1,190 research outputs found
A time series transcriptome analysis of cassava (Manihot esculenta Crantz) varieties challenged with Ugandan cassava brown streak virus
Open Access Journal; Published online: 29 August 2017A time-course transcriptome analysis of two cassava varieties that are either resistant or susceptible to cassava brown streak disease (CBSD) was conducted using RNASeq, after graft inoculation with Ugandan cassava brown streak virus (UCBSV). From approximately 1.92 billion short reads, the largest number of differentially expressed genes (DEGs) was obtained in the resistant (Namikonga) variety at 2 days after grafting (dag) (3887 DEGs) and 5 dag (4911 DEGs). At the same time points, several defense response genes (encoding LRR-containing, NBARC-containing, pathogenesis-related, late embryogenesis abundant, selected transcription factors, chaperones, and heat shock proteins) were highly expressed in Namikonga. Also, defense-related GO terms of ‘translational elongation’, ‘translation factor activity’, ‘ribosomal subunit’ and ‘phosphorelay signal transduction’, were overrepresented in Namikonga at these time points. More reads corresponding to UCBSV sequences were recovered from the susceptible variety (Albert) (733 and 1660 read counts per million (cpm)) at 45 dag and 54 dag compared to Namikonga (10 and 117 cpm respectively). These findings suggest that Namikonga’s resistance involves restriction of multiplication of UCBSV within the host. These findings can be used with other sources of evidence to identify candidate genes and biomarkers that would contribute substantially to knowledge-based resistance breeding
Analysis of factor V in zebrafish demonstrates minimal levels needed for early hemostasis
In humans, coagulation factor V (FV) deficiency is a rare, clinically heterogeneous bleeding disorder, suggesting that genetic modifiers may contribute to disease expressivity. Zebrafish possess many distinct advantages including high fecundity, optical clarity, external development, and homology with the mammalian hemostatic system, features that make it ideal for genetic studies. Our aim was to study the role of FV in zebrafish through targeted mutagenesis and apply the model to the study of human F5 variants. CRISPR-mediated genome editing of the zebrafish f5 locus was performed, generating mutants homozygous for a 49 base pair deletion in exon 4. Thrombus formation secondary to vascular endothelial injury was absent in f52/2 mutant embryos and larvae. Despite this severe hemostatic defect, homozygous mutants survived before succumbing to severe hemorrhage in adulthood. Human F5 variants of uncertain significance from patients with FV deficiency were evaluated, and the causative mutations identified and stratified by their ability to restore thrombus formation in larvae. Analysis of these novel mutations demonstrates variable residual FV function, with minimal activity being required to restore hemostasis in response to laser-induced endothelial injury. This in vivo evaluation may be beneficial for patients whose factor activity levels lack correlation with bleeding symptomatology, although limitations exist. Furthermore, homozygous mutant embryos tolerate what is a severe and lethal defect in mammals, suggesting the possibility of species-specific factors enabling survival, and allowing further study not possible in the mouse. Identification of these factors or other genetic modifiers could lead to novel therapeutic modalities
Hydrophobic and ionic-interactions in bulk and confined water with implications for collapse and folding of proteins
Water and water-mediated interactions determine thermodynamic and kinetics of
protein folding, protein aggregation and self-assembly in confined spaces. To
obtain insights into the role of water in the context of folding problems, we
describe computer simulations of a few related model systems. The dynamics of
collapse of eicosane shows that upon expulsion of water the linear hydrocarbon
chain adopts an ordered helical hairpin structure with 1.5 turns. The structure
of dimer of eicosane molecules has two well ordered helical hairpins that are
stacked perpendicular to each other. As a prelude to studying folding in
confined spaces we used simulations to understand changes in hydrophobic and
ionic interactions in nano droplets. Solvation of hydrophobic and charged
species change drastically in nano water droplets. Hydrophobic species are
localized at the boundary. The tendency of ions to be at the boundary where
water density is low increases as the charge density decreases. Interaction
between hydrophobic, polar, and charged residue are also profoundly altered in
confined spaces. Using the results of computer simulations and accounting for
loss of chain entropy upon confinement we argue and then demonstrate, using
simulations in explicit water, that ordered states of generic amphiphilic
peptide sequences should be stabilized in cylindrical nanopores
QTL associated with resistance to cassava brown streak and cassava mosaic diseases in a bi-parental cross of two Tanzanian farmer varieties, Namikonga and Albert
Article purchasedCassava production in Africa is compromised by cassava brown streak disease (CBSD) and cassava mosaic disease (CMD). To reduce costs and increase the precision of resistance breeding, a QTL study was conducted to identify molecular markers linked to resistance against these diseases. A bi-parental F1 mapping population was developed from a cross between the Tanzanian farmer varieties, Namikonga and Albert. A one-step genetic linkage map comprising 943 SNP markers and 18 linkage groups spanning 1776.2 cM was generated. Phenotypic data from 240 F1 progeny were obtained from two disease hotspots in Tanzania, over two successive seasons, 2013 and 2014. Two consistent QTLs linked to resistance to CBSD-induced root necrosis were identified in Namikonga on chromosomes II (qCBSDRNFc2Nm) and XI (qCBSDRNc11Nm) and a putative QTL on chromosome XVIII (qCBSDRNc18Nm). qCBSDRNFc2Nm was identified at Naliendele in both seasons. The same QTL was also associated with CBSD foliar resistance. qCBSDRNc11Nm was identified at Chambezi in both seasons, and was characterized by three peaks, spanning a distance of 253 kb. Twenty-seven genes were identified within this region including two LRR proteins and a signal recognition particle. In addition, two highly significant CMD resistance QTL (qCMDc12.1A and qCMDc12.2A) were detected in Albert, on chromosome 12. Both qCMDc12.1A and qCMDc12.2A lay within the range of markers reported earlier, defining the CMD2 locus. This is the first time that two loci have been identified within the CMD2 QTL, and in germplasm of apparent East African origin. Additional QTLs with minor effects on CBSD and CMD resistance were also identified
Anti-Search for the Glueball Candidate f_J(2220) in Two-Photon Interactions
Using 13.3 fb^{-1} of e^+e^- data recorded with the CLEO II and CLEO II.V
detector configurations at CESR, we have searched for f_J(2220) decays to
K^0_{S} K^0_{S} in untagged two-photon interactions. We report an upper limit
on the product of the two-photon partial width and the branching fraction,
Gamma_gamma gamma cdot B (f_J(2220) to K^0_{S} K^0_{S}) of less than 1.1 eV at
the 95% C.L: systematic uncertainties are included. This dataset is four times
larger than that used in the previous CLEO publication.Comment: 10 pages postscript, also available through
http://w4.lns.cornell.edu/public/CLNS, Submitted to PRD (R
Measurements of the Branching Fractions and Helicity Amplitudes in B --> D* rho Decays
Using 9.1 fb-1 of e+ e- data collected at the Upsilon(4S) with the CLEO
detector using the Cornell Electron Storage Ring, measurements are reported for
both the branching fractions and the helicity amplitudes for the decays B- ->
D*0 rho- and B0bar -> D*+ rho-. The fraction of longitudinal polarization in
B0bar -> D*+ rho- is found to be consistent with that in B0bar -> D*+ l- nubar
at q^2 = M^2_rho, indicating that the factorization approximation works well.
The longitudinal polarization in the B- mode is similar. The measurements also
show evidence of non-trivial final-state interaction phases for the helicity
amplitudes.Comment: 11 pages postscript, also available through
http://w4.lns.cornell.edu/public/CLNS, submitted to PR
Low-mass pre--main-sequence stars in the Magellanic Clouds
[Abridged] The stellar Initial Mass Function (IMF) suggests that sub-solar
stars form in very large numbers. Most attractive places for catching low-mass
star formation in the act are young stellar clusters and associations, still
(half-)embedded in star-forming regions. The low-mass stars in such regions are
still in their pre--main-sequence (PMS) evolutionary phase. The peculiar nature
of these objects and the contamination of their samples by the evolved
populations of the Galactic disk impose demanding observational techniques for
the detection of complete numbers of PMS stars in the Milky Way. The Magellanic
Clouds, the companion galaxies to our own, demonstrate an exceptional star
formation activity. The low extinction and stellar field contamination in
star-forming regions of these galaxies imply a more efficient detection of
low-mass PMS stars than in the Milky Way, but their distance from us make the
application of special detection techniques unfeasible. Nonetheless, imaging
with the Hubble Space Telescope yield the discovery of solar and sub-solar PMS
stars in the Magellanic Clouds from photometry alone. Unprecedented numbers of
such objects are identified as the low-mass stellar content of their
star-forming regions, changing completely our picture of young stellar systems
outside the Milky Way, and extending the extragalactic stellar IMF below the
persisting threshold of a few solar masses. This review presents the recent
developments in the investigation of PMS stars in the Magellanic Clouds, with
special focus on the limitations by single-epoch photometry that can only be
circumvented by the detailed study of the observable behavior of these stars in
the color-magnitude diagram. The achieved characterization of the low-mass PMS
stars in the Magellanic Clouds allowed thus a more comprehensive understanding
of the star formation process in our neighboring galaxies.Comment: Review paper, 26 pages (in LaTeX style for Springer journals), 4
figures. Accepted for publication in Space Science Review
First Observation of barB0 to D*0 pi+pi+pi-pi- Decays
We report on the observation of B0bar -> D*0 pi+ pi+ pi- pi- decays. The
branching ratio is (0.30 +/- 0.07 +/- 0.06)%. Interest in this particular mode
was sparked by Ligeti, Luke and Wise who propose it as a way to check the
validity of factorization tests in B0bar -> D*+ pi+ pi- pi- pi0 decays.Comment: 11 pages postscript, also available through
http://w4.lns.cornell.edu/public/CLNS, Version to appear in Phys. Rev.
Measurement of the Charge Asymmetry in
We report on a search for a CP-violating asymmetry in the charmless hadronic
decay B -> K*(892)+- pi-+, using 9.12 fb^-1 of integrated luminosity produced
at \sqrt{s}=10.58 GeV and collected with the CLEO detector. We find A_{CP}(B ->
K*(892)+- pi-+) = 0.26+0.33-0.34(stat.)+0.10-0.08(syst.), giving an allowed
interval of [-0.31,0.78] at the 90% confidence level.Comment: 7 pages postscript, also available through
http://w4.lns.cornell.edu/public/CLNS, submitted to PR
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