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SUMMARYNuclear Argonaute proteins, guided by small RNAs, mediate sequence-specific heterochromatin formation. The molecular principles that link Argonaute-small RNA complexes to cellular heterochromatin effectors upon binding to nascent target RNAs are poorly understood. Here, we elucidate the mechanism by which the PIWI interacting RNA (piRNA) pathway connects to the heterochromatin machinery in Drosophila. Piwi-mediated stabilization of the corepressor complex SFiNX on chromatin leads to SUMOylation of its subunit Panoramix. SUMOylation, together with an amphipathic LxxLL motif in Panoramix’s intrinsically disordered repressor domain, are necessary and sufficient to recruit small ovary (Sov), a multi-zinc finger protein essential for general heterochromatin formation and viability. Structure-guided mutations that abrogate the Panoramix–Sov interaction or that prevent SUMOylation of Panoramix uncouple Sov from the piRNA pathway, resulting in viable but sterile flies in which Piwi-targeted transposons are derepressed. Thus, by coupling recruitment of a corepressor to nascent transcripts with its SUMOylation, Piwi engages the heterochromatin machinery specifically at transposon loci.

Argonaute proteins of the PIWI clade complexed with PIWI-interacting RNAs (piRNAs) protect the animal germline genome by silencing transposable elements. One of the leading experimental systems for studying piRNA biology is the Drosophila melanogaster ovary. In addition to classical mutagenesis, transgenic RNA interference (RNAi), which enables tissue-specific silencing of gene expression, plays a central role in piRNA research. Here, we establish a versatile toolkit focused on piRNA biology that combines germline transgenic RNAi, GFP marker lines for key proteins of the piRNA pathway, and reporter transgenes to establish genetic hierarchies. We compare constitutive, pan-germline RNAi with an equally potent transgenic RNAi system that is activated only after germ cell cyst formation. Stage-specific RNAi allows us to investigate the role of genes essential for germline cell survival, for example, nuclear RNA export or the SUMOylation pathway, in piRNA-dependent and independent transposon silencing. Our work forms the basis for an expandable genetic toolkit provided by the Vienna Drosophila Resource Center., In eukaryotes, small RNA silencing pathways play fundamental roles in transposon control, which is of critical importance for genome stability. Drosophila is a leading study system for small RNA-guided transposon defense. Here, ElMaghraby, Tirian et al. present a set of genetic tools centered on transgenic RNA interference that will allow the dissection of the Piwi/piRNA pathway in the developing Drosophila ovary. This toolkit is particularly suited to study the intersection of piRNA biology and essential cellular processes.

Nuclear Argonaute proteins, guided by small RNAs, mediate sequence-specific heterochromatin formation. The molecular principles that link Argonaute-small RNA complexes to cellular heterochromatin effectors on binding to nascent target RNAs are poorly understood. Here, we explain the mechanism by which the PIWI-interacting RNA (piRNA) pathway connects to the heterochromatin machinery in Drosophila. We find that Panoramix, a corepressor required for piRNA-guided heterochromatin formation, is SUMOylated on chromatin in a Piwi-dependent manner. SUMOylation, together with an amphipathic LxxLL motif in Panoramix's intrinsically disordered repressor domain, are necessary and sufficient to recruit Small ovary (Sov), a multi-zinc-finger protein essential for general heterochromatin formation and viability. Structure-guided mutations that eliminate the Panoramix-Sov interaction or that prevent SUMOylation of Panoramix uncouple Sov from the piRNA pathway, resulting in viable but sterile flies in which Piwi-targeted transposons are derepressed. Thus, Piwi engages the heterochromatin machinery specifically at transposon loci by coupling recruitment of a corepressor to nascent transcripts with its SUMOylation.

Synthetic halocarbons are used for a wide range of applications, for example air conditioning or foam blowing. Many of them are long-lived greenhouse gases contributing to climate change and, in addition, may contribute to stratospheric ozone depletion if containing chlorine or bromine. Therefore, their production and use are regulated by the Montreal Protocol and its amendments. These long-lived halocarbons are increasingly replaced by a fourth generation of unsaturated short-lived halocarbons, the hydrochlorofluoroolefines (HCFOs) and hydrofluoroolefines (HFOs). The main removal process of these compounds in the atmosphere is reaction with OH radicals, and their average lifetimes are of the order of up to a few tens of days.As part of the IAGOS-CARIBIC instrument package we operate an automated air sample collection system during regular flights in the upper troposphere and lowermost stratosphere. At altitudes around 10-12 km, samples are collected in stainless steel and glass flasks at predefined times. Post-flight laboratory analyses include gas chromatography - mass spectrometry measurements of a wide range of halocarbons. The short-lived compounds HFO-1234ze(E) and HCFO-1233zd(E) were detected in a small number of samples, indicating that these compounds are sufficiently long lived for transport into the upper troposphere. There were not found in stratospheric samples.At this altitude, low abundance of OH and low temperatures may slow down chemical decay, and tracer lifetimes may increase significantly. Based on average temperatures and OH abundance, we estimate local lifetimes of HFO-1234ze(E) and HCFO-1233zd(E) in the mid-latitudes of up to 75 days and 200 days, respectively. Short-lived H(C)FOs reaching the upper troposphere could thus be transported over large distances and their degradation products may be deposited far from their emission sources.

Polyhydroxyalkanoates (PHA) are a class of biopolymers with interesting material properties and highly beneficial use in certain applications. This is the base for its market presence with a prospective increasing share over a long period. Biotechnological production with prokaryotes is, undoubtedly, the most promising way to go and may remain so for the near future. Regarding the use of substrates, three general strategies can be identified, similar to biorefinery concepts: (1) using sugar or starch as input (first-generation substrates), (2) using lignocellulosic biomass or other liquid and solid organic residues (waste streams) as input (second-generation substrates), and (3) biotechnology with photo- and autotrophic bacteria – using CO2 and sunlight as input (third-generation substrates). With a closer look at cell physiologies, the conversion yields, and the overall technological effort, the specific advantages and disadvantages of each of those strategies are made clear through comparison. This chapter focuses on the critical parameters of a phototrophic PHA production with cyanobacteria and direct output compared with some of the established biotechnological processes. It concludes with a look at the required research and process optimization for the near future and, finally, discusses the scenario of a possible long-term PHA (and PHB) production strategy.

This study evaluates a biorefinery concept for producing poly(3-hydroxybutyrate) (PHB) with the cyanobacterial strain Synechocystis salina. Due to this reason, pigment extraction and cell disruption were investigated as pre-treatment steps for the harvested cyanobacterial biomass. The results demonstrated that at least pigment removal was necessary to obtain PHB with processable quality (weight average molecular weight: 569-988kgmol-1, melting temperature: 177-182°C), which was comparable to heterotrophically produced PHB. The removed pigments could be utilised as additional by-products (chlorophylls 0.27-1.98mgg-1 TS, carotenoids 0.21-1.51mgg-1 TS, phycocyanin 0-127mgg-1 TS), whose concentration depended on the used nutrient source. Since the residual biomass still contained proteins (242mgg-1 TS), carbohydrates (6.1mgg-1 TS) and lipids (14mgg-1 TS), it could be used as animal feed or converted to biomethane (348 mn3 t-1VS) and fertiliser. The obtained results indicate that the combination of photoautotrophic PHB production with pigment extraction and utilisation of residual biomass offer the highest potential, since it contributes to decrease the environmental footprint of the process and because biomass could be used in a cascading way and the nutrient cycle could be closed.

The current commercial production of polyhydroxyalkanoates (PHA) is based on heterotrophic bacteria, using organic carbon sources from crops. To avoid the competition with food and feed production, cyanobacteria, metabolising PHA from carbon dioxide can be used. This research focuses on the investigation of the thermal and rheological properties of PHA polymers accumulated by Synechocystis salina, which had been cultivated in digestate supernatant and a mineral medium. The dried bacterial cells had a polymer content of 5.5-6.6%. The relevance of the derived PHA polymers for the common melt polymer processing was correlated with their molecular mass distribution as well as with their thermal and rheological properties. The determined thermal and rheological properties showed that PHA polymers accumulated by S. salina on digestate supernatant or mineral medium are comparable with the commercial available poly(3-hydroxybutyrate). However, the results showed that PHA polymers in general require modification before melt processing to increase their stability in the molten state.

Polyhydroxyalkanoates (PHA), polyesters accumulated by numerous prokaryotes in the form of intracellular granules, have been for decades considered being predominantly storage molecules. However, numerous recent discoveries revealed and emphasized their complex biological role for microbial cells. Most of all, it was repeatedly reported and confirmed that the presence of PHA granules in prokaryotic cells enhances stress resistance and robustness of microbes against various environmental stress factors such as high or low temperature, freezing, oxidative, and osmotic pressure. It seems that protective mechanisms of PHA granules are associated with their extraordinary architecture and biophysical properties as well as with the complex and deeply interconnected nature of PHA metabolism. Therefore, this review aims at describing novel and unexpected properties of PHA granules with respect to their contribution to stress tolerance of various prokaryotes including common mesophilic heterotrophic bacteria, but also extremophiles or photo-autotrophic cyanobacteria. KEY POINTS: • PHA granules present in bacterial cells reveal unique properties and functions. • PHA enhances stress robustness of bacterial cells.

Polyhydroxyalkanoates (PHAs) are inevitably a key biopolymer that has the potential to replace the conventional petrochemical based plastics that pose jeopardy to the environment globally. Even then the reach of PHA in the common market is so restricted. The economy of PHA is such that, even after several attempts the overall production cost seems to be high and this very factor surpasses PHAs usage when compared to the conventional polymers. The major focus of the review relies on the synthesis of PHA from Mixed Microbial Cultures (MMCs), through a 3-stage process most probably utilizing feedstocks from waste streams or models that mimic them. Emphasis was given to the works carried out in the past decade and their coherence with each and every individual criteria (Aeration, Substrate and bioprocess parameters) such that to understand their effect in enhancing the overall production of PHA.

PIWI-interacting RNAs (piRNAs) guide transposon silencing in animals. The 22-30nt piRNAs are processed in the cytoplasm from long non-coding RNAs. How piRNA precursors, which often lack RNA processing hallmarks of export-competent transcripts, achieve nuclear export is unknown. Here, we uncover the RNA export pathway specific for piRNA precursors in theDrosophilagermline. This pathway requires Nxf3-Nxt1, a variant of the hetero-dimeric mRNA export receptor Nxf1-Nxt1. Nxf3 interacts with UAP56, a nuclear RNA helicase essential for mRNA export, and CG13741/Bootlegger, which recruits Nxf3-Nxt1 and UAP56 to heterochromatic piRNA source loci. Upon RNA cargo binding, Nxf3 achieves nuclear export via the exportin Crm1, and accumulates together with Bootlegger in peri-nuclear nuage, suggesting that after export, Nxf3-Bootlegger delivers precursor transcripts to the piRNA processing sites. Our findings indicate that the piRNA pathway bypasses nuclear RNA surveillance systems to achieve export of heterochromatic, unprocessed transcripts to the cytoplasm, a strategy also exploited by retroviruses.

Within the last decades, environmental pollution with persistent plastics steadily increased; therefore the production of biodegradable materials like poly-s-hydroxybutyrate (PHB) is essential. Currently, PHB is produced with heterotrophic bacteria from crops. This leads to competition with food and feed production, which can be avoided by using photoautotrophic cyanobacteria, as Synechocystis salina, synthesizing PHB from CO2 at nutrient limitation. This study aims to increase the economic efficiency of PHB production with cyanobacteria by using nutrients from anaerobic digestate. First, growth and PHB production of S. salina in digestate fractions (supernatant and permeate, with/without precipitating agents) and dilutions thereof and then the scale-up (photobioreactor, 200 L working volume) were evaluated. With precipitated and centrifuged digestate diluted 1/3 the highest biomass (1.55gL-1) and PHB concentrations (95.4mgL-1), being 78% of those in mineral media, were achieved. In the photobioreactor-experiments biomass (1.63gL-1) and PHB concentrations (88.7mgL-1), being 79% and 72% of those in mineral medium, were reached, but in a cultivation time 10days longer than in mineral medium. The possibility to use digestate as sustainable and low cost nutrient solution for microalgae cultivation and photoautotrophic PHB production, instead of applying it on fields or processing it to achieve discharge limits, makes this application a highly valid option.

Turbidity and opaqueness are inherent properties of tissues that limit the capacity to acquire microscopic images through large tissues. Creating a uniform refractive index, known as tissue clearing, overcomes most of these issues. These methods have enabled researchers to image large and complex 3D structures with unprecedented depth and resolution. However, tissue clearing has been adopted to a limited extent due to a combination of cost, time, complexity of existing methods and potential negative impact on fluorescence signal. Here, we describe 2Eci (2nd generation ethyl cinnamate-based clearing), which can be used to clear a wide range of tissues in several species, including human organoids, Drosophila melanogaster, zebrafish, axolotl and Xenopus laevis, in as little as 1-5 days, while preserving a broad range of fluorescent proteins, including GFP, mCherry, Brainbow and Alexa-conjugated fluorophores. Ethyl cinnamate is non-toxic and can easily be used in multi-user microscope facilities. This method opens up tissue clearing to a much broader group of researchers due to its ease of use, the non-toxic nature of ethyl cinnamate and broad applicability.

The biopolymer poly-β-hydroxybutyrate (PHB) can be used as a promising bioplastic. It has a broad range of applications and is degraded relatively rapidly by soil organisms. Like many prokaryotes, the cyanobacterium Synechocystis sp. CCALA192 produces this biopolymer as a storage compound, especially under nutrient limitation. In a 200-L tubular photobioreactor, we cultivated Synechocystis sp. CCALA192 semi-continuously over a period of 75 days with CO2 as sole carbon source. A two-stage cultivation strategy was performed, where after 5–7 days nitrogen was depleted and the culture started to produce PHB and gradually turned from blue-green to yellow. After 16–20 days, 90% of the culture were harvested and the residual 10% were used as inoculum for the following cycle. The harvested culture had an average biomass concentration of 1.0 g/L with an average PHB content of 12.5% of cell dry weight. After restarting with fresh nutrients, the yellow culture turned blue-green again and degraded the PHB within 24–48 h. When nitrogen of the medium was consumed, PHB was produced again and the cycle continued. In the late stage of each production cycle, a ripening process was observed, where no CO2 was consumed but the PHB concentration was still rising at the expense of the existing glycogen rich biomass. Establishing a stable Synechocystis sp. CCALA192 culture under non-sterile conditions turned out to be difficult, as this small unicellular organism is very sensitive and easily grazed by protozoa. Therefore, a special cultivation strategy with partially anoxic conditions was necessary.

The EU Renewable Energy Directive 2009/28/EC demands bioethanol plants to reduce their greenhouse gas emissions. This can be achieved by integrating a biogas plant in the bioethanol process and consequently by using the bioethanol by-products (e.g. thin stillage) as feedstock for anaerobic digestion. Due to the large amounts of thin stillage and consequently of digestate an efficient digestate treatment is essential. For this purpose centrifugation and ultrafiltration of thin stillage digestate with and without addition of precipitating agents were carried out. Prior to centrifugation, which was carried out with a disc-stack centrifuge at pilot scale, precipitating agents (iron(III)chloride and carbonated lime) were added. The produced supernatant fractions were then used for ultrafiltration experiments, which were carried out with a αAl2O3-membrane (pore size: 50 nm). Cross flow velocity and trans membrane pressure were adjusted to 6 m s−1 and to 0.8∗105 Pa. The addition of precipitating agents increased the separation efficiency of the suspended solids from 46% to 75%. Furthermore the flux during ultrafiltration increased from 45–50 L m−2 h−1 to 79 L m−2 h−1. In addition, phosphorous could be practically entirely removed from the supernatant with the precipitating agents. For a large-scale bioethanol plant it was proposed to reutilise the digestate fractions as process water. However, depending on its influence on the process and on animal feed quality, different digestate treatment processes should be applied.

Cyanobacteria, as photoautotrophic organisms, provide the opportunity to convert CO2 to biomass with light as the sole energy source. Like many other prokaryotes, especially under nutrient deprivation, most cyanobacteria are able to produce polyhydroxyalkanoates (PHAs) as intracellular energy and carbon storage compounds. In contrast to heterotrophic PHA producers, photoautotrophic cyanobacteria do not consume sugars and, therefore, do not depend on agricultural crops, which makes them a green alternative production system. This review summarizes the recent advances in cyanobacterial PHA production. Furthermore, this study reports the working experience with different strains and cultivating conditions in a 200 L pilot plant. The tubular photobioreactor was built at the coal power plant in Durnrohr, Austria in 2013 for direct utilization of flue gases. The main challenges were the selection of robust production strains, process optimization, and automation, as well as the CO2 availability.

Political, economic and ecological reasons have recently been leading to efforts to replace fossil hydrocarbons and their products in a sustainable way. In order to replace fossil-based polymers, photoautotrophically produced polyhydroxybutryrates (PHBs), which are intracellular carbon storage products of nutrient-deprived microorganisms, seem to be a promising, biobased and biodegradable alternative. Although laboratory and pilot scale experiments have already been performed, no economic evaluation has been carried out so far. Consequently, valid claims on PHB production costs and the influence of different parameters, such as intracellular PHB-content, choice of cultivation system or location, cannot be made. In this study potential demonstration plants, equipped with different photoautotrophic cultivation systems and located at two sites, were designed to identify key parameters for a successful economic realization and implementation. Material and energy balances were determined to reveal specific PHB production costs for four different scenarios. Raw material and operating supply costs, expenditures for plant construction and operation as well as product amounts were determined using literature data for specified results from laboratory and pilot scale experiments. The lowest calculated PHB production price (24 € kg−1) accomplished in a thin-layer-system plant located in Southern Europe with 60% PHB-content of the produced biomass is significantly higher than the current market price of heterotrophically produced PHB. The most important cost factors in all scenarios are cultivation and harvesting costs accounting for 62 to 72% of the total specific production costs, followed by maintenance costs with a cost share of 11 to 14%. Therefore, the choice of a suitable cultivation system is the key driving factor for an economic PHB-production due to the currently high investment costs for photosynthetic biomass production systems. Specific production costs for a Southern compared to a Central European location amount to almost half of the costs.

Stillage processing can require more than one third of the thermal energy demand of a dry-grind bioethanol production plant. Therefore, for every stillage fraction occurring in stillage processing the potential of energy recovery by anaerobic digestion (AD) was estimated. In the case of whole stillage up to 128% of the thermal energy demand in the process can be provided, so even an energetically self-sufficient bioethanol production process is possible. For wet cake the recovery potential of thermal energy is 57%, for thin stillage 41%, for syrup 40% and for the evaporation condensate 2.5%. Specific issues for establishing AD of stillage fractions are evaluated in detail; these are high nitrogen concentrations, digestate treatment and trace element supply. If animal feed is co-produced at the bioethanol plant and digestate fractions are to be reused as process water, a sufficient quality is necessary. Most interesting stillage fractions as substrates for AD are whole stillage, thin stillage and the evaporation condensate. For these fractions process details are presented.

A polyhydroxybutyrate (PHB) producing cyanobacteria was converted through hydrothermal liquefaction (HTL) into propylene and a bio-oil suitable for advanced biofuel production. HTL of model compounds demonstrated that in contrast to proteins and carbohydrates, no synergistic effects were detected when converting PHB in the presence of algae. Subsequently, Synechocystis cf. salina, which had accumulated 7.5 wt% PHB was converted via HTL (15% dry weight loading, 340 °C). The reaction gave an overall propylene yield of 2.6%, higher than that obtained from the model compounds, in addition to a bio-oil with a low nitrogen content of 4.6%. No propylene was recovered from the alternative non-PHB producing cyanobacterial strains screened, suggesting that PHB is the source of propylene. PHB producing microorganisms could therefore be used as a feedstock for a biorefinery to produce polypropylene and advanced biofuels, with the level of propylene being proportional to the accumulated amount of PHB.

The repression of transposable elements in eukaryotes often involves their transcriptional silencing via targeted chromatin modifications. In animal gonads, nuclear Argonaute proteins of the PIWI clade complexed with small guide RNAs (piRNAs) serve as sequence specificity determinants in this process. How binding of nuclear PIWI–piRNA complexes to nascent transcripts orchestrates heterochromatin formation and transcriptional silencing is unknown. Here, we characterize CG9754/Silencio as an essential piRNA pathway factor that is required for Piwi-mediated transcriptional silencing in Drosophila. Ectopic targeting of Silencio to RNA or DNA is sufficient to elicit silencing independently of Piwi and known piRNA pathway factors. Instead, Silencio requires the H3K9 methyltransferase Eggless/SetDB1 for its silencing ability. In agreement with this, SetDB1, but not Su(var)3-9, is required for Piwi-mediated transcriptional silencing genome-wide. Due to its interaction with the target-engaged Piwi–piRNA complex, we suggest that Silencio acts as linker between the sequence specificity factor Piwi and the cellular heterochromatin machinery.

PIWI proteins and their bound PIWI-interacting RNAs (piRNAs) form the core of a gonad-specific small RNA silencing pathway that protects the animal genome against the deleterious activity of transposable elements. Recent studies linked the piRNA pathway to TUDOR biology as TUDOR domains of various proteins bind symmetrically methylated Arginine residues in PIWI proteins. We systematically analysed the Drosophila TUDOR protein family and identified four previously not characterized TUDOR domain-containing proteins (CG4771, CG14303, CG11133 and CG31755) as essential piRNA pathway factors. We characterized CG4771 (Vreteno) in detail and demonstrate a critical role for this protein in primary piRNA biogenesis. Vreteno physically and/or genetically interacts with the primary pathway components Piwi, Armitage, Yb and Zucchini. Vreteno also interacts with the Tdrd12 orthologues CG11133 (Brother of Yb) and CG31755 (Sister of Yb), which are essential for the primary piRNA pathway in the germline and probably replace the function of the related but soma-specific factor Yb.