Conservation of Arabidopsis thaliana photoperiodic flowering time genes in onion (Allium cepa L.)

The genetics underlying onion development is poorly understood. Here the characterisation of onion homologues of Arabidopsis photoperiodic flowering pathway genes is reported with the end goal of accelerating onion breeding programmes by understanding the genetic basis of adaptation to different latitudes. The expression of onion GI, FKF1 and ZTL homologues under SD and LD conditions was examined using quantitative RT-PCR. The expression of AcGI and AcFKF1 was examined in onion varieties which exhibit different daylength responses. Phylogenetic trees were constructed to confirm the identity of the homologues. AcGI and AcFKF1 showed diurnal expression patterns similar to their Arabidopsis counterparts while AcZTL was found to be constitutively expressed. AcGI showed similar expression patterns in varieties which exhibit different daylength responses whereas AcFKF1 showed differences. It is proposed that these differences could contribute to the different daylength responses in these varieties. Phylogenetic analyses showed that all the genes isolated are very closely related to their proposed homologues. The results presented here show that key genes controlling photoperiodic flowering in Arabidopsis are conserved in onion and a role for these genes in the photoperiodic control of bulb initiation is predicted. This theory is supported by expression and phylogenetic data

Selection of reference genes for diurnal and developmental time-course real-time PCR expression analyses in lettuce

Background: Real-time quantitative polymerase chain reaction (RT-qPCR) analysis is a low cost and sensitive technique that is widely used to measure levels of gene expression. Selecting and validating appropriate reference genes for normalising target gene expression should be the first step in any expression study to avoid inaccurate results. Results: In this study, ten candidate genes were tested for their suitability for use as reference genes in diurnal and developmental timecourse experiments in lettuce. The candidate reference genes were then used to normalise the expression pattern of the FLOWERING LOCUS T (FT) gene, one of key genes involved in the flowering time pathway whose expression is known to vary throughout the day and at different stages of development. Three reference genes, LsPP2A-1 (PROTEIN PHOSPHATASE 2A-1), LsPP2AA3 (PROTEIN PHOSPHATASE 2A REGULATORY SUBUNIT A3) and LsTIP41 (TAP42-INTERACTING PROTEIN OF 41 kDa), were the most stably expressed candidate reference genes throughout both the diurnal and developmental timecourse experiments. In the developmental experiment using just LsPP2A-1 and LsTIP41 as reference genes would be sufficient for accurate normalisation, whilst in the diurnal experiment all three reference genes, LsPP2A-1, LsPP2AA3 and LsTIP41, would be necessary. The FT expression pattern obtained demonstrates that the use of multiple and robust reference genes for RT-qPCR expression analyses results in a more accurate and reliable expression profile. Conclusions: Reference genes suitable for use in diurnal and developmental timecourse experiments in lettuce were identified and used to produce a more accurate and reliable analysis of lsFT expression levels than previously obtained in such timecourse experiments

FLC expression is down-regulated by cold treatment in Diplotaxis tenuifolia (wild rocket), but flowering time is unaffected

Wild rocket (Diplotaxis tenuifolia) has become a very popular salad leaf due to its peppery taste. It is part of the Brassicaceae family and thus has a high level of homology at the DNA level to other Brassica species including Arabidopsis thaliana. The vernalization and photoperiodic requirements of wild rocket have not been reported to date. Photoperiodic experiments described here demonstrate that rocket is a facultative long day plant. To investigate the vernalization requirement, both seed and young plants were given vernalization treatments at 4 °C for different lengths of time. A rocket homologue of FLOWERING LOCUS C (DtFLC) was isolated and shown to functionally complement the Arabidopsis FRI+flc3 null mutant. Whilst the expression of DtFLC was significantly reduced after just one week of cold treatment, cold treatments of two to eight weeks had no significant effect on bolting time of wild rocket indicating that rocket does not have a vernalization requirement. These findings illustrate that important fundamental differences can exist between model and crop plant species, such as in this case where down-regulation of DtFLC expression does not enable earlier flowering in wild rocket as it does in Arabidopsis and many other Brassica species

TEMPRANILLO is a regulator of juvenility in plants

Many plants are incapable of flowering in inductive daylengths during the early juvenile vegetative phase (JVP). Arabidopsis mutants with reduced expression of TEMPRANILLO (TEM), a repressor of FLOWERING LOCUS T (FT) had a shorter JVP than wild-type plants. Reciprocal changes in mRNA expression of TEM and FT were observed in both Arabidopsis and antirrhinum, which correlated with the length of the JVP. FT expression was induced just prior to the end of the JVP and levels of TEM1 mRNA declined rapidly at the time when FT mRNA levels were shown to increase. TEM orthologs were isolated from antirrhinum (AmTEM) and olive (OeTEM) and were expressed most highly during their juvenile phase. AmTEM functionally complemented AtTEM1 in the tem1 mutant and over-expression of AmTEM prolonged the JVP through repression of FT and CONSTANS (CO). We propose that TEM may have a general role in regulating JVP in herbaceous and woody species

Structural Basis of the Association of HIV-1 Matrix Protein with DNA

HIV-1 matrix (MA) is a multifunctional protein that is synthesized as a polyprotein that is cleaved by protease during viral maturation. MA contains a cluster of basic residues whose role is controversial. Proposed functions include membrane anchoring, facilitating viral assembly, and directing nuclear import of the viral DNA. Since MA has been reported to be a component of the preintegration complex (PIC), we have used NMR to probe its interaction with other PIC components. We show that MA interacts with DNA and this is likely sufficient to account for its association with the PIC

NMR Studies of the C-Terminus of alpha4 Reveal Possible Mechanism of Its Interaction with MID1 and Protein Phosphatase 2A

Alpha4 is a regulatory subunit of the protein phosphatase family of enzymes and plays an essential role in regulating the catalytic subunit of PP2A (PP2Ac) within the rapamycin-sensitive signaling pathway. Alpha4 also interacts with MID1, a microtubule-associated ubiquitin E3 ligase that appears to regulate the function of PP2A. The C-terminal region of alpha4 plays a key role in the binding interaction of PP2Ac and MID1. Here we report on the solution structure of a 45-amino acid region derived from the C-terminus of alpha4 (alpha45) that binds tightly to MID1. In aqueous solution, alpha45 has properties of an intrinsically unstructured peptide although chemical shift index and dihedral angle estimation based on chemical shifts of backbone atoms indicate the presence of a transient α-helix. Alpha45 adopts a helix-turn-helix HEAT-like structure in 1% SDS micelles, which may mimic a negatively charged surface for which alpha45 could bind. Alpha45 binds tightly to the Bbox1 domain of MID1 in aqueous solution and adopts a structure consistent with the helix-turn-helix structure observed in 1% SDS. The structure of alpha45 reveals two distinct surfaces, one that can interact with a negatively charged surface, which is present on PP2A, and one that interacts with the Bbox1 domain of MID1

Supernova Siblings: Assessing the Consistency of Properties of Type Ia Supernovae that Share the Same Parent Galaxies

While many studies have shown a correlation between properties of the light curves of SNe Ia and properties of their host galaxies, it remains unclear what is driving these correlations. We introduce a new direct method to study these correlations by analyzing "parent" galaxies that host multiple SNe Ia "siblings." Here, we search the Dark Energy Survey SN sample, one of the largest samples of discovered SNe, and find eight galaxies that hosted two likely SNe Ia. Comparing the light-curve properties of these SNe and recovered distances from the light curves, we find no better agreement between properties of SNe in the same galaxy as any random pair of galaxies, with the exception of the SN light-curve stretch. We show at 2.8σ significance that at least one-half of the intrinsic scatter of SNe Ia distance modulus residuals is not from common host properties. We also discuss the robustness with which we could make this evaluation with LSST, which will find 100x more pairs of galaxies, and pave a new line of study on the consistency of SNe Ia in the same parent galaxies. Finally, we argue that it is unlikely that some of these SNe are actually single, lensed SN with multiple images.D.S. is supported by DOE grant DE-SC0010007, the David and Lucile Packard Foundation. D.S. and R.K. are supported in part by NASA under Contract No. NNG17PX03C issued through the WFIRST Science Investigation Teams Programme. D.B. and M.S. were supported by DOE grant DE-FOA0001358 and NSF grant AST-1517742. L.G. was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 839090. This research used resources of the National Energy Research Scientific Computing Center (NERSC), a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. We are grateful for the support of the University of Chicago Research Computing Center for assistance with the calculations carried out in this work. R.F. is supported in part by NSF grants AST-1518052 and AST1815935, the Gordon & Betty Moore Foundation, the HeisingSimons Foundation, and by fellowships from the David and Lucile Packard Foundation, as well as the NASA contract above. Funding for the DES Projects has been provided by the U.S. Department of Energy, the U.S. National Science Foundation, the Ministry of Science and Education of Spain, the Science and Technology Facilities Council of the United Kingdom, the Higher Education Funding Council for England, the National Center for Supercomputing Applications at the University of Illinois at Urbana-Champaign, the Kavli Institute of Cosmological Physics at the University of Chicago, the Center for Cosmology and Astro-Particle Physics at the Ohio State University, the Mitchell Institute for Fundamental Physics and Astronomy at Texas A&M University, Financiadora de Estudos e Projetos, Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro, Conselho Nacional de Desenvolvimento Científico e Tecnológico and the Ministério da Ciência, Tecnologia e Inovação, the Deutsche Forschungsgemeinschaft and the Collaborating Institutions in the Dark Energy Survey. ...We acknowledge support from the Australian Research Council Centre of Excellence for All-sky Astrophysics (CAASTRO), through project number CE110001020, and the Brazilian Instituto Nacional de Ciência e Tecnologia (INCT) e-Universe (CNPq grant 465376/2014-2). We acknowledge support from EU/FP7-ERC grant No. 615929

Opposite Effects of HIV-1 p17 Variants on PTEN Activation and Cell Growth in B Cells

The HIV-1 matrix protein p17 is a structural protein that can act in the extracellular environment to deregulate several functions of immune cells, through the interaction of its NH2-terminal region with a cellular surface receptor (p17R). The intracellular events triggered by p17/p17R interaction have been not completely characterized yet. In this study we analyze the signal transduction pathways induced by p17/p17R interaction and show that in Raji cells, a human B cell line stably expressing p17R on its surface, p17 induces a transient activation of the transcriptional factor AP-1. Moreover, it was found to upregulate pERK1/2 and downregulate pAkt, which are the major intracellular signalling components involved in AP-1 activation. These effects are mediated by the COOH-terminal region of p17, which displays the capability of keeping PTEN, a phosphatase that regulates the PI3K/Akt pathway, in an active state through the serin/threonin (Ser/Thr) kinase ROCK. Indeed, the COOH-terminal truncated form of p17 (p17Δ36) induced activation of the PI3K/Akt pathway by maintaining PTEN in an inactive phosphorylated form. Interestingly, we show that among different p17s, a variant derived from a Ugandan HIV-1 strain, named S75X, triggers an activation of PI3K/Akt signalling pathway, and leads to an increased B cell proliferation and malignant transformation. In summary, this study shows the role of the COOH-terminal region in modulating the p17 signalling pathways so highlighting the complexity of p17 binding to and signalling through its receptor(s). Moreover, it provides the first evidence on the presence of a p17 natural variant mimicking the p17Δ36-induced signalling in B cells and displaying the capacity of promoting B cell growth and tumorigenesis

Structure of a Nudix hydrolase (MutT) in the Mg2+-­bound state from Bartonella henselae, the bacterium responsible for cat scratch fever

B. henselae is the etiological agent responsible for cat scratch fever (bartonellosis). The crystal structure of the smaller of the two Nudix hydrolases encoded in the genome of B. henselae, Bh-MutT, was determined to 2.1 Å resolution