In-depth sequencing of the siRNAs associated with peach latent mosaic viroid infection

<p>Abstract</p> <p>Background</p> <p>It has been observed that following viroid infection, there is an accumulation of viroid-derived siRNAs in infected plants. Some experimental results suggest that these small RNAs may be produced by the plant defense system to protect it from infection, indicating that viroids can elicit the RNA-silencing pathways. The objective of this study is to identify in the peach latent mosaic viroid (PLMVd), a model RNA genome, the regions that are most susceptible to RNA interference machinery.</p> <p>Results</p> <p>The RNA isolated from an infected tree have been used to sequence in parallel viroid species and small non-coding RNA species. Specifically, PLMVd RNAs were amplified, cloned and sequenced according to a conventional approach, while small non-coding RNAs were determined by high-throughput sequencing. The first led to the typing of 18 novel PLMVd variants. The second provided a library of small RNAs including 880 000 sequences corresponding to PLMVd-derived siRNAs, which makes up 11.2% of the sequences of the infected library. These siRNAs contain mainly 21-22 nucleotide RNAs and are equivalently distributed between the plus and the minus polarities of the viroid. They cover the complete viroid genome, although the amount varies depending on the regions. These regions do not necessarily correlate with the double-stranded requirement to be a substrate for Dicer-like enzymes. We noted that some sequences encompass the hammerhead self-cleavage site, indicating that the circular conformers could be processed by the RNA-silencing machinery. Finally, a bias in the relative abundance of the nature of the 5' nucleotides was observed (A, U >> G, C).</p> <p>Conclusions</p> <p>The approach used provided us a quantitative representation of the PLMVd-derived siRNAs retrieved from infected peach trees. These siRNAs account for a relatively large proportion of the small non-coding RNAs. Surprisingly, the siRNAs from some regions of the PLMVd genome appear over-represented, although these regions are not necessarily forming sufficiently long double-stranded structures to satisfy Dicer-like criteria for substrate specificity. Importantly, this large library of siRNAs gave several hints as to the components of the involved silencing machinery.</p

Recent Development with Regard to Trade of Fish and Fishery Products from Small-scale Fisheries in Africa

The trade of fish and fish products in Africa is expanding significantly as a function of increased demand for fish in the region and across the world. Several factors which could be attributed to the rising trend include increasing fish consumption due to population growth, health awareness, dwindling production from major traditional fishing nations, trade liberalization policies, harmonization of trade barriers and improved global information flow system. Such factors have indeed created a favorable business environment for increased trade. Africa has a competitive advantage in fisheries business due to the fact that the region produces over 24 percent of global fish landing from inland capture fishery; it has the remaining marine areas having a relatively higher estimated potential yield than production with increase in aquaculture activities. More importantly, the cost of production could be relatively cheaper in Africa compared to a number of other places. On the other hand, marketing of fish beyond national boundaries to meet product specifications and trading requirements of target markets has proved to be a real challenge. Major issues are post-harvest losses, technological innovation, value-addition, distribution, promotion, pricing, non-tariff barriers and entrepreneurship. These are the areas that need to be addressed to en able operators along the production chain secure greater socio-economic benefits. The paper provides a critical analysis of the business environment in Africa on small-scale fish trade, potential technical intervention and strategic marketing techniques that could improve the situation in the context of international fish trade, CCFR and MDGs

Building leaders for the UN Ocean Science Decade : a guide to supporting early career women researchers within academic marine research institutions

Diverse and inclusive marine research is paramount to addressing ocean sustainability challenges in the 21st century, as envisioned by the UN Decade of Ocean Science for Sustainable Development. Despite increasing efforts to diversify ocean science, women continue to face barriers at various stages of their career, which inhibits their progression to leadership within academic institutions. In this perspective, we draw on the collective experiences of thirty-four global women leaders, bolstered by a narrative review, to identify practical strategies and actions that will help empower early career women researchers to become the leaders of tomorrow. We propose five strategies: (i) create a more inclusive culture, (ii) ensure early and equitable career development opportunities for women ECRs, (iii) ensure equitable access to funding for women ECRs, (iv) offer mentoring opportunities and, (v) create flexible, family-friendly environments. Transformational, meaningful, and lasting change will only be achieved through commitment and collaborative action across various scales and by multiple stakeholders.Peer reviewe

Role of Trehalose Biosynthesis in Aspergillus fumigatus Development, Stress Response, and Virulence ▿

Aspergillus fumigatus is a pathogenic mold which causes invasive, often fatal, pulmonary disease in immunocompromised individuals. Recently, proteins involved in the biosynthesis of trehalose have been linked with virulence in other pathogenic fungi. We found that the trehalose content increased during the developmental life cycle of A. fumigatus, throughout which putative trehalose synthase genes tpsA and tpsB were significantly expressed. The trehalose content of A. fumigatus hyphae also increased after heat shock but not in response to other stressors. This increase in trehalose directly correlated with an increase in expression of tpsB but not tpsA. However, deletion of both tpsA and tpsB was required to block trehalose accumulation during development and heat shock. The ΔtpsAB double mutant had delayed germination at 37°C, suggesting a developmental defect. At 50°C, the majority of ΔtpsAB spores were found to be nonviable, and those that were viable had severely delayed germination, growth, and subsequent sporulation. ΔtpsAB spores were also susceptible to oxidative stress. Surprisingly, the ΔtpsAB double mutant was hypervirulent in a murine model of invasive aspergillosis, and this increased virulence was associated with alterations in the cell wall and resistance to macrophage phagocytosis. Thus, while trehalose biosynthesis is required for a number of biological processes that both promote and inhibit virulence, in A. fumigatus the predominant effect is a reduction in pathogenicity. This finding contrasts sharply with those for other fungi, in which trehalose biosynthesis acts to enhance virulence

Aspergillus Galactosaminogalactan Mediates Adherence to Host Constituents and Conceals Hyphal β-Glucan from the Immune System

International audienceAspergillus fumigatus is the most common cause of invasive mold disease in humans. The mechanisms underlying the adherence of this mold to host cells and macromolecules have remained elusive. Using mutants with different adhesive properties and comparative transcriptomics, we discovered that the gene uge3, encoding a fungal epimerase, is required for adherence through mediating the synthesis of galactosaminogalactan. Galactosaminogalactan functions as the dominant adhesin of A. fumigatus and mediates adherence to plastic, fibronectin, and epithelial cells. In addition, galactosaminogalactan suppresses host inflammatory responses in vitro and in vivo, in part through masking cell wall β-glucans from recognition by dectin-1. Finally, galactosaminogalactan is essential for full virulence in two murine models of invasive aspergillosis. Collectively these data establish a role for galactosaminogalactan as a pivotal bifunctional virulence factor in the pathogenesis of invasive aspergillosis

Defining the role of DAG, mitochondrial function, and lipid deposition in palmitate-induced proinflammatory signaling and its counter-modulation by palmitoleate

Chronic exposure of skeletal muscle to saturated fatty acids, such as palmitate (C16:0), enhances proinflammatory IKK-NFκB signaling by a mechanism involving the MAP kinase (Raf-MEK-ERK) pathway. Raf activation can be induced by its dissociation from the Raf-kinase inhibitor protein (RKIP) by diacylglycerol (DAG)-sensitive protein kinase C (PKC). However, whether these molecules mediate the proinflammatory action of palmitate, an important precursor for DAG synthesis, is currently unknown. Here, involvement of DAG-sensitive PKCs, RKIP, and the structurally related monounsaturated fatty acid palmitoleate (C16:1) on proinflammatory signaling are investigated. Palmitate, but not palmitoleate, induced phosphorylation/activation of the MEK-ERK-IKK axis and proinflammatory cytokine (IL-6, CINC-1) expression. Palmitate increased intramyocellular DAG and invoked PKC-dependent RKIP(Ser153) phosphorylation, resulting in RKIP-Raf1 dissociation and MEK-ERK signaling. These responses were mimicked by PMA, a DAG mimetic and PKC activator. However, while pharmacological inhibition of PKC suppressed PMA-induced activation of MEK-ERK-IKK signaling, activation by palmitate was upheld, suggesting that DAG-sensitive PKC and RKIP were dispensable for palmitate's proinflammatory action. Strikingly, the proinflammatory effect of palmitate was potently repressed by palmitoleate. This repression was not due to reduced palmitate uptake but linked to increased neutral lipid storage and enhanced cellular oxidative capacity brought about by palmitoleate's ability to restrain palmitate-induced mitochondrial dysfunction

Breaking down barriers: The identification of actions to promote gender equality in interdisciplinary marine research institutions

Interdisciplinary research is paramount to addressing ocean sustainability challenges in the 21st century. However, women leaders have been underrepresented in interdisciplinary marine research, and there is little guidance on how to achieve the conditions that will lead to an increased proportion of women scientists in positions of leadership. Here, we conduct in-depth qualitative research to explore the main barriers and enablers to women’s leadership in an academic interdisciplinary marine research context. We found that interdisciplinarity can present unique and additional barriers to women leaders (e.g., complexity and lack of value attributed to interdisciplinary research) and are exacerbated by existing gender-specific issues that women experience (e.g., isolation and underrepresentation and stereotyping). Together these barriers overlap forming the “glass obstacle course”—which is particularly challenging for women in minoritized groups. Here, we provide a list of concrete, ambitious, and actionable enablers that can promote and support women’s leadership in academic interdisciplinary marine research

Dendritic cells produce an increased pro-inflammatory cytokine profile in response to the GAG deficient mutant.

<p>Graphs show the cytokine content of culture supernatant after 6 h of infection of BMDDCs with hyphae of the indicated strains. LPS was used as a positive control, and medium as a negative control. Cytokine concentrations in culture supernatants were determined by multiplex EIA. Results are mean ± standard error of duplicate determination of cytokine concentrations, indicated in pg/mL. * indicates a significantly increased cytokine concentration induced by the Δ<i>uge3</i> mutant, as compared with the one induced by Af293, <i>p</i><0.05 by factor ANOVA. § indicates that actual value is above 5,000 pg TNFα/mL (measures exceeded upper limit of the test).</p

The <i>A. fumigatus</i> Δ<i>uge3</i> mutant induces a hyperinflammatory response in non-neutropenic mice that is attenuated in highly immunocompromised mice.

<p>(A.) Corticosteroid treated mice were infected by inhalation with the indicated strains of <i>A. fumigatus</i> and sacrificed three days after infection. Fungal burden was determined by pulmonary galactomannan content and pulmonary inflammation was measured by determining MPO, and TNF-α content. Pulmonary injury was quantified by measuring LDH release in BAL fluid. MPO, TNF-α, and LDH levels were normalized to the fungal burden of each strain in Panel 1. Results are median ± interquartile range of 8 mice per strain. * indicates a significant decrease in fungal burden or a significant increase in MPO, TNFα or LDH content in lungs of mice infected with the Δ<i>uge3</i> mutant as compared to the lungs of mice infected with the wild-type strain, <i>p</i><0.01 by the Wilcoxon rank sum test. (B) Corticosteroid and cyclophosphamide treated mice were infected by inhalation with the indicated strains, sacrificed and the lungs processed as in (A). MPO, TNF-α, and LDH levels were normalized to the fungal burden of each strain in Panel 1. Results are median ± interquartile range of 9 mice per strain. Note: y-axis values for all graphs are lower than those in (A).</p