Spent coffee grounds as a suitable alternative to standard soil in ecotoxicological tests

Eisenia andrei is considered in OECD and ISO guidelines to be a suitable replacement for Eisenia fetida in ecotoxicological assays. This suggests that other alternative materials and methods could also be used in standard procedures for toxicity testing. The guidelines also favor using less time-consuming procedures and reducing costs and other limitations to ecotoxicological assessments. In recent years, spent coffee grounds (SCG) have been used to produce vermicompost and biochar and as an additive to organic fertilizers. In addition, the physicochemical characteristics of SCG indicate that the material is a suitable substrate for earthworms, with the organisms performing as well as in natural soil. In the present study, a battery of ecotoxicological tests was established with unwashed and washed SCG and a natural reference soil (LUFA 2.2). The test substrates were spiked with different concentrations of silver nitrate. Survival and reproduction of the earthworm E. andrei were assessed under different conditions, along with substrate basal respiration (SBR) as a proxy for microbial activity. Seedling emergence and the germination index of Lepidium sativum were also determined, following standard guidelines. Exposure to silver nitrate had similar effects on earthworm survival and reproduction, as the estimated effective concentrations (EC10 and EC50) in unwashed SCG and LUFA 2.2 overlapped. A hormetic effect was observed for SBR in LUFA 2.2 spiked with 12.8 mg/kg but not in unwashed SCG. Both SBR and root development were inhibited by similar concentrations of silver nitrate in washed SCG. The findings indicate that unwashed SCG could potentially be used as a substrate in E. andrei toxicity tests and support the eventual inclusion of this material in the standard guidelines.

Changes in the microbiota during biological treatment of palm oil mill waste: A critical review

Palm oil mill waste has a complex cellulosic structure, is rich in nutrients, and provides a habitat for diverse microbial communities. Current research focuses on how the microbiota and organic components interact during the degradation of this type of waste. Some recent studies have described the microbial communities present in different biodegradation processes of palm oil mill waste, identifying the dominant bacteria/fungi responsible for breaking down the cellulosic components. However, understanding the degradation process's mechanisms is vital to eliminating the need for further pretreatment of lignocellulosic compounds in the waste mixture and facilitating the commercialization of palm oil mill waste treatment technology. Thus, the present work aims to review microbial community dynamics via three biological treatment systems comprehensively: composting, vermicomposting, and dark fermentation, to understand how inspiration from nature can further enhance existing degradation processes. The information presented could be used as an umbrella to current research on biological treatment processes and specific research on the bioaugmentation of indigenous microbial consortia isolated during the biological degradation of palm oil mill waste.

Influence of earthworms on the microbial properties and extracellular enzyme activities during vermicomposting of raw and distilled grape marc

The treatment of winery wastes by using appropriate management technologies is of utmost need in order to reduce to a minimum their disposal and avoid negative environmental impacts. This is of particular interest for grape marc, the main solid by-product of the winery industry. However, comparative studies on a pilot-scale dealing with the impact of earthworms on marc derived from both red and white grape varieties during vermicomposting are still scarce. The present study sought to evaluate the changes in the biochemical and microbiological properties of red and white raw marc in the presence and the absence of the earthworm species Eisenia andrei. The distilled marc obtained through distillation of the red grape marc was also considered under this scenario. Samples were taken after 14, 28, 42, and 63 days of vermicomposting. On day 14 earthworms led to a pronounced increase in most of the enzymatic activities, but only in those vermireactors fed with raw marc from the red grape variety. Alfa- and beta-glucosidase as well as chitinase and leucine-aminopeptidase activities were between 3 to 5-times higher relative to the control, while alkaline phosphomonoesterase was even up to 14-fold higher with earthworm presence. From day 28 onwards the magnitude of earthworms' effect on the studied enzymes was also dependent on the type of grape marc. Reduced values of basal respiration, ranging between 200 and 350 mg CO₂ kg OM h^-1 and indicative of stabilized materials were found in the resulting vermicomposts. Moreover, the content of macro- and micronutrients in the end products matched with those considered to have the quality criteria of a good vermicompost. Altogether, these findings reinforce the effectiveness of vermicomposting for the biological stabilization of grape marc with the dual purpose of fertilizer production and environmental protection.

A single-center comparison of our initial experiences in treating penile and urethral cancer with video-endoscopic inguinal lymphadenectomy (VEIL) and later experiences in melanoma cases

Background

Video-endoscopic inguinal lymphadenectomy (VEIL) is a minimally invasive approach that is increasingly indicated in oncological settings, with mounting evidence for its long-term oncological safety.

Objectives

To present our single-center experience of treating penile and urethral cancer with VEIL, as well as its more recent application in melanoma patients.

Methods

We prospectively recorded our experiences with VEIL from September 2010 to July 2018, registering the patient primary indication, surgical details, complications, and follow-up.

Results

Twenty-nine patients were operated in one (24) or both (5) groins; 18 had penile cancer, 1 had urethral cancer, and 10 had melanoma. A mean 8.62 ± 4.45 lymph nodes were removed using VEIL and of these, an average of 1.00 ± 2.87 were metastatic; 16 patients developed lymphocele and 10 presented some degree of lymphedema; there were no skin or other major complications. The median follow-up was 19.35 months; there were 3 penile cancer patient recurrences in the VEIL-operated side. None of the melanoma patients presented a lymphatic inguinal recurrence.

Conclusions

VEIL is a minimally invasive technique which appears to be oncologically safe showing fewer complications than open surgery. However, complications such as lymphorrhea, lymphocele, or lymphedema were not diminished by using VEIL.

Three in one: molecular phylogeny of the genus Helodrilus (Crassiclitellata: Lumbricidae) with a description of two new genera and two new species

The earthworm genus Helodrilus comprises about 20 species with distributions ranging from the Iberian Peninsula to the Caucasus, through Central Europe, the Balkans, Anatolia and the Levant. The species prefer moist habitats and are often found in the mud of river banks, in swamps or in caves. Although a high degree of morphological variability is observed in the taxonomic characters, the genus shares a common feature: the absence of nephridial bladders. In this study, we clarify the phylogeny and taxonomy of the genus Helodrilus using an integrated approach including a multilocus molecular phylogenetic analysis and thorough morphological examination of several species across the putative Helodrilus area of distribution. The findings of this study have led to the genus Helodrilus being split and to the description of two new genera and two new species: Coventina Szederjesi, Sarbu & Csuzdi gen. nov. and Imetescolex movilensis Szederjesi, Sarbu & Csuzdi gen. & sp. nov. The highly homoplasic nature of the absence of nephridial bladders was also revealed.

Host taxonomy determines the composition, structure, and diversity of the earthworm cast microbiome under homogenous feeding conditions

Host evolutionary history is a key factor shaping the earthworm cast microbiome, although its effect can be shadowed by the earthworm's diet. To untangle dietary from taxon effects, we raised nine earthworm species on a uniform diet of cow manure and compared cast microbiome across species while controlling for diet. Our results showed that, under controlled laboratory conditions, earthworm microbiomes are species-specific, more diverse than that of the controlled diet, and mainly comprised of native bacteria (i.e., not acquired from the diet). Furthermore, diet has a medium to large convergence effect on microbiome composition since earthworms shared 16 to 74% of their bacterial amplicon sequence variants (ASV). The inter-species core microbiome included 10 ASVs, while their intra-species core microbiomes were larger and varied in ASV richness (24-48%) and sequence abundance across earthworm species. This specificity in core microbiomes and variable degree of similarity in bacterial composition suggest that phylosymbiosis could determine earthworm microbiome assembly. However, lack of congruence between the earthworm phylogeny and the microbiome dendrogram suggests that a consistent diet fed over several generations may have weakened potential phylosymbiotic effects. Thus, cast microbiome assembly in earthworms seem to be the result of an interplay among host phylogeny and diet.

Comparative Analysis of Metagenomics and Metataxonomics for the Characterization of Vermicompost Microbiomes

The study of microbial communities or microbiotas in animals and environments is important because of their impact in a broad range of industrial applications, diseases and ecological roles. High throughput sequencing (HTS) is the best strategy to characterize microbial composition and function. Microbial profiles can be obtained either by shotgun sequencing of genomes, or through amplicon sequencing of target genes (e.g., 16S rRNA for bacteria and ITS for fungi). Here, we compared both HTS approaches at assessing taxonomic and functional diversity of bacterial and fungal communities during vermicomposting of white grape marc. We applied specific HTS workflows to the same 12 microcosms, with and without earthworms, sampled at two distinct phases of the vermicomposting process occurring at 21 and 63 days. Metataxonomic profiles were inferred in DADA2, with bacterial metabolic pathways predicted via PICRUSt2. Metagenomic taxonomic profiles were inferred in PathoScope, while bacterial functional profiles were inferred in Humann2. Microbial profiles inferred by metagenomics and metataxonomics showed similarities and differences in composition, structure, and metabolic function at different taxonomic levels. Microbial composition and abundance estimated by both HTS approaches agreed reasonably well at the phylum level, but larger discrepancies were observed at lower taxonomic ranks. Shotgun HTS identified ~1.8 times more bacterial genera than 16S rRNA HTS, while ITS HTS identified two times more fungal genera than shotgun HTS. This is mainly a consequence of the difference in resolution and reference richness between amplicon and genome sequencing approaches and databases, respectively. Our study also revealed great differences and even opposite trends in alpha- and beta-diversity between amplicon and shotgun HTS. Interestingly, amplicon PICRUSt2-imputed functional repertoires overlapped ~50% with shotgun Humann2 profiles. Finally, both approaches indicated that although bacteria and fungi are the main drivers of biochemical decomposition, earthworms also play a key role in plant vermicomposting. In summary, our study highlights the strengths and weaknesses of metagenomics and metataxonomics and provides new insights on the vermicomposting of white grape marc. Since both approaches may target different biological aspects of the communities, combining them will provide a better understanding of the microbiotas under study.

Composition, Structure and Diversity of Soil Bacterial Communities before, during and after Transit through the Gut of the Earthworm Aporrectodea caliginosa

Earthworms heavily modify the soil microbiome as it passes throughout their guts. However, there are no detailed studies describing changes in the composition, structure and diversity of soil microbiomes during gut transit and once they are released back to the soil as casts. To address this knowledge gap, we used 16S rRNA next-generation sequencing to characterize the microbiomes of soil, gut and casts from the earthworm Aporrectodea caliginosa. We also studied whether these three microbiomes are clearly distinct in composition or can be merged into metacommunities. A large proportion of bacteria was unique to each microbiome—soil (82%), gut (89%) and casts (75%), which indicates that the soil microbiome is greatly modified during gut transit. The three microbiomes also differed in alpha diversity, which peaked during gut transit and decreased in casts. Furthermore, gut transit also modified the structure of the soil microbiome, which clustered away from those of the earthworm gut and cast samples. However, this clustering pattern was not supported by metacommunity analysis, which indicated that soil and gut samples make up one metacommunity and cast samples another. These results have important implications for understanding the dynamics of soil microbial communities and nutrient cycles.

Establishment of the upstream processing for renewable production of hydrogen using vermicomposting-tea and molasses as substrate

This study aimed to establish the optimal operational conditions for hydrogen production using vermicomposting-tea and sugarcane molasses as substrate. The experiments were carried out by triplicate in 110 ml serological bottles, a Box-Behnken design of experiments was performed in anaerobic dark conditions. The maximal hydrogen production (HP), hydrogen production rate (HPR), and hydrogen yield (HY) attained were 1021.0 mlL^-1, 5.32 mlL^-1h^-1, and 60.3 mlL_H2^-1/g_TCC, respectively. The statistical model showed that the optimal operational conditions for pH, molasses concentration, and temperature were 6.5; 30 % (v/v) and 25 °C. The bioreactor run showed 17.202 L of hydrogen, 0.58 Lh^-1, and 77.2 ml_H2g_TCC^-1 For HP, HPR, and HY. Chemometric analysis for the volatile fatty acids obtained at the fermentation showed that only two principal components are required to explain 90 % of the variance. The representative pathways for hydrogen production were acetic and butyric acids. This study established the operational conditions for the upstream processing amenable to pilot and industrial-scale operations. Our results add value to molasses within the circular economy for hydrogen production using a novel consortium from vermicompost.

Vermicomposting of cow manure: Effect of time on earthworm biomass and chemical, physical, and biological properties of vermicompost

Vermicomposting is a biological process for efficient cattle manure treatment, but the vermicomposting time determines the quality of the vermicompost. The objective of this study was to evaluate the effect of cattle manure vermicomposting time on earthworm biomass and the changes in physical, chemical, and biological in properties of the vermicompost. The cattle manure was inoculated with Eisenia andrei earthworms and conducted vermicomposting for 0, 15, 30, 45, 60, and 120 days. The analysis of 44 chemical, physical, and biological properties allowed the vermicomposting process to be divided into initial (<45 days) and final (45-120 days) phases. The initial phase was characterized by high microbial activity and the final by high physical-chemical transformation of the vermicompost and an increase in earthworm density. The organic matter aromaticity increased until the 45th day, subsequently decreasing. Although 30 d of vermicompost are sufficient to obtain a high-quality organic fertilizer, 120 d are necessary for producing matrices.

Bacterial Succession during Vermicomposting of Silver Wattle (Acacia dealbata Link)

Vermicomposting is the process of organic waste degradation through interactions between earthworms and microbes. A variety of organic wastes can be vermicomposted, producing a nutrient-rich final product that can be used as a soil biofertilizer. Giving the prolific invasive nature of the Australian silver wattle Acacia dealbata Link in Europe, it is important to find alternatives for its sustainable use. However, optimization of vermicomposting needs further comprehension of the fundamental microbial processes. Here, we characterized bacterial succession during the vermicomposting of silver wattle during 56 days using the earthworm species Eisenia andrei. We observed significant differences in α- and β-diversity between fresh silver wattle (day 0) and days 14 and 28, while the bacterial community seemed more stable between days 28 and 56. Accordingly, during the first 28 days, a higher number of taxa experienced significant changes in relative abundance. A microbiome core composed of 10 amplicon sequence variants was identified during the vermicomposting of silver wattle (days 14 to 56). Finally, predicted functional profiles of genes involved in cellulose metabolism, nitrification, and salicylic acid also changed significantly during vermicomposting. This study, hence, provides detailed insights of the bacterial succession occurring during vermicomposting of the silver wattle and the characteristics of its final product as a sustainable plant biofertilizer.

Changes in the nutrient dynamics and microbiological properties of grape marc in a continuous-feeding vermicomposting system

Finding strategies to reuse and treat organic wastes is of utmost need. Biological processes offer the possibility to transform them into safer end products with benefits for both agriculture and the environment. Moreover, it represents an ecologically-sound and economically attractive alternative to landfill disposal and incineration. In this work, we evaluated the feasibility of vermicomposting to treat and process grape marc, the main solid by-product of the wine industry. The long-term changes in grape marc derived from both white and red winemaking processes were assessed throughout the process of vermicomposting from a physico-chemical and microbiological perspective. New layers of fresh marc were added sequentially in the presence and absence of earthworms (Eisenia andrei) forming an age gradient during a 42-week period. An optimal moisture level of 70% was maintained over the course of the process. The pH fell within weak-alkaline levels through the layerś profile and the electrical conductivity was between 200 and 300 µS cm^-1, providing optimum conditions for earthworm growth. The mass loss caused by earthworm activity led to an increased content of macro- and micronutrients at the end of the trial. An overall decrease in microbial biomass and its activity, indicative of a stabilised material, was also recorded with depth of layer. Altogether, this points to vermicomposting as a suitable management system for processing grape marc with a dual purpose, that is fertilizer production and environment protection. This is especially relevant in the current attempts to reach a fully circular economy.

Gut microbiome and telomere length in gull hatchlings

In many animals, recent evidence indicates that the gut microbiome may be acquired during early development, with possible consequences on newborns' health. Thus, it has been hypothesized that a healthy microbiome protects telomeres and genomic integrity against cellular stress. However, the link between the early acquired microbiome and telomere dynamics has not hitherto been investigated. In birds, this link may also be potentially modulated by the transfer of maternal glucocorticoids, since these substances dysregulate microbiome composition during postnatal development. Here, we examined the effect of the interplay between the microbiome and stress hormones on the telomere length of yellow-legged gull hatchlings by using a field experiment in which we manipulated the corticosterone content in eggs. We found that the hatchling telomere length was related to microbiome composition, but this relationship was not affected by the corticosterone treatment. Hatchlings with a microbiome dominated by potential commensal bacteria (i.e. Catellicoccus and Cetobacterium) had larger telomeres, suggesting that an early establishment of the species-specific microbiome during development may have important consequences on offspring health and survival.

Systematic revision of Gatesona (Crassiclitellata, Lumbricidae), an endemic earthworm genus from the Massif Central (France)

The Massif Central in France could potentially harbor numerous ancient endemic lineages owing to its long history of continuous geological stability. Several endemic earthworm species inhabit the area, with Allolobophora (Gatesona) chaetophora, Helodrilus (Acystodrilus) and Avelona ligra showing hints of a common evolutionary origin. However, the phylogenetic relationships and taxonomic status of the species remain to be studied through integrative molecular and morphological methods. To this end, eight species including most of the known species and subspecies of All. (Gatesona), Helodrilus (Acystodrilus) musicus, and Avelona ligra were sequenced for a set of five molecular markers. The species were grouped on the basis of the molecular findings in a phylogenetic framework. All. (Gatesona) was included within the same clade as Helodrilus (Acystodrilus) and Avelona, separated from Allolobophora sensu stricto, supporting its status as a good genus. Branch lengths and average pairwise genetic distances suggested the subspecies of All. (Gatesona) chaetophora examined should be considered species-level taxa. Thus, a generic diagnosis for Gatesona stat. nov. is provided, along with redescriptions of Gatesona chaetophora comb. nov., Gatesona rutena comb. nov. stat. nov., Gatesona lablacherensis comb. nov. stat. nov. and Gatesona serninensis comb. nov. stat. nov. The study findings highlight the need for further sampling of earthworm diversity in the Massif Central (and Southern France), in addition to an increased focus on the Eastern European species of Helodrilus.

Complexities underlying the breeding and deployment of Dutch elm disease resistant elms

Dutch elm disease (DED) is a vascular wilt disease caused by the pathogens Ophiostoma ulmi and Ophiostoma novo-ulmi with multiple ecological phases including pathogenic (xylem), saprotrophic (bark) and vector (beetle flight and beetle feeding wound) phases. Due to the two DED pandemics during the twentieth century the use of elms in landscape and forest restoration has declined significantly. However new initiatives for elm breeding and restoration are now underway in Europe and North America. Here we discuss complexities in the DED 'system' that can lead to unintended consequences during elm breeding and some of the wider options for obtaining durability or 'field resistance' in released material, including (1) the phenotypic plasticity of disease levels in resistant cultivars infected by O. novo-ulmi; (2) shortcomings in test methods when selecting for resistance; (3) the implications of rapid evolutionary changes in current O. novo-ulmi populations for the choice of pathogen inoculum when screening; (4) the possibility of using active resistance to the pathogen in the beetle feeding wound, and low attractiveness of elm cultivars to feeding beetles, in addition to resistance in the xylem; (5) the risk that genes from susceptible and exotic elms be introgressed into resistant cultivars; (6) risks posed by unintentional changes in the host microbiome; and (7) the biosecurity risks posed by resistant elm deployment. In addition, attention needs to be paid to the disease pressures within which resistant elms will be released. In the future, biotechnology may further enhance our understanding of the various resistance processes in elms and our potential to deploy trees with highly durable resistance in elm restoration. Hopefully the different elm resistance processes will prove to be largely under durable, additive, multigenic control. Elm breeding programmes cannot afford to get into the host-pathogen arms races that characterise some agricultural host-pathogen systems.

Sorry atlanticus, you are not my type: molecular assessment splits Zophoscolex (Lumbricidae: Crassiclitellata) into French and Iberian genera

Molecular phylogenetics contributes to making important advances in the challenging field of earthworm taxonomy. Use of this type of analysis has enabled clarification of the phylogenetic relationships between early-branching genera of Lumbricidae within the highly diverse Franco-Iberian realm. However, molecular phylogenetic studies of the genus Zophoscolex are scarce and have led to taxonomic uncertainty due to insufficient sampling and the absence of the type species, Z. atlanticus, from such studies. The present study investigated 11 species of Zophoscolex (including Z. atlanticus), and the phylogenetic relationships were deduced from seven molecular markers (COI, COII, 16S, tRNAs, ND1, 12S, 28S) by Bayesian and maximum likelihood inference. The findings show that species of Zophoscolex did not belong to a single clade. Zophoscolex atlanticus was placed in a clade with Z. micellus, Z. graffi and Ethnodrilus zajonci. Other species of the genus were found to belong to the genera Cataladrilus and Compostelandrilus. Finally, most of the Iberian species form a distinct clade, which was formally described as the revised genus Castellodrilus. Based on these findings, Zophoscolex is restricted to French representatives. These results highlight the importance of incorporating type species in molecular phylogenetic analyses in order to reconcile taxonomy and systematics.

Pituitary Abscess: Two Case Reports and Review of the Literature

Pituitary abscesses are infrequent entities, often forgotten and hence rarely included in the differential diagnosis of sellar lesions. However, given that they share the clinical manifestations of other more common pathologies in this region, the treatment of pituitary abscesses is usually performed correctly without demonstrating a relevant delay in therapeutic decisions when surgical options are considered as the alternative of choice. Two patients with intrasellar expansive processes and endocrinological alterations who were diagnosed intraoperatively as having pituitary abscesses are presented. In both cases, transsphenoidal surgery was performed; adjuvant antibiotic treatment was established for just one of them. Both patients are currently without symptoms due to mass-effect; one of the patients continues exhibiting residual endocrinological alteration and no signs of relapse in imaging studies.

Unraveling the environmental impacts of bioactive compounds and organic amendment from grape marc

In a society that produces large amounts of solid waste, the search for new methods of valorisation has led to the development of techniques that make it possible to obtain new products from waste. In the case of bio-waste, biological treatment such as anaerobic digestion or composting appear to be suitable options for producing bio-energy or bio-fertilizers respectively. Vermicomposting is a method of converting solid organic waste into resources through bio-oxidation and stabilization of the organic waste by earthworms. The purpose of this study is to establish the environmental impacts of a complete route for the valorisation of grape pomace in order to identify environmental hotspots. In this valorisation route, different value-added products are produced with potential application in the cosmetic, food and pharmaceutical sectors. Priority was given to the use of primary data in the elaboration of the data inventories needed to perform the life cycle assessment (LCA). The main findings from this study reported that the energy requirement of the distillation process is an important hot spot of the process. Although the valorisation route has some poor results in terms of the two environmental indicators (carbon footprint and normalised impact index), when economic revenues were included in this analysis, its environmental performance was better than that of other alternatives for bio-waste recovery.

Effectiveness of vermicomposting for bioconversion of grape marc derived from red winemaking into a value-added product

Grape marc, the main solid by-product of the wine industry, can be used as a nutrient-rich organic amendment if treated appropriately before its application into soil. In this study, we evaluated the potential of vermicomposting to process grape marc derived from the red winemaking of Mencía grapes in order to yield a high-quality, polyphenol-free organic vermicompost that could be used as an environmentally friendly fertiliser. We observed that the grape marc from this cultivar appears to be an optimum substrate for feeding earthworms providing optimum conditions for growth and reproduction, and sufficient energy to sustain large populations. Moreover, earthworm activity favoured the stabilisation of the grape marc resulting in a final vermicompost characterised by a higher concentration of macro- and micro-nutrients and a reduced polyphenol content after 112 days of vermicomposting. Lower values of microbial activity, indicative of stabilised materials, were recorded at the end of the process. These findings highlight vermicomposting as an environmentally sound management system for processing grape marc that could easily be scaled up for industrial application.

Expression of Siglec-1, -3, -5 and -10 in porcine cDC1 and cDC2 subsets from blood, spleen and lymph nodes and functional capabilities of these cells

Dendritic cells are professional antigen-presenting cells that play a critical role in the development of immune responses. DCs express a variety of Siglecs on their surface, which play a regulatory role modulating their activation through interaction with sialylated structures expressed by cells or pathogens. Here, we characterized the phenotype of porcine conventional dendritic cells subsets from blood, spleen and lymph nodes, emphasizing the analysis of the expression of Siglecs. Siglec-1 was detected in type 1 cDC and, at lower levels, in type 2 cDC in the spleen, being low to negative in blood and lymph node cDC. Siglec-3 and Siglec-5 were expressed in cDC1 at lower levels than in cDC2. Porcine cDCs did not express Siglec-10. cDC2 showed a higher capacity to phagocytose microspheres and to process DQ™-OVA than cDC1, but none of these functions was affected by engagement of Siglec-3 and -5 with antibodies on blood cDC.

Data-Driven Computational Simulation in Bone Mechanics

The data-driven approach was formally introduced in the field of computational mechanics just a few years ago, but it has gained increasing interest and application as disruptive technology in many other fields of physics and engineering. Although the fundamental bases of the method have been already settled, there are still many challenges to solve, which are often inherently linked to the problem at hand. In this paper, the data-driven methodology is applied to a particular problem in tissue biomechanics, a context where this approach is particularly suitable due to the difficulty in establishing accurate and general constitutive models, due to the intrinsic intra and inter-individual variability of the microstructure and associated mechanical properties of biological tissues. The problem addressed here corresponds to the characterization and mechanical simulation of a piece of cortical bone tissue. Cortical horse bone tissue was mechanically tested using a biaxial machine. The displacement field was obtained by means of digital image correlation and then transformed into strains by approximating the displacement derivatives in the bone virtual geometric image. These results, together with the approximated stress state, assumed as uniform in the small pieces tested, were used as input in the flowchart of the data-driven methodology to solve several numerical examples, which were compared with the corresponding classical model-based fitted solution. From these results, we conclude that the data-driven methodology is a useful tool to directly simulate problems of biomechanical interest without the imposition (model-free) of complex spatial and individually-varying constitutive laws. The presented data-driven approach recovers the natural spatial variation of the solution, resulting from the complex structure of bone tissue, i.e. heterogeneity, microstructural hierarchy and multifactorial architecture, making it possible to add the intrinsic stochasticity of biological tissues into the data set and into the numerical approach.

Activation of pro- and anti-inflammatory responses in lung tissue injury during the acute phase of PRRSV-1 infection with the virulent strain Lena

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Lena virulent strain caused an increase in sera levels of IFN-γ and IL-6.

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Lung viral load and PRRSV-N-protein⁺ cells were inversely correlated with CD163⁺ macrophages in the lung.

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CD14⁺ cells infiltrated interstitium to possibly replenish macrophages subsets.

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Lena-induced microscopic lung injury was linked to an increase of iNOS⁺ cells.

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The increase of CD200R1⁺ and FoxP3⁺ cells was associated with the course of lung injury.

Porcine reproductive and respiratory syndrome virus (PRRSV) plays a key role in porcine respiratory disease complex modulating the host immune response and favouring secondary bacterial infections. Pulmonary alveolar macrophages (PAMs) are the main cells supporting PRRSV replication, with CD163 as the essential receptor for viral infection. Although interstitial pneumonia is by far the representative lung lesion, suppurative bronchopneumonia is described for PRRSV virulent strains. This research explores the role of several immune markers potentially involved in the regulation of the inflammatory response and sensitisation of lung to secondary bacterial infections by PRRSV-1 strains of different virulence. Conventional pigs were intranasally inoculated with the virulent subtype 3 Lena strain or the low virulent subtype 1 3249 strain and euthanised at 1, 3, 6 and 8 dpi. Lena-infected pigs exhibited more severe clinical signs, macroscopic lung score and viraemia associated with an increase of IL-6 and IFN-γ in sera compared to 3249-infected pigs. Extensive areas of lung consolidation corresponding with suppurative bronchopneumonia were observed in Lena-infected pigs. Lung viral load and PRRSV-N-protein⁺ cells were always higher in Lena-infected animals. PRRSV-N-protein⁺ cells were linked to a marked drop of CD163⁺ macrophages. The number of CD14⁺ and iNOS⁺ cells gradually increased along PRRSV-1 infection, being more evident in Lena-infected pigs. The frequency of CD200R1⁺ and FoxP3⁺ cells peaked late in both PRRSV-1 strains, with a strong correlation between CD200R1⁺ cells and lung injury in Lena-infected pigs. These results highlight the role of molecules involved in the earlier and higher extent of lung lesions in piglets infected with the virulent Lena strain, pointing out the activation of routes potentially involved in the restraint of the local inflammatory response.

Temporal Dynamics of Bacterial Communities in a Pilot-Scale Vermireactor Fed with Distilled Grape Marc

Vermicomposting has been found as a profitable approach to dispose of and treat large quantities of raw grape marc. However, less information is available with regard to its efficiency for treating distillery winery byproducts, even though distillation has been widely used as a way to economically valorize grape marc. As such, we sought to characterize the compositional and functional changes in bacterial communities during vermicomposting of distilled grape marc by using 16S rRNA high-throughput sequencing. Samples were collected at the initiation of vermicomposting and at days 14, 21, 28, 35 and 42. There were significant changes (p < 0.0001) in the bacterial community composition of distilled grape marc after 14 days of vermicomposting that were accompanied by twofold increases in bacterial richness and diversity from a taxonomic and phylogenetic perspective. This was followed by significant increases in functional diversity of the bacterial community, including metabolic capacity, lignin and cellulose metabolism, and salicylic acid synthesis. These findings indicate that the most striking compositional and functional bacterial community changes took place during the active phase of the process. They also pinpoint functional attributes that may be related to the potential beneficial effects of distilled grape marc vermicompost when applied on soil and plants.

Comparison of the viscoelastic properties of human abdominal and breast adipose tissue and its incidence on breast reconstruction surgery. A pilot study

BACKGROUND

Breast cancer is the leading malignant tumor in women in the world. Reconstruction after mastectomy plays a key role in the physical and psychological recuperation, being the abdominal skin and adipose tissue the best current option for the DIEP surgery. The aim of the surgery is to obtain a reconstructed breast which looks and behaves naturally. Therefore, it would be useful to characterize the mechanical behaviour of the adipose tissue in the abdomen and breast to compare their mechanical properties, also investigating possible regional differences.

METHODS

Experimental tests have been carried out in breast and abdominal adipose tissue samples, obtaining their viscoelastic properties. The specimens have been subjected to uniaxial compression relaxation tests and a mechanical behaviour model has been fitted to the experimental curves. Afterwards, statistical analyses have been used to detect differences between different individuals' abdominal fat tissue and finally between different areas of the same individual's breast and abdominal adipose tissue.

FINDINGS

Several conclusions could be extracted from the results: 1) inter-individual differences may exist in the abdominal adipose tissue; 2) the breast fat could be regarded as a unique tissue from the mechanical point of view; 3) significant differences were detected between the superficial breast and all the locations of the abdomen, except for the superficial lateral one and 4) the mechanical properties of the abdominal adipose tissue seem to change with the depth. These conclusions can be of great value for DIEP surgeries and other surgeries in which the adipose tissue is involved.

Exploring the potential enzymatic bioremediation of vermicompost through pesticide-detoxifying carboxylesterases

Vermicompost is a known biofertilizer of potential use in soil bioremediation. This study was undertaken to explore the capacity of grape marc-derived vermicompost to inactivate methyl carbamate (MC) and organophosphorus (OP) pesticides via exploring the carboxylesterase (CE) activity level and its response to pesticide exposure. We first optimized the method for enzyme activity assay comparing the CE activity in two contrasting homogenization procedures (30-min mixing and mortar grinding). Thereafter, we assessed the sensitivity of the enzyme by both in vitro and vermicompost incubation trials with selected pesticides. The main findings can be summarized as follows: i) grinding the vermicompost in water (2% w/v) yielded maximum enzyme activity; ii) at concentrations around 10^-4 M, highly toxic oxygen-analog metabolites of OPs strongly inhibited the CE activity (76-93% inhibition), but MC did not inhibit the enzyme activity; iii) liquid vermicompost was able to degrade chlorpyrifos and inactivate its highly toxic metabolite chlorpyrifos-oxon. Our results suggest that liquid vermicompost is the most appropriate preparation to increase the enzymatic potential of vermicompost in pesticide-contaminated soils.

Analysis of the expression of porcine CD200R1 and CD200R1L by using newly developed monoclonal antibodies

CD200R1 and CD200R1-like are paired receptors which modulate activation of immune cells. Here, we describe the characterisation of their porcine homologues. Analysis of database porcine sequences shows an exceptionally high homology between the extracellular Ig-like domains of these receptors, being the rest more dissimilar. We have obtained two mAbs, PCT1 and PCT3, against a CD200R1-Fc recombinant protein, that bind on CHO cells expressing GFP-tagged CD200R1. The specificity of these mAbs was analysed on CD200R1 L, and also on a CD200R1 splicing variant that lacks the V-type Ig domain. PCT1 bound to both CD200R1 and CD200R1L, but not to the splicing variant, what suggests that recognises an epitope in the V-type Ig domain. PCT3 reacted with both CD200R1 variants, but not CD200R1L, probably binding to an epitope in the N-terminal sequence of CD200R1. Analysis of porcine cells with these mAbs showed expression of CD200R1/CD200R1L on B cells, monocytes and alveolar macrophages.

Changes in the composition and function of bacterial communities during vermicomposting may explain beneficial properties of vermicompost

Vermicomposting is the process by which organic waste is broken down through the synergistic actions of earthworms and microbial communities. Although vermicomposting has been shown to effectively reduce organic biomass and generate high-quality fertilizer for plants, little is known about the bacterial communities that are involved in this decomposition process. Since optimization of vermicomposting for commercial use necessitates additional knowledge of the underlying biological processes, this study sought to characterize the bacterial succession involved in the vermicomposting of Scotch broom (Cytisus scoparius), a leguminous shrub that has become invasive around the world with consequences for the dynamics and productivity of the ecosystems they occupy. Scotch broom was processed in a pilot-scale vermireactor for 91 days with the earthworm species Eisenia andrei. Samples were taken at the initiation of vermicomposting, and days 14, 42 and 91, representing both active and mature stages of vermicomposting. Significant changes (P < 0.0001) in the bacterial community composition (richness and evenness) were observed throughout the process. Increases in taxonomic diversity were accompanied by increases in functional diversity of the bacterial community, including metabolic capacity, streptomycin and salicylic acid synthesis, and nitrification. These results highlight the role of bacterial succession during the vermicomposting process and provide evidence of microbial functions that may explain the beneficial effects of vermicompost on soil and plants.

Strategies for recycling and valorization of grape marc

Grapes are one of the most cultivated fruit crops worldwide. Either for wine or juice production, grape processing generates a large amount of residues that must be treated, disposed of or reused properly to reduce their pollution load before being applied to the soil. In this review, a special focus is given to the treatment and valorization of the winemaking by-product like grape marc via anaerobic digestion, composting and vermicomposting at laboratory, pilot, and industrial scales. The impact of the final products (digestates, composts, and vermicomposts) on soil properties is briefly addressed. Moreover, the role of grape marc and seeds as a valuable source of natural phytochemicals that include polyphenols and other bioactive compounds of interest for pharmaceutical, cosmetic, and food industries is also discussed. This is of paramount importance given the fact that sustainability requires the use of management and valorization strategies that allow the recovery of valuable compounds (e.g. antioxidants) with minimum disposal of waste streams.

Use of IP-10 detection in dried plasma spots for latent tuberculosis infection diagnosis in contacts via mail

The aim of this study was to test the use of IP-10 detection in dried plasma from contact studies individuals (contacts of smear positive patients), by comparing it with IP-10 and IFN-γ detection in direct plasma, to establish IP-10 detection in DPS as a useful assay for LTBI diagnosis. Whole blood samples were collected from 80 subjects: 12 with active tuberculosis (TB), and 68 from contact studies. The amount of IFN-γ produced by sensitized T cells was determined in direct plasma by QuantiFERON Gold In-Tube test. IP-10 levels were determined in direct and dried plasma by an in-house ELISA. For dried plasma IP-10 determination, two 25 µl plasma drops were dried in Whatman903 filter paper and sent by mail to the laboratory. Regarding TB patients, 100.0%, 91.7% and 75.0% were positive for IFN-γ detection and IP-10 detection in direct and dried plasma, respectively. In contacts, 69.1%, 60.3% and 48.5% had positive results after IFN-γ and IP-10 in direct and dried plasma, respectively. The agreement among in vitro tests was substantial and IP-10 levels in direct and dried plasma were strongly correlated (r = 0.897). In conclusion, IP-10 detection in dried plasma is a simple and safe method that would help improve LTBI management.

Multigene phylogeny reveals a new Iranian earthworm genus (Lumbricidae: Philomontanus) with three new species

Lumbricidae taxonomy is vastly restricted by the morphological simplicity of earthworms and their lack of complex appendices. This has led to confusing results in the Lumbricidae classifications, which in turn, has hindered our ability to identify and assign new and cryptic species to the family. Here we propose the addition of a new Lumbricidae genus from the Zagros and Elburz Mountains of Iran, i.e. Philomontanus gen. nov, including three new species. Our taxonomic inferences were based on the phylogenetic analysis of two nuclear gene regions (28S rDNA and 18S rDNA) and 11 mitochondrial gene regions (16S rDNA, 12S rDNA, NADH dehydrogenase I, cytochrome oxidase subunits I and II and tRNAs Asn, Asp, Val, Leu, Ala and Ser). Philomontanus gen. nov comprises the earthworm species Philomontanus sarii sp. nov., Philomontanus mahmoudi sp. nov. and Philomontanus baloutchi sp. nov. These three species are morphologically similar to each other with only a few characters separating them (e.g. size, pigmentation and position of clitellum). Our findings support the adoption of an integrative approach including molecular information (e.g., DNA sequences) to aid earthworm classification and develop a robust taxonomy.

Bioconversion of Scotch broom into a high-quality organic fertiliser: Vermicomposting as a sustainable option

Wild Scotch broom ( Cytisus scoparius (L.) Link) shrubs are widely distributed throughout the world and, in some countries, are considered to be a threat to other plant species. The use of plant biomass from Scotch broom as a fertiliser seems to be the optimum solution for its disposal because it contains considerable amounts of macronutrients. However, its direct application to soils may cause phytotoxicity due to the release of polyphenols, which could negatively affect crop growth. This study evaluated the efficiency of vermicomposting in processing this leguminous plant on an industrial scale. Vermicomposting substantially reduced the biomass of Scotch broom (by 84%), mainly as a result of the loss of volatile solids. Simultaneously, the initial population of earthworms ( Eisenia andrei) increased remarkably throughout the process, offering the possibility of obtaining earthworm protein for animal feed. A nutrient-rich and stabilised peat-like material without polyphenol-associated phytotoxicity was obtained after 42 days of vermicomposting. Lower values of microbial biomass and activity, indicative of stabilised materials, were recorded at the end of the trial. These findings suggest that vermicomposting is an environmentally sound management system for Scotch broom and could easily be scaled up for industrial application.

Genetic diversity of mycobacterium tuberculosis in northern Greece

The aim of the present study was to describe the genetic diversity of Mycobacterium tuberculosis (M.tuberculosis) strains circulating in the region of Northern Greece. A total of thirty-seven M. tuberculosis clinical isolates were analysed by the spoligotyping method. According to the results, six clusters comprising seventeen strains were detected, and the remaining twenty strains showed unique patterns. The M.tuberculosis families according to SITVITWEB were distributed as follows: Haarlem (H) (27.0%); T (24.3%); Beijing (13.5%); Latin-America and Mediterranean (LAM) (5.4%) and S (2.7%). The remaining isolates (27%) did not match any isolates within the database and they were characterized as orphans. Regarding GenoType MTBDRplus results, two strains (5.4%) were Multi-Drug-Resistant, four strains (10.8%), were isoniazid monoresistant, while the remaining thirty-one strains (83.8%) were susceptible. In conclusion, in the region of Macedonia-Thrace (Northern Greece), there was high phylogenetic diversity among M. tuberculosis isolates. Molecular tools used and data presented can have regional and national impact on tuberculosis control.

Diversity, structure and sources of bacterial communities in earthworm cocoons

Animals start interactions with the bacteria that will constitute their microbiomes at embryonic stage. After mating, earthworms produce cocoons externally which will be colonized with bacteria from their parents and the environment. Due to the key role bacterial symbionts play on earthworm fitness, it is important to study bacterial colonization during cocoon formation. Here we describe the cocoon microbiome of the earthworms Eisenia andrei and E. fetida, which included 275 and 176 bacterial species, respectively. They were dominated by three vertically-transmitted symbionts, Microbacteriaceae, Verminephrobacter and Ca. Nephrothrix, which accounted for 88% and 66% of the sequences respectively. Verminephrobacter and Ca. Nephrothrix showed a high rate of sequence variation, suggesting that they could be biparentally acquired during mating. The other bacterial species inhabiting the cocoons came from the bedding, where they accounted for a small fraction of the diversity (27% and 7% of bacterial species for E. andrei and E. fetida bedding). Hence, earthworm cocoon microbiome includes a large fraction of the vertically-transmitted symbionts and a minor fraction, but more diverse, horizontally and non-randomly acquired from the environment. These data suggest that horizontally-transmitted bacteria to cocoons may play an important role in the adaptation of earthworms to new environments or diets.

Glucocorticoids modulate gastrointestinal microbiome in a wild bird

It has recently been hypothesized that stress exposure (e.g. via glucocorticoid secretion) may dysregulate the bacterial gut microbiome, a crucial 'organ' in animal health. However, whether stress exposure (e.g. via glucocorticoid secretion) affects the bacterial gut microbiome of natural populations is unknown. We have experimentally altered the basal glucocorticoid level (corticosterone implants) in a wild avian species, the yellow-legged gull Larus michahellis, to assess its effects on the gastrointestinal microbiota. Our results suggest underrepresentation of several microbial taxa in the corticosterone-implanted birds. Importantly, such reduction included potentially pathogenic avian bacteria (e.g. Mycoplasma and Microvirga) and also some commensal taxa that may be beneficial for birds (e.g. Firmicutes). Our findings clearly demonstrate a close link between microbiome communities and glucocorticoid levels in natural populations. Furthermore, they suggest a beneficial effect of stress in reducing the risk of infection that should be explored in future studies.

PyroTyping, a novel pyrosequencing-based assay for Mycobacterium tuberculosis genotyping

We developed a novel method, PyroTyping, for discrimination of Mycobacterium tuberculosis isolates combining pyrosequencing and IS6110 polymorphism. A total of 100 isolates were analysed with IS6110-restriction fragment length polymorphism (RFLP), spoligotyping, mycobacterial interspersed repetitive units - variable number tandem repeats (MIRU-VNTR), and PyroTyping. PyroTyping results regarding clustering or discrimination of the isolates were highly concordant with the other typing methods performed. PyroTyping is more rapid than RFLP and presents the same discriminatory power, thus, it may be useful for taking timely decisions for tuberculosis control.

Earthworm-induced carboxylesterase activity in soil: Assessing the potential for detoxification and monitoring organophosphorus pesticides

Soil enzyme activities are attracting widespread interest due to its potential use in contaminant breakdown, and as indicators of soil deterioration. However, given the multiple environmental and methodological factors affecting their activity levels, assessment of soil pollution using these biochemical endpoints is still complex. Taking advantage of the well-known stimulatory effect of earthworms on soil microbes, and their associated enzyme activities, we explored some toxicological features of carboxylesterases (CbEs) in soils inoculated with Lumbricus terrestris. A microplate-scale spectrophotometric assay using soil-water suspensions was first optimized, in which kinetic assay parameters (Km, Vmax, dilution of soil homogenate, and duration of soil homogenization) were established for further CbE determinations. Optimal conditions included a soil-to-water ratio of 1:50 (w/v), 30-min of shaking, and 2.5mM of substrate concentration. As expected, CbE activity increased significantly in soils treated with L. terrestris. This bioturbed soil was used for exploring the role of CbE activity as a bioscavenger for organophosphorus (OP) pesticides. Soil treated with two formulations of chlorpyrifos revealed that CbE activity was a significant molecular sink for this pesticide, reducing its impact on soil microbial activity as shown by the unchanged dehydrogenase activity. Dose-dependent curves were adjusted to an exponential kinetic model, and the median ecological dose (ED50) for both pesticide formulations was calculated. ED50 values decreased as the time of pesticide exposure increased (14 d-ED50s=20.4-26.7 mg kg(-1), and 28 d-ED50s=1.8-2.3 mg kg(-1)), which suggested that chlorpyrifos was progressively transformed into its highly toxic metabolite chlorpyrifos-oxon, but simultaneously was inactivated by CbEs. These results were confirmed by in vitro assays that showed chlorpyrifos-oxon was a more potent CbE inhibitor (IC50=35.5-4.67 nM) than chlorpyrifos (0.41-0.84 μM). The results showed that earthworm-induced CbE activity is an efficient bioscavengers for OP pesticides, acting as a soil safeguarding system. Moreover, the simple dose-response curves against OP exposure suggest that this enzyme--combined with other enzyme activities (e.g., dehydrogenase)--may be a suitable biomarker of pesticide exposure.