%, 30%w/w), charring temperatures (600,700°C) and charring times (1,2h) has been carried out. The surface characteristics and removal efficiencies of cadmium, copper and zinc ions from aqueous solutions were affected by the activation conditions. The sulphonated lignin-based activated carbons (SLACs) with the highest specific surface area, total pore and micropore volume were produced at the lowest dehydrating salt concentration (10%w/w) and at 700°C and 2-h charring. These optimal sulphonated lignin-based ACs were named SLAC-ZC (optimal grass-derived SLAC activated by zinc chloride); SLAC-PC (optimal grass-derived SLAC activated by potassium chloride) and SLAC-FS (optimal grass-derived SLAC activated by ferric sulphate). The central composite design and surface response methodology of different SLACs characteristics showed that the optimal responses were achieved at the same operating conditions. These SLACs also achieved the highest removal efficiencies of Cd2+, Cu2+ and Zn2+ ions from aqueous solutions. The chemical activation had significantly increased the total porosity, microporosity and surface area of water-soluble SL. The activation mechanism depended on the used dehydrating salt where the porosity developed by the dehydration effect of ZnCl2, and by a series of hydrolysis and redox reactions for the other two salts. The results of this research demonstrated that water-soluble SL has a great potential as a novel precursor for the production of activated carbons

Confirmation of a pi_1^0 Exotic Meson in the \eta \pi^0 System

The exclusive reaction $\pi^- p \to \eta \pi^0 n$, $\eta \to \pi^+ \pi^- \pi^0$ at 18 GeV$/c$ has been studied with a partial wave analysis on a sample of 23~492 $\eta \pi^0 n$ events from BNL experiment E852. A mass-dependent fit is consistent with a resonant hypothesis for the $P_+$ wave, thus providing evidence for a neutral exotic meson with $J^{PC} = 1^{-+}$, a mass of $1257 \pm 20 \pm 25$ MeV$/c^2$, and a width of $354 \pm 64 \pm 60$ MeV$/c^2$. New interpretations of the meson exotics in neutral $\eta \pi^0$ system observed in E852 and Crystal Barrel experiments are discussed.Comment: p3, rewording the paragraph (at the bottom) about the phase variations. p4, rewording paragrath "The second method ..." . p4, at the bottom of paragrath "The third method ..." added consistent with the results of methods 1 and 2

Exotic Meson Production in the f1(1285)π−f_{1}(1285)\pi^{-} System observed in the Reaction π−p→ηπ+π−π−p\pi^{-} p \to \eta\pi^{+}\pi^{-}\pi^{-} p at 18 GeV/c

This letter reports results from the partial wave analysis of the $\pi^{-}\pi^{-}\pi^{+}\eta$ final state in $\pi^{-}p$ collisions at 18GeV/c. Strong evidence is observed for production of two mesons with exotic quantum numbers of spin, parity and charge conjugation, $J^{PC} = 1^{-+}$ in the decay channel $f_{1}(1285)\pi^{-}$. The mass $M = 1709 \pm 24 \pm 41$ MeV/c^2 and width $\Gamma = 403 \pm 80 \pm 115$ MeV/c^2 of the first state are consistent with the parameters of the previously observed $\pi_{1}(1600)$. The second resonance with mass $M = 2001 \pm 30 \pm 92$ MeV/c^2 and width $\Gamma = 333 \pm 52 \pm 49$ MeV/c^2 agrees very well with predictions from theoretical models. In addition, the presence of $\pi_{2}(1900)$ is confirmed with mass $M = 2003 \pm 88 \pm 148$ MeV/c^2 and width $\Gamma = 306 \pm 132 \pm 121$ MeV/c^2 and a new state, $a_{1}(2096)$, is observed with mass $M = 2096 \pm 17 \pm 121$ MeV/c^2 and width $\Gamma = 451 \pm 41 \pm 81$ MeV/c^2. The decay properties of these last two states are consistent with flux tube model predictions for hybrid mesons with non-exotic quantum numbers

Observation of Pseudoscalar and Axial Vector Resonances in pi- p -> K+ K- pi0 n at 18 GeV

A new measurement of the reaction pi- p -> K+ K- pi0 n has been made at a beam energy of 18 GeV. A partial wave analysis of the K+ K- pi0 system shows evidence for three pseudoscalar resonances, eta(1295), eta(1416), and eta(1485), as well as two axial vectors, f1(1285), and f1(1420). Their observed masses, widths and decay properties are reported. No signal was observed for C(1480), an IG J{PC} = 1+ 1{--} state previously reported in phi pi0 decay.Comment: 7 pages, 6 figs, to be submitted to Phys. Let

Exploring definitions of retention in care for people living with HIV in the United States in the modern treatment era

Objective: To describe retention in HIV care based on various definitions of retention in the modern treatment era. Design: A cohort study of people enrolled in care at seven mostly urban HIV clinics across the United States, 2010 - 2018. Methods: We estimated retention based on missed visits, kept visits, kept encounters (clinical visits, CD4þ cell counts, and viral loads), and HIV labs. We contrasted risk factors for retention by different definitions and estimated odds ratios for viral suppression and hazard ratios for mortality in 2 years immediately following the year in which retention was defined (the study year). Results: Across 108 171 person-years (N ¼ 21 481 people), in 71% of years, people kept ≥75% of scheduled visits; in 78%, people kept ≥2 visits >90 days apart; in 74%, people had ≥2 HIV labs >90 days apart; and in 47%, people had no gaps >6 months in clinic visits. Missing >25% of scheduled visits despite attending ≥2 visits >90 days apart was associated with nonwhite non-Hispanic race/ethnicity, history of injection drug use, and prior AIDS diagnosis. In contrast, attending ≥75% of scheduled visits while not attending ≥2 visits >90 days apart was associated with male sex, white race, no injection drug use history, and no prior AIDS diagnosis. Subsequent viral nonsuppression was more strongly associated with missed- than kept-visit measures of retention; 2-year mortality was only associated with failure to be retained by missed-visit measures. Discussion: Missed and kept-visit definitions of retention capture different constructs. Missed-visit measures are more strongly associated with poor HIV outcomes

Origins of the Ambient Solar Wind: Implications for Space Weather

The Sun's outer atmosphere is heated to temperatures of millions of degrees, and solar plasma flows out into interplanetary space at supersonic speeds. This paper reviews our current understanding of these interrelated problems: coronal heating and the acceleration of the ambient solar wind. We also discuss where the community stands in its ability to forecast how variations in the solar wind (i.e., fast and slow wind streams) impact the Earth. Although the last few decades have seen significant progress in observations and modeling, we still do not have a complete understanding of the relevant physical processes, nor do we have a quantitatively precise census of which coronal structures contribute to specific types of solar wind. Fast streams are known to be connected to the central regions of large coronal holes. Slow streams, however, appear to come from a wide range of sources, including streamers, pseudostreamers, coronal loops, active regions, and coronal hole boundaries. Complicating our understanding even more is the fact that processes such as turbulence, stream-stream interactions, and Coulomb collisions can make it difficult to unambiguously map a parcel measured at 1 AU back down to its coronal source. We also review recent progress -- in theoretical modeling, observational data analysis, and forecasting techniques that sit at the interface between data and theory -- that gives us hope that the above problems are indeed solvable.Comment: Accepted for publication in Space Science Reviews. Special issue connected with a 2016 ISSI workshop on "The Scientific Foundations of Space Weather." 44 pages, 9 figure