Inflammation in Development and Aging: Insights from the Zebrafish Model

Zebrafish are an emergent animal model to study human diseases due to their significant genetic similarity to humans, swift development, and genetic manipulability. Their utility extends to the exploration of the involvement of inflammation in host defense, immune responses, and tissue regeneration. Additionally, the zebrafish model system facilitates prompt screening of chemical compounds that affect inflammation. This study explored the diverse roles of inflammatory pathways in zebrafish development and aging. Serving as a crucial model, zebrafish provides insights into the intricate interplay of inflammation in both developmental and aging contexts. The evidence presented suggests that the same inflammatory signaling pathways often play instructive or beneficial roles during embryogenesis and are associated with malignancies in adults.

A zebrafish model of Ifih1-driven Aicardi-Goutières syndrome reproduces the interferon signature and the exacerbated inflammation of patients

Type I interferonopathies are a heterogenic group of rare diseases associated with an increase in type I interferon (IFN). The main challenge for the study of Type I interferonopathies is the lack of a well-founded animal model to better characterize the phenotype as well as to perform fast and large drug screenings to offer the best treatment options. In this study, we report the development of a transgenic zebrafish model of Type I interferonopathy overexpressing ifih1 carrying the mutation p.Arg742His (Tg(ifih1_mut)), corresponding to the human mutation p.Arg779His. RNA sequence analysis from Tg(ifih1_mut) larvae revealed a systemic inflammation and IFN signature upon a suboptimal poly I:C induction compared with wild-type larvae, confirming the phenotype observed in patients suffering from Type I interferonopathies. More interestingly, the phenotype was manifested in the zebrafish inflammation and Type I IFN reporters nfkb:eGFP and isg15:eGFP, respectively, making this zebrafish model suitable for future high-throughput chemical screening (HTS). Using the unique advantages of the zebrafish model for gene editing, we have generated Tg(ifih1_mut) knocked down for mavs and ikbke, which completely abrogated the Poly I:C induction and activation of the GFP of the reporters. Finally, we used an FDA-approved drug, Baricitinib (Jak1/Jak2 inhibitor), which was able to reduce the inflammation and the ISG expression. Our results demonstrate the potential of this model to further understand AGS pathological mechanisms and to identify novel therapeutic drugs by HTS.

ZAKα/P38 kinase signaling pathway regulates hematopoiesis by activating the NLRP1 inflammasome

Chronic inflammatory diseases are associated with hematopoietic lineage bias, including neutrophilia and anemia. We have recently identified that the canonical inflammasome mediates the cleavage of the master erythroid transcription factor GATA1 in hematopoietic stem and progenitor cells (HSPCs). We report here that genetic inhibition of Nlrp1 resulted in reduced number of neutrophils and increased erythrocyte counts in zebrafish larvae. We also found that the NLRP1 inflammasome in human cells was inhibited by LRRFIP1 and FLII, independently of DPP9, and both inhibitors regulated hematopoiesis. Mechanistically, erythroid differentiation resulted in ribosomal stress-induced activation of the ZAKα/P38 kinase axis which, in turn, phosphorylated and promoted the assembly of NLRP1 in both zebrafish and human. Finally, inhibition of Zaka with the FDA/EMA-approved drug Nilotinib alleviated neutrophilia in a zebrafish model of neutrophilic inflammation and promoted erythroid differentiation and GATA1 accumulation in K562 cells. In conclusion, our results reveal that the NLRP1 inflammasome regulates hematopoiesis and pave the way to develop novel therapeutic strategies for the treatment of hematopoietic alterations associated with chronic inflammatory and rare diseases.

Telomerase RNA-based aptamers restore defective myelopoiesis in congenital neutropenic syndromes

Telomerase RNA (TERC) has a noncanonical function in myelopoiesis binding to a consensus DNA binding sequence and attracting RNA polymerase II (RNA Pol II), thus facilitating myeloid gene expression. The CR4/CR5 domain of TERC is known to play this role, since a mutation of this domain found in dyskeratosis congenita (DC) patients decreases its affinity for RNA Pol II, impairing its myelopoietic activity as a result. In this study, we report that two aptamers, short single-stranded oligonucleotides, based on the CR4/CR5 domain were able to increase myelopoiesis without affecting erythropoiesis in zebrafish. Mechanistically, the aptamers functioned as full terc; that is, they increased the expression of master myeloid genes, independently of endogenous terc, by interacting with RNA Pol II and with the terc-binding sequences of the regulatory regions of such genes, enforcing their transcription. Importantly, aptamers harboring the CR4/CR5 mutation that was found in DC patients failed to perform all these functions. The therapeutic potential of the aptamers for treating neutropenia was demonstrated in several preclinical models. The findings of this study have identified two potential therapeutic agents for DC and other neutropenic patients.

NAMPT and PARylation Are Involved in the Pathogenesis of Atopic Dermatitis

Atopic dermatitis (AD) is a chronic inflammatory skin disease of very high prevalence, especially in childhood, with no specific treatment or cure. As its pathogenesis is complex, multifactorial and not fully understood, further research is needed to increase knowledge and develop new targeted therapies. We have recently demonstrated the critical role of NAD⁺ and poly (ADP-ribose) (PAR) metabolism in oxidative stress and skin inflammation. Specifically, we found that hyperactivation of PARP1 in response to DNA damage induced by reactive oxygen species, and fueled by NAMPT-derived NAD⁺, mediated inflammation through parthanatos cell death in zebrafish and human organotypic 3D skin models of psoriasis. Furthermore, the aberrant induction of NAMPT and PARP activity was observed in the lesional skin of psoriasis patients, supporting the role of these signaling pathways in psoriasis and pointing to NAMPT and PARP1 as potential novel therapeutic targets in treating skin inflammatory disorders. In the present work, we report, for the first time, altered NAD⁺ and PAR metabolism in the skin of AD patients and a strong correlation between NAMPT and PARP1 expression and the lesional status of AD. Furthermore, using a human 3D organotypic skin model of AD, we demonstrate that the pharmacological inhibition of NAMPT and PARP reduces pathology-associated biomarkers. These results help to understand the complexity of AD and reveal new potential treatments for AD patients.

Evolution of LPS recognition and signaling: The bony fish perspective

Fish are the most diverse and successful group of vertebrate animals, with about 30,000 species. The study of fish immunity is of great importance for understanding the evolution of vertebrate immunity, as they are the first animals to show both innate and adaptive immune responses. Although fish immunity is similar to that of mammals, there are obvious differences, such as their dependence of ambient temperature, their poor antibody response, and lack of antibody switching and lymph nodes. In addition, several important differences have also been found between the innate immune responses of fish and mammals. Among these, we will discuss in this review the high resistance of fish to the toxic effects of lipopolysaccharide (LPS) which can be explained by the absence of a Toll-like receptor 4 (Tlr4) ortholog in most fish species or by the inability of the Tlr4/Md2 (Myeloid differentiation 2) complex to recognize LPS, together with the presence of a negative regulator of the LPS signaling complex formed by the TLR-like molecule Rp105 (Radioprotective 105) and Md1. Taken together, these data support the idea that, although TLR4 and RP105 arose from a common ancestor to fish and tetrapods, the TLR4/MD2 receptor complex for LPS recognition arose after their divergence about 450 million years ago.

The Spike protein of SARS-CoV-2 signals via Tlr2 in zebrafish

One of the most studied defense mechanisms against invading pathogens, including viruses, are Toll-like receptors (TLRs). Among them, TLR3, TLR7, TLR8 and TLR9 detect different forms of viral nucleic acids in endosomal compartments, whereas TLR2 and TLR4 recognize viral structural and nonstructural proteins outside the cell. Although many different TLRs have been shown to be involved in SARS-CoV-2 infection and detection of different structural proteins, most studies have been performed in vitro and the results obtained are rather contradictory. In this study, we report using the unique advantages of the zebrafish model for in vivo imaging and gene editing that the S1 domain of the Spike protein from the Wuhan strain (S1WT) induced hyperinflammation in zebrafish larvae via a Tlr2/Myd88 signaling pathway and independently of interleukin-1β production. In addition, S1WT also triggered emergency myelopoiesis, but in this case through a Tlr2/Myd88-independent signaling pathway. These results shed light on the mechanisms involved in the fish host responses to viral proteins.

Nitrogen availability in biochar-based fertilizers depending on activation treatment and nitrogen source

Different activation and N-doping treatments were used to produce biochar-based fertilizers (BBFs) with increased N concentration and slow N release. Pristine biochars were produced by pyrolysis of olive tree pruning feedstock at low and high temperatures (400 and 800 °C). These biochars were activated either by ultrasonication, or oxidation with hydrogen peroxide (H₂O₂) or nitric acid (HNO₃) to increase their N retention potential. Subsequently biochars were enriched with N with either urea or ammonium sulfate. The activation of low-temperature biochars with HNO₃ was the most effective treatment leading to new surface carboxylic groups that facilitated the later enrichment with N. When treated with urea, BBFs reached 7.0 N%, whereas the H₂O₂ activation only allowed an increase up to 2.0 N%. The use of urea as the external N source was the most efficient for incorporating N. Urea treated biochars had a water-soluble fraction that represented up to 14.5 % of the total N. The hydrolyzable N fraction, composed by amides and simple N heterocycles originated by the N-doping treatments, and nitro groups generated from HNO₃ activation, represented up to 60 % of the total N. This study relates the N chemical forms in the new BBFs to potential N availability in soil. The presence of water-soluble, hydrolyzable and non-hydrolyzable N implied that these BBFs may supply N that would be progressively available for plants, acting as slow-release fertilizers.

Analysis of 16S rRNA Gene Sequence of Nasopharyngeal Exudate Reveals Changes in Key Microbial Communities Associated with Aging

Functional or compositional perturbations of the microbiome can occur at different sites, of the body and this dysbiosis has been linked to various diseases. Changes in the nasopharyngeal microbiome are associated to patient's susceptibility to multiple viral infections, supporting the idea that the nasopharynx may be playing an important role in health and disease. Most studies on the nasopharyngeal microbiome have focused on a specific period in the lifespan, such as infancy or the old age, or have other limitations such as low sample size. Therefore, detailed studies analyzing the age- and sex-associated changes in the nasopharyngeal microbiome of healthy people across their whole life are essential to understand the relevance of the nasopharynx in the pathogenesis of multiple diseases, particularly viral infections. One hundred twenty nasopharyngeal samples from healthy subjects of all ages and both sexes were analyzed by 16S rRNA sequencing. Nasopharyngeal bacterial alpha diversity did not vary in any case between age or sex groups. Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were the predominant phyla in all the age groups, with several sex-associated. Acinetobacter, Brevundimonas, Dolosigranulum, Finegoldia, Haemophilus, Leptotrichia, Moraxella, Peptoniphilus, Pseudomonas, Rothia, and Staphylococcus were the only 11 bacterial genera that presented significant age-associated differences. Other bacterial genera such as Anaerococcus, Burkholderia, Campylobacter, Delftia, Prevotella, Neisseria, Propionibacterium, Streptococcus, Ralstonia, Sphingomonas, and Corynebacterium appeared in the population with a very high frequency, suggesting that their presence might be biologically relevant. Therefore, in contrast to other anatomical areas such as the gut, bacterial diversity in the nasopharynx of healthy subjects remains stable and resistant to perturbations throughout the whole life and in both sexes. Age-associated abundance changes were observed at phylum, family, and genus levels, as well as several sex-associated changes probably due to the different levels of sex hormones present in both sexes at certain ages. Our results provide a complete and valuable dataset that will be useful for future research aiming for studying the relationship between changes in the nasopharyngeal microbiome and susceptibility to or severity of multiple diseases.

Zebrafish models of COVID-19

Although COVID-19 has only recently appeared, research studies have already developed and implemented many animal models for deciphering the secrets of the disease and provided insights into the biology of SARS-CoV-2. However, there are several major factors that complicate the study of this virus in model organisms, such as the poor infectivity of clinical isolates of SARS-CoV-2 in some model species, and the absence of persistent infection, immunopathology, severe acute respiratory distress syndrome, and, in general, all the systemic complications which characterize COVID-19 clinically. Another important limitation is that SARS-CoV-2 mainly causes severe COVID-19 in older people with comorbidities, which represents a serious problem when attempting to use young and immunologically naïve laboratory animals in COVID-19 testing. We review here the main animal models developed so far to study COVID-19 and the unique advantages of the zebrafish model that may help to contribute to understand this disease, in particular to the identification and repurposing of drugs to treat COVID-19, to reveal the mechanism of action and side-effects of Spike-based vaccines, and to decipher the high susceptibility of aged people to COVID-19.

Differential proinflammatory activities of Spike proteins of SARS-CoV-2 variants of concern

The coronavirus disease 2019 (COVID-19) pandemic turned the whole world upside down in a short time. One of the main challenges faced has been to understand COVID-19-associated life-threatening hyperinflammation, the so-called cytokine storm syndrome (CSS). We report here the proinflammatory role of Spike (S) proteins from different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern in zebrafish. We found that wild-type/Wuhan variant S1 (S1WT) promoted neutrophil and macrophage recruitment, local and systemic hyperinflammation, emergency myelopoiesis, and hemorrhages. In addition, S1γ was more proinflammatory S1δ was less proinflammatory than S1WT, and, notably, S1β promoted delayed and long-lasting inflammation. Pharmacological inhibition of the canonical inflammasome alleviated S1-induced inflammation and emergency myelopoiesis. In contrast, genetic inhibition of angiotensin-converting enzyme 2 strengthened the proinflammatory activity of S1, and angiotensin (1-7) fully rescued S1-induced hyperinflammation and hemorrhages. These results shed light into the mechanisms orchestrating the COVID-19-associated CSS and the host immune response to different SARS-CoV-2 S protein variants.

NAMPT-derived NAD+ fuels PARP1 to promote skin inflammation through parthanatos cell death

Several studies have revealed a correlation between chronic inflammation and nicotinamide adenine dinucleotide (NAD+) metabolism, but the precise mechanism involved is unknown. Here, we report that the genetic and pharmacological inhibition of nicotinamide phosphoribosyltransferase (Nampt), the rate-limiting enzyme in the salvage pathway of NAD+ biosynthesis, reduced oxidative stress, inflammation, and keratinocyte DNA damage, hyperproliferation, and cell death in zebrafish models of chronic skin inflammation, while all these effects were reversed by NAD+ supplementation. Similarly, genetic and pharmacological inhibition of poly(ADP-ribose) (PAR) polymerase 1 (Parp1), overexpression of PAR glycohydrolase, inhibition of apoptosis-inducing factor 1, inhibition of NADPH oxidases, and reactive oxygen species (ROS) scavenging all phenocopied the effects of Nampt inhibition. Pharmacological inhibition of NADPH oxidases/NAMPT/PARP/AIFM1 axis decreased the expression of pathology-associated genes in human organotypic 3D skin models of psoriasis. Consistently, an aberrant induction of NAMPT and PARP activity, together with AIFM1 nuclear translocation, was observed in lesional skin from psoriasis patients. In conclusion, hyperactivation of PARP1 in response to ROS-induced DNA damage, fueled by NAMPT-derived NAD+, mediates skin inflammation through parthanatos cell death.

Telomerase reverse transcriptase activates transcription of miR500A to inhibit Hedgehog signalling and promote cell invasiveness

Telomerase reverse transcriptase (TERT) maintains telomere homeostasis, thus ensuring chromosome stability and cell proliferation. In addition, several telomere-independent functions of human TERT have been described. In this study, we report that TERT binds directly to the TCF binding elements located upstream of the oncomiR miR500A, and induces its transcription. This function was independent of the telomerase activity, as shown with experiments using catalytically inactive TERT and inhibitors of TERT and the TERT RNA component. miR500A was in turn found to target three key components of the Hedgehog signalling pathway: Patched 1; Gli family zinc finger 3; and Cullin 3, thereby promoting cell invasion. Our results point to the crucial role of the TERT-miR500A-Hedgehog axis in tumour aggressiveness and highlight the therapeutic potential of targeting noncanonical TERT functions in cancer.

Zebrafish Models to Study Inflammasome-Mediated Regulation of Hematopoiesis

Hematopoiesis is a complex process through which immature bone marrow precursor cells mature into all types of blood cells. Although the association of hematopoietic lineage bias (including anemia and neutrophilia) with chronic inflammatory diseases has long been appreciated, the causes involved are obscure. Recently, cytosolic multiprotein inflammasome complexes were shown to activate inflammatory and immune responses, and directly regulate hematopoiesis in zebrafish models; this was deemed to occur via cleavage and inactivation of the master erythroid transcription factor GATA1. Herein summarized are the zebrafish models that are currently available to study this unappreciated role of inflammasome-mediated regulation of hematopoiesis. Novel putative therapeutic strategies, for the treatment of hematopoietic alterations associated with chronic inflammatory diseases in humans, are also proposed.

Biochar as electron donor for reduction of N2O by Paracoccus denitrificans

Biochar (BC) has been shown to influence microbial denitrification and mitigate soil N2O emissions. However, it is unclear if BC is able to directly stimulate the microbial reduction of N2O to N2. We hypothesized that the ability of BC to lower N2O emissions could be related not only to its ability to store electrons, but to donate them to bacteria that enzymatically reduce N2O. Therefore, we carried out anoxic incubations with Paracoccus denitrificans, known amounts of N2O, and nine contrasting BCs, in the absence of any other electron donor or acceptor. We found a strong and direct correlation between the extent and rates of N2O reduction with BC's EDC/EEC (electron donating capacity/electron exchange capacity). Apart from the redox capacity, other BC properties were found to regulate the BC's ability to increase N2O reduction by P. denitrificans. For this specific BC series, we found that a high H/C and ash content, low surface area and poor lignin feedstocks favored N2O reduction. This provides valuable information for producing tailored BCs with the potential to assist and promote the reduction of N2O in the pursuit of reducing this greenhouse gas emissions.

The vitamin B6-regulated enzymes PYGL and G6PD fuel NADPH oxidases to promote skin inflammation

Psoriasis is a skin inflammatory disorder that affects 3% of the human population. Although several therapies based on the neutralization of proinflammatory cytokines have been used with relative success, additional treatments are required. The in silico analysis of gene expression data of psoriasis lesional skin and an analysis of vitamin B6 metabolites in the sera of psoriasis patients point to altered vitamin B6 metabolism at both local and systemic levels. Functional studies showed that vitamin B6 vitamers reduced skin neutrophil infiltration, oxidative stress and Nfkb activity in two zebrafish models of skin inflammation. Strikingly, inhibition of glycogen phosphorylase L (Pygl) and glucose-6-phosphate dehydrogenase (G6pd), two vitamin B6-regulated enzymes, alleviated oxidative-stress induced inflammation in zebrafish skin inflammation models. Despite the central role of G6pd in antioxidant defenses, the results of the study demonstrate that glycogen stores and G6pd fuel NADPH oxidase to promote skin inflammation, revealing novel targets for the treatment of skin inflammatory disorders.

Hydrogen peroxide in neutrophil inflammation: Lesson from the zebrafish

The zebrafish has become an excellent model for the study of inflammation and immunity. Its unique advantages for in vivo imaging and gene and drug screening have allowed the visualization of dual oxidase 1 (Duox1)-derived hydrogen peroxide (H₂O₂) tissue gradients and its crosstalk with neutrophil infiltration to inflamed tissue. Thus, it has been shown that H₂O₂ directly recruits neutrophils via the Src-family tyrosine kinase Lyn and indirectly by the activation of several signaling pathways involved in inflammation, such as nuclear factor κB (NF-κB), mitogen activated kinases and the transcription factor AP1. In addition, this model has also unmasked the unexpected ability of H₂O₂ to induce the expression of the gene encoding the key neutrophil chemoattractant CXC chemokine ligand 8 by facilitating the accessibility of transcription factors to its promoter through histone covalent modifications. Finally, zebrafish models of psoriasis have shown that a H₂O₂/NF-κB/Duox1 positive feedback inflammatory loop operates in this chronic inflammatory disorder and that pharmacological inhibition of Duox1, but not of downstream mediators, inhibits inflammation and restores epithelial homeostasis. Therefore, these results have pointed out DUOX1 and H₂O₂ as therapeutic targets for the treatment of skin inflammatory disorders, such as psoriasis.

Zebrafish modeling reveals that SPINT1 regulates the aggressiveness of skin cutaneous melanoma and its crosstalk with tumor immune microenvironment

BACKGROUND

Skin cutaneous melanoma (SKCM) is the most lethal form of skin cancer and while incidence rates are declining for most cancers, they have been steadily rising for SKCM. Serine protease inhibitor, kunitz-type, 1 (SPINT1) is a type II transmembrane serine protease inhibitor that has been shown to be involved in the development of several types of cancer, such as squamous cell carcinoma and colorectal cancer.

METHODS

We used the unique advantages of the zebrafish to model the impact of Spint1a deficiency in early transformation, progression and metastatic invasion of SKCM together with in silico analysis of the occurrence and relevance of SPINT1 genetic alterations of the SKCM TCGA cohort.

RESULTS

We report here a high prevalence of SPINT1 genetic alterations in SKCM patients and their association with altered tumor immune microenvironment and poor patient survival. The zebrafish model reveals that Spint1a deficiency facilitates oncogenic transformation, regulates the tumor immune microenvironment crosstalk, accelerates the onset of SKCM and promotes metastatic invasion. Notably, Spint1a deficiency is required at both cell autonomous and non-autonomous levels to enhance invasiveness of SKCM.

CONCLUSIONS

These results reveal a novel therapeutic target for SKCM.

Biochar reduces volatile organic compounds generated during chicken manure composting

The efficiency of biochar for reducing the levels of volatile organic compounds (VOC) was investigated in a composting mixture containing 90% poultry manure and 10% straw (with and without 3% biochar addition) at three different stages of the process. The use of a low application rate of biochar reduced the concentration of VOC during the thermophilic phase. Biochar significantly reduced the levels of nitrogen volatile compounds, which are the most abundant VOC family, originated from microbial transformation of the N-compounds originally present in manure. The most efficient VOC reduction was observed in oxygenated volatile compounds (ketones, phenols and organic acids), which are intermediates of organic matter degradation, whereas there was no effect on other VOC families (aliphatic, aromatic and terpenes). These results suggest the importance of not only the sorption capacity of biochar but also its impact in the composting progress as main drivers for VOC reduction.

Inflammasome Regulates Hematopoiesis through Cleavage of the Master Erythroid Transcription Factor GATA1

Chronic inflammatory diseases are associated with altered hematopoiesis that could result in neutrophilia and anemia. Here we report that genetic or chemical manipulation of different inflammasome components altered the differentiation of hematopoietic stem and progenitor cells (HSPC) in zebrafish. Although the inflammasome was dispensable for the emergence of HSPC, it was intrinsically required for their myeloid differentiation. In addition, Gata1 transcript and protein amounts increased in inflammasome-deficient larvae, enforcing erythropoiesis and inhibiting myelopoiesis. This mechanism is evolutionarily conserved, since pharmacological inhibition of the inflammasome altered erythroid differentiation of human erythroleukemic K562 cells. In addition, caspase-1 inhibition rapidly upregulated GATA1 protein in mouse HSPC promoting their erythroid differentiation. Importantly, pharmacological inhibition of the inflammasome rescued zebrafish disease models of neutrophilic inflammation and anemia. These results indicate that the inflammasome plays a major role in the pathogenesis of neutrophilia and anemia of chronic diseases and reveal druggable targets for therapeutic interventions.

Biochar reduces the efficiency of nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) mitigating N2O emissions

Among strategies suggested to decrease agricultural soil N₂O losses, the use of nitrification inhibitors such as DMPP (3,4-dimethylpyrazole phosphate) has been proposed. However, the efficiency of DMPP might be affected by soil amendments, such as biochar, which has been shown to reduce N₂O emissions. This study evaluated the synergic effect of a woody biochar applied with DMPP on soil N₂O emissions. A incubation study was conducted with a silt loam soil and a biochar obtained from Pinus taeda at 500 °C. Two biochar rates (0 and 2% (w/w)) and three different nitrogen treatments (unfertilized, fertilized and fertilized + DMPP) were assayed under two contrasting soil water content levels (40% and 80% of water filled pore space (WFPS)) over a 163 day incubation period. Results showed that DMPP reduced N₂O emissions by reducing ammonia-oxidizing bacteria (AOB) populations and promoting the last step of denitrification (measured by the ratio nosZI + nosZII/nirS + nirK genes). Biochar mitigated N₂O emissions only at 40% WFPS due to a reduction in AOB population. However, when DMPP was applied to the biochar amended soil, a counteracting effect was observed, since the N₂O mitigation induced by DMPP was lower than in control soil, demonstrating that this biochar diminishes the efficiency of the DMPP both at low and high soil water contents.

Relationships between emitted volatile organic compounds and their concentration in the pile during municipal solid waste composting

Composting operations taking place at municipal solid waste (MSW) treatment plants represent a source of volatile organic compounds (VOC) to the atmosphere. Understanding the variables governing the release of VOC at these facilities is crucial to assess potential health risks for site workers and local residents. In this work the changes in the VOC composition of a composting pile were monitored and compared to the VOC emmited from the same pile in order to understand the impact of composting operations on the release of VOC. More than one hundred VOC were indentified in the solid phase of the composting piles, which were dominated by terpenes (about 50% of the total amount of VOC) and in a lower quantity alcohols, volatile fatty acids and aromatic compounds. There was a reduction in the total concentration of VOC in the pile during composting, from 45 to 35 mg/kg, but the compostion and distribution of VOC families remained stable in the pile even in the mature compost. However, there was no correlation between the emitted VOC and their concentration in the composting pile. The VOC emission pattern was affected by the biological activity in the pile (measured by temperature, CO₂ evolution and the presence of CH₄ emissions). The highest VOC emissions were detected at early stages of the process, alongside with the generation of CH₄ in the pile, and then decreased sharply in the mature compost as a consequence of biodegradation and volatilisation. These results pointed to the importance of composting operation rather than the composition of the raw materials on the release of VOC in composting plants.

Role of biochar as an additive in organic waste composting

The use of biochar in organic waste composting has attracted interest in the last decade due to the environmental and agronomical benefits obtained during the process. Biochar presents favourable physicochemical properties, such as large porosity, surface area and high cation exchange capacity, enabling interaction with major nutrient cycles and favouring microbial growth in the composting pile. The enhanced environmental conditions can promote a change in the microbial communities that can affect important microbially mediated biogeochemical cycles: organic matter degradation and humification, nitrification, denitrification and methanogenesis. The main benefits of the use of biochar in composting are reviewed in this article, with special attention to those related to the process performance, compost microbiology, organic matter degradation and humification, reduction of N losses and greenhouse gas emissions and fate of heavy metals.

Identification of an Evolutionarily Conserved Ankyrin Domain-Containing Protein, Caiap, Which Regulates Inflammasome-Dependent Resistance to Bacterial Infection

Many proteins contain tandemly repeated modules of several amino acids, which act as the building blocks that form the underlying architecture of a specific protein-binding interface. Among these motifs and one of the most frequently observed is ankyrin repeats (ANK), which consist of 33 amino acid residues that are highly conserved. ANK domains span a wide range of functions, including protein–protein interactions, such as the recruitment of substrate to the catalytic domain of an enzyme, or the assembly of stable multiprotein complexes. Here, we report the identification of an evolutionarily conserved protein, that we term Caiap (from CARD- and ANK-containing Inflammasome Adaptor Protein), which has an N-terminal CARD domain and 16 C-terminal ANK domains and is required for the inflammasome-dependent resistance to Salmonella Typhimurium in zebrafish. Intriguingly, Caiap is highly conserved from cartilaginous fish to marsupials but is absent in placental mammals. Mechanistically, Caiap acts downstream flagellin and interacts with catalytic active Caspa, the functional homolog of mammalian caspase-1, through its ANK domain, while its CARD domain promotes its self-oligomerization. Our results therefore point to ANK domain-containing proteins as key inflammasome adaptors required for the stabilization of active caspase-1 in functionally stable, high molecular weight complexes.

Biochar accelerates organic matter degradation and enhances N mineralisation during composting of poultry manure without a relevant impact on gas emissions

A composting study was performed to assess the impact of biochar addition to a mixture of poultry manure and barley straw. Two treatments: control (78% poultry manure + 22% barley straw, dry weight) and the same mixture amended with biochar (3% dry weight), were composted in duplicated windrows during 19 weeks. Typical monitoring parameters and gaseous emissions (CO2, CO, CH4, N2O and H2S) were evaluated during the process as well as the agronomical quality of the end-products. Biochar accelerated organic matter degradation and ammonium formation during the thermophilic phase and enhanced nitrification during the maturation phase. Our results suggest that biochar, as composting additive, improved the physical properties of the mixture by preventing the formation of clumps larger than 70 mm. It favoured microbiological activity without a relevant impact on N losses and gaseous emissions. It was estimated that biochar addition at 3% could reduce the composting time by 20%.

High concentrations of polycyclic aromatic hydrocarbons (naphthalene, phenanthrene and pyrene) failed to explain biochar's capacity to reduce soil nitrous oxide emissions

The presence of polycyclic aromatic hydrocarbons (PAHs) has been postulated as a mechanism by which biochar might mitigate N(2)O emissions. We studied whether and to what extent N(2)O emissions were influenced by the three most abundant PAHs in biochar: naphthalene, phenanthrene and pyrene. We hypothesised that biochars contaminated with PAHs would show a larger N(2)O mitigation capacity and that increasing PAH concentrations in biochar would lead to higher mitigation potentials. Our results demonstrate that the high-temperature biochar (550 °C) had a higher capacity to mitigate soil N(2)O emissions than the low-temperature biochar (350 °C). At low PAH concentrations, PAHs do not significantly contribute to the reductions in soil N(2)O emissions; while biochar stimulated soil N(2)O emissions when it was spiked with high concentrations of PAHs. This study suggests that the impact of biochar on soil N(2)O emissions is due to other compositional and/or structural properties of biochar rather than to PAH concentration.

Tnfa signaling through tnfr2 protects skin against oxidative stress-induced inflammation

A new zebrafish model of skin inflammatory disease explains new-onset and worsening psoriasis and lichen planus in patients receiving anti-TNFα therapy.

TNFα overexpression has been associated with several chronic inflammatory diseases, including psoriasis, lichen planus, rheumatoid arthritis, and inflammatory bowel disease. Paradoxically, numerous studies have reported new-onset psoriasis and lichen planus following TNFα antagonist therapy. Here, we show that genetic inhibition of Tnfa and Tnfr2 in zebrafish results in the mobilization of neutrophils to the skin. Using combinations of fluorescent reporter transgenes, fluorescence microscopy, and flow cytometry, we identified the local production of dual oxidase 1 (Duox1)-derived H₂O₂ by Tnfa- and Tnfr2-deficient keratinocytes as a trigger for the activation of the master inflammation transcription factor NF-κB, which then promotes the induction of genes encoding pro-inflammatory molecules. In addition, pharmacological inhibition of Duox1 completely abrogated skin inflammation, placing Duox1-derived H₂O₂ upstream of this positive feedback inflammatory loop. Strikingly, DUOX1 was drastically induced in the skin lesions of psoriasis and lichen planus patients. These results reveal a crucial role for TNFα/TNFR2 axis in the protection of the skin against DUOX1-mediated oxidative stress and could establish new therapeutic targets for skin inflammatory disorders.

Psoriasis and lichen planus are chronic, debilitating skin diseases that affect millions of people worldwide. TNFα is a multifunctional cytokine that mediates acute and chronic inflammation. While TNFα antagonist therapy is used for autoimmune or chronic inflammatory diseases, such as inflammatory bowel disease (IBD), numerous studies have reported new-onset psoriasis and lichen planus following such therapy. We have used the unique advantages of the zebrafish embryo to identify a novel phenotype that mirrors this unexplained and paradoxical onset of psoriasis and lichen planus. We found that depletion of Tnfa or its receptor Tnfr2 caused skin inflammation and hyperproliferation of keratinocytes through the activation of a Duox1/H₂O₂/NF-κB positive feedback inflammatory loop. Strikingly, DUOX1 was drastically induced in the skin lesions of psoriasis and lichen planus patients, and pharmacological inhibition of Duox1 abrogated skin inflammation, placing Duox1-derived H₂O₂ upstream of this inflammatory loop. Our results suggest that therapies targeting DUOX1 and H₂O₂ could provide innovative approaches to the management of skin inflammatory disorders.

Premature aging in telomerase-deficient zebrafish

The study of telomere biology is crucial to the understanding of aging and cancer. In the pursuit of greater knowledge in the field of human telomere biology, the mouse has been used extensively as a model. However, there are fundamental differences between mouse and human cells. Therefore, additional models are required. In light of this, we have characterized telomerase-deficient zebrafish (Danio rerio) as the second vertebrate model for human telomerase-driven diseases. We found that telomerase-deficient zebrafish show p53-dependent premature aging and reduced lifespan in the first generation, as occurs in humans but not in mice, probably reflecting the similar telomere length in fish and humans. Among these aging symptoms, spinal curvature, liver and retina degeneration, and infertility were the most remarkable. Although the second-generation embryos died in early developmental stages, restoration of telomerase activity rescued telomere length and survival, indicating that telomerase dosage is crucial. Importantly, this model also reproduces the disease anticipation observed in humans with dyskeratosis congenita (DC). Thus, telomerase haploinsufficiency leads to anticipation phenomenon in longevity, which is related to telomere shortening and, specifically, with the proportion of short telomeres. Furthermore, p53 was induced by telomere attrition, leading to growth arrest and apoptosis. Importantly, genetic inhibition of p53 rescued the adverse effects of telomere loss, indicating that the molecular mechanisms induced by telomere shortening are conserved from fish to mammals. The partial rescue of telomere length and longevity by restoration of telomerase activity, together with the feasibility of the zebrafish for high-throughput chemical screening, both point to the usefulness of this model for the discovery of new drugs able to reactivate telomerase in individuals with DC.

TNF receptors regulate vascular homeostasis in zebrafish through a caspase-8, caspase-2 and P53 apoptotic program that bypasses caspase-3

Although it is known that tumor necrosis factor receptor (TNFR) signaling plays a crucial role in vascular integrity and homeostasis, the contribution of each receptor to these processes and the signaling pathway involved are still largely unknown. Here, we show that targeted gene knockdown of TNFRSF1B in zebrafish embryos results in the induction of a caspase-8, caspase-2 and P53-dependent apoptotic program in endothelial cells that bypasses caspase-3. Furthermore, the simultaneous depletion of TNFRSF1A or the activation of NF-κB rescue endothelial cell apoptosis, indicating that a signaling balance between both TNFRs is required for endothelial cell integrity. In endothelial cells, TNFRSF1A signals apoptosis through caspase-8, whereas TNFRSF1B signals survival via NF-κB. Similarly, TNFα promotes the apoptosis of human endothelial cells through TNFRSF1A and triggers caspase-2 and P53 activation. We have identified an evolutionarily conserved apoptotic pathway involved in vascular homeostasis that provides new therapeutic targets for the control of inflammation- and tumor-driven angiogenesis.

Behaviour of telomere and telomerase during aging and regeneration in zebrafish

Telomere length and telomerase activity are important factors in the pathobiology of human diseases. Age-related diseases and premature aging syndromes are characterized by short telomeres, which can compromise cell viability, whereas tumour cells can prevent telomere loss by aberrantly upregulating telomerase. The zebrafish (Danio rerio) offers multiple experimental manipulation advantages over other vertebrate models and, therefore, it has been recently considered as a potential model for aging, cancer, and regeneration studies. However, it has only partially been exploited to shed light on these fundamental biological processes. The aim of this study was, therefore, to investigate telomere length and telomerase expression and activity in different strains of zebrafish obtained from different stock centres to determine whether they undergo any changes during aging and regeneration. We found that although both telomerase expression and telomere length increased from embryo to adulthood stages, they drastically declined in aged fish despite telomerase activity was detected in different tissues of old fish. In addition, we observed a weaker upregulation of telomerase expression in regenerating fins of old fish, which well correlates with their impaired regeneration capacity. Strikingly, telomeres were elongated or maintained during the fin regeneration process at all ages and after repeated amputations, likely to support high cell proliferation rates. We conclude that the expression of telomerase and telomere length are closely related during the entire life cycle of the fish and that these two parameters can be used as biomarkers of aging in zebrafish. Our results also reveal a direct relationship between the expression of telomerase, telomere length and the efficiency of tissue regeneration.

Evolution of lipopolysaccharide (LPS) recognition and signaling: fish TLR4 does not recognize LPS and negatively regulates NF-kappaB activation

It has long been established that lower vertebrates, most notably fish and amphibians, are resistant to the toxic effect of LPS. Furthermore, the lack of a TLR4 ortholog in some fish species and the lack of the essential costimulatory molecules for LPS activation via TLR4 (i.e., myeloid differentiation protein 2 (MD-2) and CD14) in all the fish genomes and expressed sequence tag databases available led us to hypothesize that the mechanism of LPS recognition in fish may be different from that of mammals. To shed light on the role of fish TLRs in LPS recognition, a dual-luciferase reporter assay to study NF-kappaB activation in whole zebrafish embryos was developed and three different bony fish models were studied: 1) the gilthead seabream (Sparus aurata, Perciformes), an immunological-tractable teleost model in which the presence of a TLR4 ortholog is unknown; 2) the spotted green pufferfish (Tetraodon nigroviridis, Tetraodontiformes), which lacks a TLR4 ortholog; and 3) the zebrafish (Danio rerio, Cypriniformes), which possesses two TLR4 orthologs. Our results show that LPS signaled via a TLR4- and MyD88-independent manner in fish, and, surprisingly, that the zebrafish TLR4 orthologs negatively regulated the MyD88-dependent signaling pathway. We think that the identification of TLR4 as a negative regulator of TLR signaling in the zebrafish, together with the absence of this receptor in most fish species, explains the resistance of fish to endotoxic shock and supports the idea that the TLR4 receptor complex for LPS recognition arose after the divergence of fish and tetrapods.

Telomerase reverse transcriptase delays aging in cancer-resistant mice

Telomerase confers limitless proliferative potential to most human cells through its ability to elongate telomeres, the natural ends of chromosomes, which otherwise would undergo progressive attrition and eventually compromise cell viability. However, the role of telomerase in organismal aging has remained unaddressed, in part because of the cancer-promoting activity of telomerase. To circumvent this problem, we have constitutively expressed telomerase reverse transcriptase (TERT), one of the components of telomerase, in mice engineered to be cancer resistant by means of enhanced expression of the tumor suppressors p53, p16, and p19ARF. In this context, TERT overexpression improves the fitness of epithelial barriers, particularly the skin and the intestine, and produces a systemic delay in aging accompanied by extension of the median life span. These results demonstrate that constitutive expression of Tert provides antiaging activity in the context of a mammalian organism.

Application of the dual-luciferase reporter assay to the analysis of promoter activity in Zebrafish embryos

BACKGROUND

The dual-luciferase assay has been widely used in cell lines to determine rapidly but accurately the activity of a given promoter. Although this strategy has proved very useful, it does not allow the promoter and gene function to be analyzed in the context of the whole organism.

RESULTS

Here, we present a rapid and sensitive assay based on the classical dual-luciferase reporter technique which can be used as a new tool to characterize the minimum promoter region of a gene as well as the in vivo response of inducible promoters to different stimuli. We illustrate the usefulness of this system for studying both constitutive (telomerase) and inducible (NF-kappaB-dependent) promoters. The flexibility of this assay is demonstrated by induction of the NF-kappaB-dependent promoters using simultaneous microinjection of different pathogen-associated molecular patterns as well as with the use of morpholino-gene mediated knockdown.

CONCLUSION

This assay has several advantages compared with the classical in vitro (cell lines) and in vivo (transgenic mice) approaches. Among others, the assay allows a rapid and quantitative measurement of the effects of particular genes or drugs in a given promoter in the context of a whole organism and it can also be used in high throughput screening experiments.

Potential of olive mill waste and compost as biobased pesticides against weeds, fungi, and nematodes

The phytotoxic and antimicrobial properties of olive mill wastes have been widely investigated and demonstrated over the past decade. However, their potential utilization as biodegradable pesticides against plant pathogens is still poorly understood. In this study, a series of laboratory bioassays was designed to test the inhibitory effects of sterile water extracts of two-phase olive mill waste (TPOMW) and TPOMW composts with different degrees of stabilization on several different plant pathogens. Fungicidal properties of TPOMW extracts, assayed in a microwell assay format, showed that the growth of Phytophthora capsici was consistently and strongly inhibited by all TPOMW extracts diluted 1:10 (w:v). In contrast, suppression of Pythium ultimum and Botrytis cinerea by the extracts was not as strong and depended on the specific TPOMW sample. Mature compost inhibited P. capsici and B. cinerea at dilutions as great as 1:50, w:v. Neither TPOMW nor TPOMW compost extracts were able to inhibit the growth of the basidiomycete root rot agent Rhizoctonia solani. In addition, studies were conducted on the allelopathic effects of TPOMW extracts on seed germination of four highly invasive and globally distributed weeds (Amaranthus retroflexus, Solanum nigrum, Chenopodium album and Sorghum halepense). Both the TPOMW and immature TPOMW compost extracts substantially inhibited germination of A. retroflexus and S. nigrum, whereas mature composts extracts only partially reduced the germination of S. nigrum. Finally, TPOMW extracts strongly inhibited egg hatch and second-stage juvenile (J2) motility of the root-knot nematode Meloidogyne incognita. However, only higher concentrations of stage-one and stage-two TPOMW compost extracts exerted a suppressive effect on both J2 motility and on egg hatch. The study shows the high potential of naturally occurring chemicals present in TPOMW and TPOMW composts that should be further investigated as bio-pesticides for their use in sustainable agricultural systems.

Chemical properties and hydrolytic enzyme activities for the characterisation of two-phase olive mill wastes composting

Two-phase olive mill waste (TPOMW) is a semisolid sludge generated during the extraction of olive oil by the two-phase centrifugation system. Among all the available disposal options, composting is gaining interest as a sustainable strategy to recycle TPOMW for agricultural purposes. The quality of compost for agronomical use depends on the degree of organic matter stabilization, but despite several studies on the topic, there is not a single method available which alone can give a certain indication of compost stability. In addition, information on the biological and biochemical properties, including the enzymatic activity (EA) of compost, is rare. The aim of this work was to investigate the suitability of some enzymatic activities (beta-glucosidase, arylsulphatase, acid-phosphatase, alkaline-phosphatase, urease and fluorescein diacetate hydrolysis (FDA)) as parameters to evaluate organic matter stability during the composting of TPOMW. These enzymatic indices were also compared to conventional stability indices. For this purpose two composting piles were prepared by mixing TPOMW with sheep manure and grape stalks in different proportions, with forced aeration and occasional turnings. The composting of TPOMW followed the common pattern reported previously for this kind of material with a reduction of 40-50% of organic matter, a gradual increase in pH, disappearance of phytotoxicity and formation of humic-like C. All EA increased during composting except acid-phosphatase. Significant correlations were found between EA and some important conventional stability indices indicating that EA can be a simple and reliable tool to determine the degree of stability of TPOMW composts.

The mineralisation of fresh and humified soil organic matter by the soil microbial biomass

Soil organic matter comprises all dead plant and animal residues, from the most recent inputs to the most intensively humified. We have found that traces of fresh substrates at microg g(-1) soil concentrations (termed 'trigger molecules') activate the biomass to expend more energy than is contained in the original 'trigger molecules'. In contrast, we suggest that the rate limiting step in soil organic matter mineralisation is independent of microbial activity, but is governed by abiological processes (which we term the Regulatory Gate theory). These two findings have important implications for our understanding of carbon mineralisation in soil, a fundamental process in the sequestration of soil organic matter.

Potential of olive mill wastes for soil C sequestration

The present work deals with the potential of olive mill wastes as a C source for soil C sequestration strategy, which is based on the high lignocellulosic content that makes these wastes to degrade slowly during composting and after land application. A C balance was performed during the whole life cycle of two different two-phase olive mill wastes (TPOMW): C losses were calculated during the composting process and after soil application of the composting mixtures under laboratory conditions. The effect of the degree of stabilization of TPOMW on the overall C waste conservation efficiency was also evaluated. C losses after 34 weeks of TPOMW composting ranged from 40.58% to 45.19% of the initial C, whereas the amount of C evolved as CO2 after 8 months of incubation of soil amended with mature composts only represented between 20.6% and 21.9% of the added C. The total C losses considering the whole life cycle of the TPOMW showed lower losses compared to composts prepared with organic residues of different origin. Conversely to the typical behaviour of other organic wastes, the stabilisation degree of the TPOMW composting mixtures did not show any significant effect on the total C losses measured during composting and later land application. The low rate of degradation of TPOMW both during composting and after soil application makes the use of TPOMW as a C source an attractive strategy for soil C sequestration.

Carbon mineralization dynamics in soils amended with meat meals under laboratory conditions

Meat and bone meal (MBM) is obtained from the wastes produced during slaughtering operations. Its high concentration of N and P makes it interesting as an organic fertiliser but its use in soil has been barely studied previously. In this work four laboratory experiments were performed to study the influence of different variables (MBM composition, rate of application, temperature of incubation and the type of soil) on C mineralization dynamics of MBM in agricultural soils. The total CO2-C evolved (as % of added C) after 2 weeks ranged between 10% and 20%. The kinetics of mineralization were rapid, with C evolved as CO2 within the first 4 days representing more than 50% of total C mineralized. A linear correlation was found between the rate of application (added-C) and CO2-C evolved (r2: 0.997; P<0.001). A temperature coefficient (Q10) was used to assess the difference in biological activity at 5 degrees C intervals. Q10, which ranged from 1.0 to 2.7 (250h), was higher for the lower temperature range (Q10 (15-20 degrees C)>Q10 (20-25 degrees C)) and it was found to be related to the soil properties. Finally, the mineralization process was found to be highly dependent upon the different soil factors, although no simple linear correlation was found between mineralization and soil properties.

Duckweed (Lemna gibba) growth inhibition bioassay for evaluating the toxicity of olive mill wastes before and during composting

Two-phase olive mill waste (TPOMW) is considered the main problem confronting the modern oil extraction and processing industry. Composting has been recently proposed as a suitable method to treat TPOMW so that it is suitable for use in agriculture. In the work reported here, the Lemna gibba bioassay was tested to assess the toxicity of TPOMW before and during the composting process. The method was compared with the Lepidium sativum bioassay and with other chemical maturity indices traditionally reported in the literature. The L. gibba test proved to be a simple, sensitive, and accurate method to evaluate toxicity before and during the composting of TPOMW. Plant growth response was measured by two methods: counting the number of fronds (leaves) and measuring total frond area (TFA) with image analysis software. Compared to the counting of fronds (L. gibba) or seeds (L. sativum), the use of area-measuring software permitted a very rapid, unbiased and easy way of analysing the toxicity of TPOMW before and during composting. Although the accuracy of the frond count method was similar to the traditional cress seed test, data analysis showed that the TFA measurement method was statistically more accurate (significantly lower variance) than the frond count approach. Highly significant correlations were found between TFA and some important maturation indices commonly reported in literature indicating that the L. gibba bioassay can be a useful tool to determine the degree of maturity of TPOMW composts.

Post-transcriptional regulation of cytokine genes in fish: A role for conserved AU-rich elements located in the 3′-untranslated region of their mRNAs

The overproduction of cytokines, such us interleukin-1beta (IL-1beta) and tumor necrosis factor alpha (TNFalpha), contributes to the pathological complications observed in many inflammatory diseases caused by bacterial endotoxins. The synthesis of these cytokines is tightly regulated at both transcriptional and post-transcriptional levels. Post-transcriptional regulation of gene expression depends on specific cis-acting sequences and trans-acting factors. Thus, the presence of adenylate- and uridylate-rich (AU-rich) elements (AREs) has been described in the 3'-untranslated regions (UTRs) of many unstable mammalian mRNAs. Although, it represents the most widespread, phylogenetically conserved and efficient determinant of mRNA stability among those so far characterized in mammalian cells, no studies are available on the functional relevance of this sequence in non-mammalian vertebrates. In this contribution, we study the enzymatic activity of various luciferase reporter constructs, containing or lacking the 3'UTR of IL-1beta and TNFalpha from different fish species, and report the finding that bony fish AREs are able to decrease luciferase activity but are less potent than their mammalian counterparts. Surprisingly, the 3'UTR of the IL-1beta from the cartilaginous fish small spotted catshark had the greatest ability to decrease luciferase activity. Lastly, the functional significance of the above was confirmed by measuring the half-life of IL-1beta and TNFalpha mRNAs in gilthead seabream leukocytes by blocking transcription with actinomycin D. Both cytokine mRNAs were unstable with an estimated half-life of about 45 min in control and activated cells.

An overview on olive mill wastes and their valorisation methods

Olive mill wastes represent an important environmental problem in Mediterranean areas where they are generated in huge quantities in short periods of time. Their high phenol, lipid and organic acid concentrations turn them into phytotoxic materials, but these wastes also contain valuable resources such as a large proportion of organic matter and a wide range of nutrients that could be recycled. In this article, recent research studies for the valorisation of olive mill wastes performed by several authors were reviewed: second oil extraction, combustion, gasification, anaerobic digestion, composting and solid fermentation are some of the methods proposed. Special attention was paid to the new solid waste generated during the extraction of olive oil by the two-phase system. The peculiar physicochemical properties of the new solid waste, called two-phase olive mill waste, caused specific management problems in the olive mills that have led to the adaptation and transformation of the traditional valorisation strategies. The selection of the most suitable or appropriate valorisation strategy will depend on the social, agricultural or industrial environment of the olive mill. Although some methods are strongly consolidated in this sector, other options, more respectful with the environment, should also be considered.

Effects of telomerase and telomere length on epidermal stem cell behavior

A key process in organ homeostasis is the mobilization of stem cells out of their niches. We show through analysis of mouse models that telomere length, as well as the catalytic component of telomerase, Tert, are critical determinants in the mobilization of epidermal stem cells. Telomere shortening inhibited mobilization of stem cells out of their niche, impaired hair growth, and resulted in suppression of stem cell proliferative capacity in vitro. In contrast, Tert overexpression in the absence of changes in telomere length promoted stem cell mobilization, hair growth, and stem cell proliferation in vitro. The effects of telomeres and telomerase on stem cell biology anticipate their role in cancer and aging.

Germline mutational dynamics in myotonic dystrophy type 1 males: allele length and age effects

BACKGROUND

The CTG repeat expansion causing myotonic dystrophy type 1 is unstable in the germline, and frequent intergenerational length changes are observed, giving rise to the unusual genetics of the disorder. The repeat is also somatically unstable, and expanded alleles accumulate throughout life, thus compromising simple measures of intergenerational stability.

OBJECTIVE

To gain a better understanding of the intergenerational dynamics of the DM1 repeat in the male germline.

METHODS

We used sensitive small pool PCR procedures to analyze sperm and somatic DNA from 22 DM1 men of different ages, CTG repeat length, and clinical form.

RESULTS

High levels of repeat length variation heavily biased toward further expansions were observed in the sperm of all DM1 men. Progenitor allele length was revealed as a major modifier of interindividual variation, with the largest length changes observed for premutation and protomutation alleles and the highest frequency of contractions in full mutation alleles. However, despite clear increases in the degree of somatic mosaicism, no differences were observed in replicate sperm samples obtained from two men during a 4-year period.

CONCLUSIONS

Progenitor allele length is a major modifier of the mutational dynamics of the DM1 repeat in the male germline, but surprisingly age is not. Therefore, other as yet unidentified modifiers must be responsible for the considerable residual interindividual variation that cannot be accounted for by these factors.

The use of elemental sulphur as organic alternative to control pH during composting of olive mill wastes

High values of pH may represent a limitation for the agricultural use of the composts, not only when used as soil-less substrate but also as soil amendment in high pH soils. The addition of elemental S during the maturation phase of the composting process was evaluated as suitable method to reduce pH of the composts under the organic agriculture regulations. A compost prepared with two phase olive mill waste (OMW) and sheep litter (SL) was used to study the effect of elemental sulphur addition on the pH of the composting mixture. Initially, different bench scale experiments were designed in order to study the influence of moisture, sulphur concentration, and incubation temperature on the sulphur oxidation rate and thus on the pH of the compost. A concentration of 0.5% in sulphur (dry weight basis) and moisture of 40% were proposed as the optimum conditions to decrease the compost pH by 1.1 units without increasing in EC to levels that may suppose a limitation for its agricultural use. Finally, these optimum experimental conditions found at bench scale were tested at full scale in a commercial composting plant treating the same organic materials by windrowing. The pH values of the composting mixture were reduced by one unit after 2 weeks following the addition of elemental S causing no negative effects on the final compost quality.

The Stigmatella aurantiaca homolog of Myxococcus xanthus high-mobility-group A-type transcription factor CarD: insights into the functional modules of CarD and their distribution in bacteria

Transcriptional factor CarD is the only reported prokaryotic analog of eukaryotic high-mobility-group A (HMGA) proteins, in that it has contiguous acidic and AT hook DNA-binding segments and multifunctional roles in Myxococcus xanthus carotenogenesis and fruiting body formation. HMGA proteins are small, randomly structured, nonhistone, nuclear architectural factors that remodel DNA and chromatin structure. Here we report on a second AT hook protein, CarD(Sa), that is very similar to CarD and that occurs in the bacterium Stigmatella aurantiaca. CarD(Sa) has a C-terminal HMGA-like domain with three AT hooks and a highly acidic adjacent region with one predicted casein kinase II (CKII) phosphorylation site, compared to the four AT hooks and five CKII sites in CarD. Both proteins have a nearly identical 180-residue N-terminal segment that is absent in HMGA proteins. In vitro, CarD(Sa) exhibits the specific minor-groove binding to appropriately spaced AT-rich DNA that is characteristic of CarD or HMGA proteins, and it is also phosphorylated by CKII. In vivo, CarD(Sa) or a variant without the single CKII phosphorylation site can replace CarD in M. xanthus carotenogenesis and fruiting body formation. These two cellular processes absolutely require that the highly conserved N-terminal domain be present. Thus, three AT hooks are sufficient, the N-terminal domain is essential, and phosphorylation in the acidic region by a CKII-type kinase can be dispensed with for CarD function in M. xanthus carotenogenesis and fruiting body development. Whereas a number of hypothetical proteins homologous to the N-terminal region occur in a diverse array of bacterial species, eukaryotic HMGA-type domains appear to be confined primarily to myxobacteria.

Genomic instability in a PARP-1(-/-) cell line expressing PARP-1 DNA-binding domain

Poly(ADP-ribose) polymerase-1 (PARP-1) is a nuclear DNA binding protein that participates in processes involving nicking and resealing DNA strands. A genomically unstable subpopulation of PARP-1(-/-) cells has recently been described, which disappears after stable transfection of the cells with complete PARP-1 cDNA. Here we investigate the role played by PARP-1 in the maintenance of genomic stability, independently of its enzymatic activity. We used a PARP-1-deficient cell line to express a DNA construct encoding the PARP-1 DNA-binding domain (DBD) fragment and one encoding the mutant DBDbd-, defective in binding to DNA strand breaks. We found that, in the absence of DNA damage, expression of DBD or DBDbd- mutant induces increased genomic instability in the PARP-1(-/-) cells. These results suggest that the DBD fragment of PARP-1, apart from its classical role of nick detection and DNA binding, is likely to participate in molecular complexes with proteins involved in genomic integrity.

Very large (CAG)(n) DNA repeat expansions in the sperm of two spinocerebellar ataxia type 7 males

Genetic anticipation, i.e. increasing disease severity and decreasing age of onset from one generation to the next, is observed in a number of diseases, including myotonic dystrophy type 1, Huntington's disease and several of the spinocerebellar ataxias. All of these disorders are associated with the expansion of a trinucleotide repeat and array length is positively correlated with disease severity and inversely correlated with the age of onset. The expanded repeat is highly unstable and continues to expand from one generation to the next, providing a molecular explanation for anticipation. Spinocerebellar ataxia type 7 (SCA7) is one of the latest additions to the list of triplet repeat diseases and is distinct from the other SCAs in that it is accompanied by retinal degeneration. Pedigree analyses have previously revealed that the SCA7 repeat is highly unstable and liable to expand, in particular when transmitted by a male. Surprisingly, though, an under-representation of male transmission has also been reported. We now demonstrate directly by single molecule analyses that the expanded repeat is extraordinarily unstable in the male germline and biased toward massive increases. Nearly all of the mutant sperm of two SCA7 males contain alleles that are so large that most of the affected offspring would at best have a severe infantile form of the disease. Indeed, the gross under-representation of such very large expanded alleles in patients suggests that a significant proportion of such alleles might be associated with embryonic lethality or dysfunctional sperm.

High mobility group I(Y)-like DNA-binding domains on a bacterial transcription factor

The bacterium Myxococcus xanthus responds to blue light by producing carotenoids. It also responds to starvation conditions by developing fruiting bodies, where the cells differentiate into myxospores. Each response entails the transcriptional activation of a separate set of genes. However, a single gene, carD, is required for the activation of both light- and starvation-inducible genes. Gene carD has now been sequenced. Its predicted amino acid sequence includes four repeats of a DNA-binding domain present in mammalian high mobility group I(Y) proteins and other nuclear proteins from animals and plants. Other peptide stretches on CarD also resemble functional domains typical of eukaryotic transcription factors, including a very acidic region and a leucine zipper. High mobility group yI(Y) proteins are known to bind the minor groove of A+T-rich DNA. CarD binds in vitro an A+T-rich element that is required for the proper operation of a carD-dependent promoter in vivo.