Biomolecular Analyses Research Articles

Isolation of DNA from plant tissues using a miniaturized matrix solid-phase dispersion approach featuring ionic liquid and magnetic ionic liquid solvents

The isolation of high-quality plant genomic DNA is a major prerequisite in many plant biomolecular analyses involving nucleic acid amplification. Conventional plant cell lysis and DNA extraction methods involve lengthy sample preparation procedures that often require large amounts of sample and chemicals, high temperatures and multiple liquid transfer steps which can introduce challenges for high throughput applications. In this study, a simple, rapid, miniaturized ionic liquid (IL)-based extraction method was developed for the isolation of genomic DNA from milligram fragments of Arabidopsis thaliana plant tissue. This method is based on a modification of vortex-assisted matrix solid-phase dispersion (VA-MSPD) in which the trihexyl(tetradecyl)phosphonium bis(trifluoromethylsulfonyl)imide ([P6,6,6,14+][NTf2-]) IL or trihexyl(tetradecyl)phosphonium tris(hexafluoroacetylaceto)nickelate(II) ([P6,6,6,14+][Ni(hfacac)3-]) magnetic IL (MIL) was directly applied to treated plant tissue (∼1.5 mg) and dispersed in an agate mortar to facilitate plant cell lysis and DNA extraction, followed by recovery of the mixture with a qPCR compatible co-solvent. This study represents the first approach to use ILs and MILs in a MSPD procedure to facilitate plant cell lysis and DNA extraction. The DNA-enriched IL- and MIL-cosolvent mixtures were directly integrated into the qPCR buffer without inhibiting the reaction while also circumventing the need for additional purification steps prior to DNA amplification. Under optimum conditions, the IL and MIL yielded 2.87 ± 0.28 and 1.97 ± 0.59 ng of DNA/mg of plant tissue, respectively. Furthermore, the mild extraction conditions used in the method enabled plant DNA in IL- and MIL-cosolvent mixtures to be preserved from degradation at room temperature.

Morphological Methods to Evaluate Peripheral Nerve Fiber Regeneration: A Comprehensive Review.

Regeneration of damaged peripheral nerves remains one of the main challenges of neurosurgery and regenerative medicine, a nerve functionality is rarely restored, especially after severe injuries. Researchers are constantly looking for innovative strategies for tackling this problem, with the development of advanced tissue-engineered nerve conduits and new pharmacological and physical interventions, with the aim of improving patients' life quality. Different evaluation methods can be used to study the effectiveness of a new treatment, including functional tests, morphological assessment of regenerated nerve fibers and biomolecular analyses of key factors necessary for good regeneration. The number and diversity of protocols and methods, as well as the availability of innovative technologies which are used to assess nerve regeneration after experimental interventions, often makes it difficult to compare results obtained in different labs. The purpose of the current review is to describe the main morphological approaches used to evaluate the degree of nerve fiber regeneration in terms of their usefulness and limitations.

Pemafibrate prevents choroidal neovascularization in a mouse model of neovascular age-related macular degeneration.

Pathological choroidal neovascularization (CNV) is one of the major causes of visual impairment in neovascular age-related macular degeneration (AMD). CNV has been suppressed by using anti-vascular endothelial growth factor (VEGF) antibodies. However, some clinical cases have demonstrated the failure of anti-VEGF therapies. Furthermore, anti-VEGF agents might induce the development of ocular atrophy. Recently, peroxisome proliferator-activated receptor alpha (PPARα) activation using pemafibrate treatment was suggested as one of the promising therapeutic targets in the prevention of ocular ischemia. However, the preventive role of pemafibrate remains unclear in CNV. We aimed to examine the preventive role of pemafibrate on laser-induced pathological CNV. Adult male C57BL/6 mice were orally supplied pemafibrate (0.5 mg/kg) for four days, followed by laser irradiation. Then, pemafibrate was consecutively given to mice with the same condition. CNV was visualized with isolectin-IB4. The eye (retina and/or retinal pigment epithelium [RPE]-choroid), liver, and serum were used for biomolecular analyses. We found that pemafibrate administration suppressed CNV volumes. Pemafibrate administration activated PPARα downstream genes in the liver and eye (especially, RPE-choroid). Furthermore, pemafibrate administration elevated serum fibroblast growth factor 21 levels and reduced serum levels of triglycerides. Our data suggest a promising pemafibrate therapy for suppressing CNV in AMD.

Short-Term In Vitro ROS Detection and Oxidative Stress Regulators in Epiretinal Membranes and Vitreous from Idiopathic Vitreoretinal Diseases.

A plethora of inflammatory, angiogenic, and tissue remodeling factors has been reported in idiopathic epiretinal membranes (ERMs). Herein we focused on the expression of a few mediators (oxidative, inflammatory, and angiogenic/vascular factors) by means of short-term vitreal cell cultures and biomolecular analysis. Thirty-nine (39) ERMs and vitreal samples were collected at the time of vitreoretinal surgery and biomolecular analyses were performed in clear vitreous, vitreal cell pellets, and ERMs. ROS products and iNOS were investigated in adherent vitreal cells and/or ERMs, and iNOS, VEGF, Ang-2, IFNγ, IL18, and IL22 were quantified in vitreous (ELISA/Ella, IF/WB); transcripts specific for iNOS, p65NFkB, KEAP1, NRF2, and NOX1/NOX4 were detected in ERMs (PCR). Biomolecular changes were analyzed and correlated with disease severity. The higher ROS production was observed in vitreal cells at stage 4, and iNOS was found in ERMs and increased in the vitreous as early as at stage 3. Both iNOS and NOX4 were upregulated at all stages, while p65NFkB was increased at stage 3. iNOS and NOX1 were positively and inversely related with p65NFkB. While NOX4 transcripts were always upregulated, NRF2 was upregulated at stage 3 and inverted at stage 4. No significant changes occurred in the release of angiogenic (VEGF, Ang-2) and proinflammatory (IL18, IL22 and IFNγ) mediators between all stages investigated. ROS production was strictly associated with iNOS and NOX4 overexpression and increased depending on ERM stadiation. The higher iNOS expression occurred as early as stage 3, with respect to p65NFkB and NRF2. These last mediators might have potential prognostic values in ERMs as representative of an underneath retinal damage.

Analysis of Ancient Microbial DNA.

The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of ancient human skeletal remains have revolutionized our understanding of human evolution. This research led to the discovery of a new hominin lineage, and demonstrated multiple admixture events with more distantly related archaic human populations such as Neandertals and Denisovans over the last 100,000years. Moreover, it has also yielded novel insights into the evolution of ancient pathogens. The analysis of ancient microbial genomes enables the study of their recent evolution, presently covering the last several millennia. These spectacular results have been obtained despite the degradation of DNA that takes place after the death of the host and increases with time. This cumulative degradation results in very short ancient DNA molecules, low in quantity, and highly prone to contamination by modern DNA molecules, especially from human and animal DNA present in reagents used in downstream biomolecular analyses. Finally, the minute amounts of ancient molecules are further diluted in environmental DNA from the soil microorganisms that colonize bones and teeth. Thus, ancient skeletal remains can share DNA profiles with environmental samples, and the identification of ancient microbial genomes among the more recent, presently poorly characterized, environmental microbiome is particularly challenging. Here, we describe the methods developed and/or in use in our laboratory to produce reliable and reproducible paleogenomic results from ancient skeletal remains that can be used to identify the presence of ancient microbiota.

Lake Erie field trials to advance autonomous monitoring of cyanobacterial harmful algal blooms

Biomolecular analyses are used to investigate the dynamics of cyanobacterial harmful algal blooms (cyanoHABs), with samples collected during monitoring often analyzed by qPCR and sometimes amplicon and metagenomic sequencing. However, cyanoHAB research and monitoring programs face operational constraints due to the reliance on human resources for sample collections. To address this impediment, a third-generation Environmental Sample Processor (3G ESP) integrated with a long-range autonomous underwater vehicle (LRAUV) was tested during seasonal blooms of Microcystis in western Lake Erie (WLE) in 2018 and 2019. The LRAUV-3G ESP successfully performed flexible, autonomous sampling across a wide range of cyanoHAB conditions, and results indicated equivalency between autonomous and manual methods. No significant differences were found between LRAUV-3G ESP and manual sample collection and handling methods in the 12 parameters tested. Analyzed parameters included concentrations of total cyanobacteria and microcystin toxin gene via qPCR; relative abundances of bacterial amplicon sequence variants (ASVs) from 16S rRNA gene amplicon sequencing; and community diversity measures from both 16S amplicon and metagenomic sequencing. The LRAUV-3G ESP provided additional sampling capacity and revealed differences between field seasons for bacterial taxa and concentrations of total cyanobacteria and microcystin toxin gene. Metagenomic analysis of multiple microcystin toxin genes corroborated the use of the mcyE gene as a proxy for the genomic potential of WLE cyanoHABs to produce microcystin. Overall, this study provides support for the use of autonomous ‘omics capability in WLE to help expand the spatial and temporal coverage of cyanoHAB monitoring operations.

New integrated molecular approaches for investigating lake settlements in north-western Europe

Lake settlements, particularly crannogs, pose several contradictions—visible yet inaccessible, widespread yet geographically restricted, persistent yet vulnerable. To further our understanding, we developed the integrated use of palaeolimnological (scanning XRF, pollen, spores, diatoms, chironomids, Cladocera, microcharcoal, biogenic silica, SEM-EDS, stable-isotopes) and biomolecular (faecal stanols, bile acids, sedaDNA) analyses of crannog cores in south-west Scotland and Ireland. Both can be effective methods sets for revealing occupation chronologies and identifying on-crannog activities and practices. Strong results from sedaDNA and lipid biomarker analyses demonstrate probable on-site animal slaughter, food storage and possible feasting, suggesting multi-period, elite site associations, and the storage and protection of valuable resources.

Peripheral gene signatures reveal distinct cancer patient immunotypes with therapeutic implications for autologous DC-based vaccines

ABSTRACT Dendritic cells (DCs) have received considerable attention as potential targets for the development of novel cancer immunotherapies. However, the clinical efficacy of DC-based vaccines remains suboptimal, largely reflecting local and systemic immunosuppression at baseline. An autologous DC-based vaccine (DCVAC) has recently been shown to improve progression-free survival and overall survival in randomized clinical trials enrolling patients with lung cancer (SLU01, NCT02470468) or ovarian carcinoma (SOV01, NCT02107937), but not metastatic castration-resistant prostate cancer (SP005, NCT02111577), despite a good safety profile across all cohorts. We performed biomolecular and cytofluorometric analyses on peripheral blood samples collected prior to immunotherapy from 1000 patients enrolled in these trials, with the objective of identifying immunological biomarkers that may improve the clinical management of DCVAC-treated patients. Gene signatures reflecting adaptive immunity and T cell activation were associated with favorable disease outcomes and responses to DCVAC in patients with prostate and lung cancer, but not ovarian carcinoma. By contrast, the clinical benefits of DCVAC were more pronounced among patients with ovarian carcinoma exhibiting reduced expression of T cell-associated genes, especially those linked to TH2-like signature and immunosuppressive regulatory T (TREG) cells. Clinical responses to DCVAC were accompanied by signs of antitumor immunity in the peripheral blood. Our findings suggest that circulating signatures of antitumor immunity may provide a useful tool for monitoring the potency of autologous DC-based immunotherapy.

Comparison of Different Fixation Methods for Combined Histological and Biomolecular Analysis of Fixed and Decalcified Bone Samples.

The combination of histological and biomolecular analyses provides deep understanding of different biological processes and is of high interest for basic and applied research. However, the available analytical methods are still limited, especially when considering bone samples. This study compared different fixation media to identify a sufficient analytical method for the combination of histological, immuno-histological and biomolecular analyses of the same fixed, processed and paraffin embedded bone sample. Bone core biopsies of rats’ femurs were fixed in different media (RNAlater + formaldehyde (R + FFPE), methacarn (MFPE) or formaldehyde (FFPE)) for 1 week prior to decalcification by EDTA and further histological processing and paraffin embedding. Snap freezing (unfixed frozen tissue, UFT) and incubation in RNAlater were used as additional controls. After gaining the paraffin sections for histological and immunohistological analysis, the samples were deparaffined and RNA was isolated by a modified TRIZOL protocol. Subsequently, gene expression was evaluated using RT-qPCR. Comparable histo-morphological and immuno-histological results were evident in all paraffin embedded samples of MFPE, FFPE and R + FFPE. The isolated RNA in the group of MFPE showed a high concentration and high purity, which was comparable to the UFT and RNAlater groups. However, in the groups of FFPE and R + FFPE, the RNA quality and quantity were statistically significantly lower when compared to MFPE, UFT and RNAlater. RT-qPCR results showed a comparable outcome in the group of MFPE and UFT, whereas the groups of FFPE and R + FFPE did not result in a correctly amplified gene product. Sample fixation by means of methacarn is of high interest for clinical samples to allow a combination of histological, immunohistological and biomolecular analysis. The implementation of such evaluation method in clinical research may allow a deeper understanding of the processes of bone formation and regeneration.

High-accuracy methodology for the integrative restoration of archaeological teeth by using reverse engineering techniques and rapid prototyping

The reconstruction of the original morphology of bones and teeth after sampling for physicochemical (e.g., radiocarbon and uranium series dating, stable isotope analysis, paleohistology, trace element analysis) and biomolecular analyses (e.g., ancient DNA, paleoproteomics) is appropriate in many contexts and compulsory when dealing with fossil human remains. The reconstruction protocols available to date are mostly based on manual re-integration of removed portions and can lead to an imprecise recovery of the original morphology.In this work, to restore the original external morphology of sampled teeth we used computed microtomography (microCT), reverse engineering (RE), computer-aided design (CAD) and rapid prototyping (RP) techniques to fabricate customized missing parts. The protocol was tested by performing the reconstruction of two Upper Palaeolithic human teeth from the archaeological excavations of Roccia San Sebastiano (Mondragone, Caserta, southern Italy) and Riparo I of Grotte Verdi di Pradis (Clauzetto, Pordenone, north-eastern Italy) (RSS2 and Pradis 1, respectively), which were sampled for physicochemical and biomolecular analyses.It involved a composite procedure consisting in: a) the microCT scanning of the original specimens; b) sampling; c) the microCT scanning of the specimens after sampling; d) the reconstruction of the digital 3D surfaces of the specimens before and after sampling; e) the creation of digital models of the missing/sampled portions by subtracting the 3D images of the preserved portions (after the sampling) from the images of the intact specimens (before the sampling) by using reverse engineering techniques; f) the prototyping of the missing/sampled portions to be integrated; g) the painting and application of the prototypes through the use of compatible and reversible adhesives.By following the proposed protocol, in addition to the fabrication of a physical element which is faithful to the original, it was possible to obtain a remarkable correspondence between the contact surfaces of the two portions (the original and the reconstructed one) without having to resort to any manipulation/adaptation of either element.

Therapeutic Effect of Crocin on the NASH Model by Targeting the Fas Receptor Signaling Pathway.

The role of hepatocyte apoptosis and inflammation has been implicated in the progression of nonalcoholic steatohepatitis (NASH). Overproduction of reactive oxygen species (ROS) appears to accelerate these pathways through the activation of Fas receptor signaling. Therefore, we explored the hepatoprotective effects of crocin as a strong free radical scavenger against oxidative damages leading to NASH development. Thirty-two male mice were randomly divided into control, NASH, NASH + crocin, and crocin groups. They received an intraperi- toneal injection of crocin twice a week, for 3 weeks. For NASH model induction, the animals were fed with a Western diet and exposed to cigarette smoke for 8 weeks. At the end of the experiment, liver histology, biochemical, and biomolecular analyses were done to evaluate the antioxidant, anti-inflammatory, and anti-apoptotic activities of crocin in the NASH model. Evaluation of the features of the NASH model revealed steatosis, inflammatory infiltrate, and ballooning degeneration. Metabolic dysfunction was associated with elevated serum levels of the lipid profile and decreased hepatic liver enzymes. The increased content of malondialdehyde (MDA) and reduced antioxidant activities confirmed hepatotoxicity induction. There was a significant increase in expression level of Fas, caspase 3, and NF-κB genes that was also associated with elevation in hepatic TNF-α content. Moreover, expression the of Fas receptor protein was significantly detected on the hepatocyte membrane. Treatment with crocin effectively improved NASH-related parameters, and the histopathological findings were also parallel with the resulting changes. Crocin can be introduced as a candidate hepatoprotective agent against NASH by virtue of its anti-inflammatory, antioxi- dant, and anti-apoptotic properties, possibly through regulation of the Fas death receptor pathway.

Atypical Mycosis in Psittacine Birds: A Retrospective Study.

A retrospective study was conducted on parrots submitted from necropsy to the Department of Veterinary Pathology, School of Biosciences and Veterinary, University of Camerino, Italy, from 2007 to 2018. From a total of 2,153 parrots examined at post-mortem, four cases were diagnosed with atypical mycosis and were considered for determination of the fungus species by PCR. A Fischer's lovebird (Agapornis fischeri), Peach-faced lovebirds (Agapornis roseicollis), and two Blue and Gold Macaws (Ara ararauna) from four different aviaries died after some days of lethargy and ruffled feathers. Records of gross necropsy and histopathological exams (H&E, PAS, and Grocott stain) were described and biomolecular analyses were carried out. No specific gross lesions were appreciated at necropsy, while histopathology evidenced a systemic mycosis in several organs, particularly in the lungs. In affected organs, broad and non-septate hyphae, suggestive of mycoses, were observed. Molecularly, Mucor racemosus (Fischer's lovebird) and M. circinelloides (Peach-faced lovebirds) were identified from formalin-fixed and paraffin-embedded (FFPE) lung and liver tissue. In addition, Alternaria alternata and Fusicladium spp. (respectively in male and female Blue and Gold macaws) were identified in FFPE tissue from several organs; whereas the role of Mucor spp. as true pathogens is well-demonstrated, and the behavior of A. alternata and Fusicladium spp. in macaws as opportunistic pathogens have been discussed. To our knowledge, this report is the first one reporting mucormycosis caused by M. racemosus and M. circinelloides in lovebirds, and A. alternata and Fusicladium spp. in macaws.

Ketamine administration in early postnatal life as a tool for mimicking Autism Spectrum Disorders core symptoms

Autism Spectrum Disorders (ASD) core symptoms include deficits of social interaction, stereotyped behaviours, dysfunction in language and communication. Beyond them, several additional symptoms, such as cognitive impairment, anxiety-like states and hyperactivity are often occurring, mainly overlapping with other neuropsychiatric diseases. To untangle mechanisms underlying ASD etiology, and to identify possible pharmacological approaches, different factors, such as environmental, immunological and genetic ones, need to be considered. In this context, ASD animal models, aiming to reproduce the wide range of behavioural phenotypes of this uniquely human disorder, represent a very useful tool. Ketamine administration in early postnatal life of mice has already been studied as a suitable animal model resembling psychotic-like symptoms.Here, we investigated whether ketamine administration, at postnatal days 7, 9 and 11, might induce behavioural features able to mimic ASD typical symptoms in adult mice. To this aim, we developed a 4-days behavioural tests battery, including Marble Burying, Hole Board, Olfactory and Social tests, to assess repetitive and stereotyped behaviour, social deficits and anxiety-like symptoms. Moreover, by using this mouse model, we performed neurochemical and biomolecular analyses, quantifying neurotransmitters belonging to excitatory-inhibitory pathways, such as glutamate, glutamine and gamma-aminobutyric acid (GABA), as well as immune activation biomarkers related to ASD, such as CD11b and glial fibrillary acidic protein (GFAP), in the hippocampus and amygdala. Possible alterations in levels of brain-derived neurotrophic factor (BDNF) expression in the hippocampus and amygdala were also evaluated.Our results showed an increase in stereotyped behaviours, together with social impairments and anxiety-like behaviour in adult mice, receiving ketamine administration in early postnatal life. In addition, we found decreased BDNF and enhanced GFAP hippocampal expression levels, accompanied by elevations in glutamate amount, as well as reduction in GABA content in amygdala and hippocampus.In conclusion, early ketamine administration may represent a suitable animal model of ASD, exhibiting face validity to mimic specific ASD symptoms, such as social deficits, repetitive repertoire and anxiety-like behaviour.

Exploitation history of Atlantic bluefin tuna in the eastern Atlantic and Mediterranean—insights from ancient bones

Abstract Overexploitation has directly, negatively affected marine fish populations in the past half-century, modifying not only their abundance but their behaviour and life-history traits. The recovery and resilience of such populations is dependent upon their exploitation history, which often extends back millennia. Hence, data on when exploitation intensified and how populations were composed in historical periods, have the potential to reveal long-term population dynamics and provide context on the baselines currently used in fisheries management and conservation. Here, we setup a framework for investigations on the exploitation history of Atlantic bluefin tuna (Thunnus thynnus; BFT) in the eastern Atlantic and Mediterranean by collating records of their zooarchaeological remains and critically reviewing these alongside the literature. Then, we outline how novel multidisciplinary applications on BFT remains may be used to document long-term population dynamics. Our review of literature provides clear evidence of BFT overexploitation during the mid-20th century ce. Furthermore, a strong case could be made that the intensification of BFT exploitation extends back further to at least the 19th century ce, if not the 13th–16th century ce, in the eastern Atlantic and Mediterranean. However, a host of archaeological evidence would suggest that BFT exploitation may have been intensive since antiquity. Altogether, this indicates that by the currently used management baselines of the 1970s, population abundance and complexity was already likely to have declined from historical levels, and we identify how biomolecular and morphometric analyses of BFT remains have the potential to further investigate this.

Biomolecular, Histological, Clinical, and Radiological Analyses of Dental Implant Bone Sites Prepared Using Magnetic Mallet Technology: A Pilot Study in Animals.

Background. A new instrumentation exploiting magneto-dynamic technology (mallet) proposed for implant site preparation was investigated. Methods. In the tibias of three minipigs, two sites were prepared by mallet and two by drill technique. Primary stability (ISQ) was detected after implant positioning (T0) and at 14 days (T14). X-rays and computed tomography were performed. At T14, bone samples were utilized for histological and biomolecular analyses. Results. In mallet sites, histological evaluations evidenced a significant increase in the newly formed bone, osteoblast number, and a smaller quantity of fibrous tissue. These results agree with the significant BMP-4 augmentation and the positive trend in other osteogenic factors (biological and radiological investigations). Major, albeit IL-10-controlled, inflammation was present. For both techniques, at T14 a significant ISQ increase was evidenced, but no significant difference was observed at T0 and T14 between the mallet and drill techniques. In mallet sites, lateral bone condensation was observed on computed tomography. Conclusions. Using biological, histological, clinical, and radiological analyses, this study first shows that the mallet technique is effective for implant site preparation. Based on its ability to cause osseocondensation and improve newly formed bone, mallet technology should be chosen in all clinical cases of poor bone quality.

Biobox: a toolbox for biomolecular modelling.

MotivationThe implementation of biomolecular modelling methods and analyses can be cumbersome, often carried out with in-house software reimplementing common tasks, and requiring the integration of diverse software libraries.ResultsWe present Biobox, a Python-based toolbox facilitating the implementation of biomolecular modelling methods.Availability and implementationBiobox is freely available on https://github.com/degiacom/biobox, along with its API and interactive Jupyter notebook tutorials.

Phenotypic Features and Genetic Findings in a Cohort of Italian Pseudoxanthoma Elasticum Patients and Update of the Ophthalmologic Evaluation Score.

Background: Pseudoxanthoma elasticum (PXE) is a rare ectopic calcification genetic disease mainly caused by ABCC6 rare sequence variants. The clinical phenotype is characterized by typical dermatological, ophthalmological and cardiovascular manifestations, whose frequency and severity are differently reported in the literature. Methods: A retrospective study was performed on 377 PXE patients of Italian origin, clinically evaluated according to the Phenodex Index, who underwent ABCC6 biomolecular analyses. Moreover, 53 PXE patients were further characterized by in-depth ophthalmological examinations. Results: A total of 117 different ABCC6 rare sequence variants were detected as being spread through the whole gene. The severity of the clinical phenotype was dependent on age, but it was not influenced by gender or by the type of sequence variants. In-depth ophthalmological examinations focused on the incidences of coquille d’oeuf, comet lesions, pattern dystrophy-like lesions, optic disk drusen and posterior-pole atrophy. Conclusion: Given the large number of patients analyzed, we were able to better evaluate the occurrence of less frequent alterations (e.g., stroke, myocardial infarction, nephrolithiasis). A more detailed description of ophthalmological abnormalities allowed us to stratify patients and better evaluate disease progression, thus suggesting a further update of the PXE score system.

Tannery Wastewater Recalcitrant Compounds Foster the Selection of Fungi in Non-Sterile Conditions: A Pilot Scale Long-Term Test.

This study demonstrated that a microbial community dominated by fungi can be selected and maintained in the long-term under non-sterile conditions, in a pilot-scale packed-bed reactor fed with tannery wastewater. During the start-up phase, the reactor, filled with 0.6 m3 of polyurethane foam cubes, was inoculated with a pure culture of Aspergillus tubingensis and Quebracho tannin, a recalcitrant compound widely used by tannery industry, was used as sole carbon source in the feeding. During the start-up, fungi grew attached as biofilm in carriers that filled the packed-bed reactor. Subsequently, the reactor was tested for the removal of chemical oxygen demand (COD) from an exhaust tanning bath collected from tanneries. The entire experiment lasted 121 days and average removals of 29% and 23% of COD and dissolved organic carbon (DOC) from the tannins bath were achieved, respectively. The evolution of the microbial consortium (bacteria and fungi) was described through biomolecular analyses along the experiment and also developed as a function of the size of the support media.

Proteomic analysis of archaeological ceramics from Tell Khaiber, southern Iraq

Archaeological ceramics are a rich source of ancient biomolecules and their analysis provides valuable information with regard to ancient diet. Traditionally, biomolecular analyses on archaeological ceramics have focused on lipid analysis, with milk, ruminant and non-ruminant adipose fats, plant resins, as well as both marine fish and marine mammals among the resources successfully identified. However, lipidomic analyses can underestimate the presence of lipid-poor resources (e.g. cereals and grains) and are usually less specific at tissue and taxonomic levels. Proteomic analysis can be complementary, allowing for the identification of a greater variety of resources and with increased specificity. Here, we analyse eight ceramic sherds from Tell Khaiber, a Sealand Dynasty (mid-2nd millennium BCE) settlement in modern day southern Iraq, using LC-MS/MS based shotgun proteomics. Our results provide the first proteomic evidence of soybeans from archaeological ceramics and confirmation of the early appearance of soybean products in the Middle East by the mid-second millennium BCE.

A comprehensive tool box for large animal studies of intervertebral disc degeneration.

Preclinical studies involving large animal models aim to recapitulate the clinical situation as much as possible and bridge the gap from benchtop to bedside. To date, studies investigating intervertebral disc (IVD) degeneration and regeneration in large animal models have utilized a wide spectrum of methodologies for outcome evaluation. This paper aims to consolidate available knowledge, expertise, and experience in large animal preclinical models of IVD degeneration to create a comprehensive tool box of anatomical and functional outcomes. Herein, we present a Large Animal IVD Scoring Algorithm based on three scales: macroscopic (gross morphology, imaging, and biomechanics), microscopic (histological, biochemical, and biomolecular analyses), and clinical (neurologic state, mobility, and pain). The proposed algorithm encompasses a stepwise evaluation on all three scales, including spinal pain assessment, and relevant structural and functional components of IVD health and disease. This comprehensive tool box was designed for four commonly used preclinical large animal models (dog, pig, goat, and sheep) in order to facilitate standardization and applicability. Furthermore, it is intended to facilitate comparison across studies while discerning relevant differences between species within the context of outcomes with the goal to enhance veterinary clinical relevance as well. Current major challenges in pre‐clinical large animal models for IVD regeneration are highlighted and insights into future directions that may improve the understanding of the underlying pathologies are discussed. As such, the IVD research community can deepen its exploration of the molecular, cellular, structural, and biomechanical changes that occur with IVD degeneration and regeneration, paving the path for clinically relevant therapeutic strategies.