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Recent Submissions

  • Investigating calcification-related candidates in a non-symbiotic scleractinian coral, Tubastraea spp.

    Capasso, Laura; Aranda, Manuel; Cui, Guoxin; Pousse, Melanie; Tambutté, Sylvie; Zoccola, Didier (Scientific Reports, Springer Science and Business Media LLC, 2022-08-06) [Article]
    In hermatypic scleractinian corals, photosynthetic fixation of CO2 and the production of CaCO3 are intimately linked due to their symbiotic relationship with dinoflagellates of the Symbiodiniaceae family. This makes it difficult to study ion transport mechanisms involved in the different pathways. In contrast, most ahermatypic scleractinian corals do not share this symbiotic relationship and thus offer an advantage when studying the ion transport mechanisms involved in the calcification process. Despite this advantage, non-symbiotic scleractinian corals have been systematically neglected in calcification studies, resulting in a lack of data especially at the molecular level. Here, we combined a tissue micro-dissection technique and RNA-sequencing to identify calcification-related ion transporters, and other candidates, in the ahermatypic non-symbiotic scleractinian coral Tubastraea spp. Our results show that Tubastraea spp. possesses several calcification-related candidates previously identified in symbiotic scleractinian corals (such as SLC4-γ, AMT-1like, CARP, etc.). Furthermore, we identify and describe a role in scleractinian calcification for several ion transporter candidates (such as SLC13, -16, -23, etc.) identified for the first time in this study. Taken together, our results provide not only insights about the molecular mechanisms underlying non-symbiotic scleractinian calcification, but also valuable tools for the development of biotechnological solutions to better control the extreme invasiveness of corals belonging to this particular genus.
  • Spectrochemistry of Firefly Bioluminescence

    Al-Handawi, Marieh B.; Polavaram, Srujana; Kurlevskaya, Anastasiya; Commins, Patrick; Schramm, Stefan; Carrasco-López, César; Lui, Nathan M.; Solntsev, Kyril M.; Laptenok, Siarhei; Navizet, Isabelle; Naumov, Panče (Chemical Reviews, American Chemical Society (ACS), 2022-08-04) [Article]
    The chemical reactions underlying the emission of light in fireflies and other bioluminescent beetles are some of the most thoroughly studied processes by scientists worldwide. Despite these remarkable efforts, fierce academic arguments continue around even some of the most fundamental aspects of the reaction mechanism behind the beetle bioluminescence. In an attempt to reach a consensus, we made an exhaustive search of the available literature and compiled the key discoveries on the fluorescence and chemiluminescence spectrochemistry of the emitting molecule, the firefly oxyluciferin, and its chemical analogues reported over the past 50+ years. The factors that affect the light emission, including intermolecular interactions, solvent polarity, and electronic effects, were analyzed in the context of both the reaction mechanism and the different colors of light emitted by different luciferases. The collective data points toward a combined emission of multiple coexistent forms of oxyluciferin as the most probable explanation for the variation in color of the emitted light. We also highlight realistic research directions to eventually address some of the remaining questions related to firefly bioluminescence. It is our hope that this extensive compilation of data and detailed analysis will not only consolidate the existing body of knowledge on this important phenomenon but will also aid in reaching a wider consensus on some of the mechanistic details of firefly bioluminescence.
  • A new species of Bathypathes (Cnidaria, Anthozoa, Antipatharia, Schizopathidae) from the Red Sea and its phylogenetic position

    Chimienti, Giovanni; Terraneo, Tullia Isotta; Vicario, Silvia; Marchese, Fabio; Purkis, Sam J.; Abdulla Eweida, Ameer; Rodrigue, Mattie; Benzoni, Francesca (ZooKeys, Pensoft Publishers, 2022-08-04) [Article]
    A black coral, Bathypathes thermophila Chimienti, sp. nov. is described from the Saudi Arabian coasts of the Gulf of Aqaba and north Red Sea (Neom area) using an integrated taxonomic approach. The morphological distinctiveness of the new species is confirmed by molecular analyses. The species thrives in warm and high salinity waters typical of the Red Sea at bathyal depths. It can form colony aggregations on muddy bottoms with scattered, small hard substrates. Colonies are monopodial, feather-like, and attached to a hard substrate through a thorny basal plate. Pinnules are simple, arranged biserially and alternately, and all the same length (up to approximately 20 cm) except for few, proximal ones. Spines are triangular, laterally compressed, subequal, smooth, and simple or rarely bifurcated. Polyps are elongated transversely, 1.5–2.0 mm in transverse diameter. Large colonies can have one or few branches, whose origin is discussed. The phylogenetic position of B. thermophila sp. nov. within the order Antipatharia, recovered using three mitochondrial markers, shows that it is nested within the family Schizopathidae. It is close to species in the genera Parantipathes, Lillipathes, Alternatipathes, and Umbellapathes rather than to the other available representatives of the genus Bathypathes, as currently defined based on morphology. In agreement with previous findings, our results question the evolutionary significance of morphological characters traditionally used to discriminate Antipatharia at higher taxonomic level.
  • Coverage Enhancement of Underwater Internet of Things Using Multi-Level Acoustic Communication Networks

    Xu, Jiajie; Kishk, Mustafa Abdelsalam; Alouini, Mohamed-Slim (IEEE Internet of Things Journal, Institute of Electrical and Electronics Engineers (IEEE), 2022-08-03) [Article]
    Underwater acoustic communication networks (UACNs) are considered a key-enabler to the underwater internet of things (UIoT). UACN is regarded as essential for various marine applications such as monitoring, exploration, and trading. However, a large part of existing literature disregards the 3-dimensional (3D) nature of the underwater communication system. In this paper, we propose a K-tier UACN that acts as a gateway that connects the UIoT with the Space-Air-Ground-Sea Integrated System (SAGSIS). The proposed network architecture consists of several tiers along the vertical direction with adjustable depths. On the horizontal dimension, the best coverage probability (CP) is computed and maximized by optimizing the densities of surface stations (SSs) in each tier. On the vertical dimension, the depth of each tier is also optimized to minimize inter-tier interference and maximize overall system performance. Using tools from stochastic geometry, the total CP of the proposed K-tier network is analyzed. For given spatial distribution of UIoT device’s depth, the best CP can be achieved by optimizing the depths of the transceivers connected to the SSs through a tether. We verify the accuracy of the analysis using Monte-Carlo simulations. In addition, we draw multiple useful system-level insights that help optimize the design of underwater 3D networks based on the given distribution of UIoT device’s depths.
  • Differential role of neuronal glucose and PFKFB3 in memory formation during development

    Cruz, Emmanuel; Bessières, Benjamin; Magistretti, Pierre J.; Alberini, Cristina M (Glia, 2022-08-02) [Article]
    The consumption of glucose in the brain peaks during late childhood; yet, whether and how glucose metabolism is differentially regulated in the brain during childhood compared to adulthood remains to be understood. In particular, it remains to be determined how glucose metabolism is involved in behavioral activations such as learning. Here we show that, compared to adult, the juvenile rat hippocampus has significantly higher mRNA levels of several glucose metabolism enzymes belonging to all glucose metabolism pathways, as well as higher levels of the monocarboxylate transporters MCT1 and MCT4 and the glucose transporters endothelial-GLUT1 and GLUT3 proteins. Furthermore, relative to adults, long-term episodic memory formation in juvenile animals requires significantly higher rates of aerobic glycolysis and astrocytic-neuronal lactate coupling in the hippocampus. Only juvenile but not adult long-term memory formation recruits GLUT3, neuronal 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3) and more efficiently engages glucose in the hippocampus. Hence, compared to adult, the juvenile hippocampus distinctively regulates glucose metabolism pathways, and formation of long-term memory in juveniles involves differential neuronal glucose metabolism mechanisms.
  • Investigation of Antibiotic Resistome in Hospital Wastewater during the COVID-19 Pandemic: Is the Initial Phase of the Pandemic Contributing to Antimicrobial Resistance?

    Wang, Changzhi; Mantilla Calderon, David; Xiong, Yanghui; Alkahtani, Mohsen; Bashawri, Yasir M.; Al Qarni, Hamed; Hong, Pei-Ying (Environmental Science & Technology, American Chemical Society (ACS), 2022-08-02) [Article]
    Since the COVID-19 pandemic started, there has been much speculation about how COVID-19 and antimicrobial resistance may be interconnected. In this study, untreated wastewater was sampled from Hospital A designated to treat COVID-19 patients during the first wave of the COVID-19 pandemic alongside Hospital B that did not receive any COVID-19 patients. Metagenomics was used to determine the relative abundance and mobile potential of antibiotic resistant genes (ARGs), prior to determining the correlation of ARGs with time/incidence of COVID-19. Our findings showed that ARGs resistant to macrolides, sulfonamides, and tetracyclines were positively correlated with time in Hospital A but not in Hospital B. Likewise, minor extended spectrum beta-lactamases (ESBLs) and carbapenemases of classes B and D were positively correlated with time, suggesting the selection of rare and/or carbapenem-resistant genes in Hospital A. Non-carbapenemase blaVEB also positively correlated with both time and intI1 and was copresent with other ARGs including carbapenem-resistant genes in 6 metagenome-assembled genomes (MAGs). This study highlighted concerns related to the dissemination of antimicrobial resistance (AMR) during the COVID-19 pandemic that may arise from antibiotic use and untreated hospital wastewater.
  • Genetic networks underlying salinity tolerance in wheat uncovered with genome-wide analyses and selective sweeps.

    Shan, Danting; Ali, Mohsin; Shahid, Mohammed; Arif, Anjuman; Waheed, Muhammad Qandeel; Xia, Xianchun; Trethowan, Richard; Tester, Mark A.; Poland, Jesse; Ogbonnaya, Francis C; Rasheed, Awais; He, Zhonghu; Li, Huihui (TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, Springer Science and Business Media LLC, 2022-08-01) [Article]
    A genetic framework underpinning salinity tolerance at reproductive stage was revealed by genome-wide SNP markers and major adaptability genes in synthetic-derived wheats, and trait-associated loci were used to predict phenotypes. Using wild relatives of crops to identify genes related to improved productivity and resilience to climate extremes is a prioritized area of crop genetic improvement. High salinity is a widespread crop production constraint, and development of salt-tolerant cultivars is a sustainable solution. We evaluated a panel of 294 wheat accessions comprising synthetic-derived wheat lines (SYN-DERs) and modern bread wheat advanced lines under control and high salinity conditions at two locations. The GWAS analysis revealed a quantitative genetic framework of more than 200 loci with minor effect underlying salinity tolerance at reproductive stage. The significant trait-associated SNPs were used to predict phenotypes using a GBLUP model, and the prediction accuracy (r2) ranged between 0.57 and 0.74. The r2 values for flag leaf weight, days to flowering, biomass, and number of spikes per plant were all above 0.70, validating the phenotypic effects of the loci discovered in this study. Furthermore, the germplasm sets were compared to identify selection sweeps associated with salt tolerance loci in SYN-DERs. Six loci associated with salinity tolerance were found to be differentially selected in the SYN-DERs (12.4 Mb on chromosome (chr)1B, 7.1 Mb on chr2A, 11.2 Mb on chr2D, 200 Mb on chr3D, 600 Mb on chr6B, and 700.9 Mb on chr7B). A total of 228 reported markers and genes, including 17 well-characterized genes, were uncovered using GWAS and EigenGWAS. A linkage disequilibrium (LD) block on chr5A, including the Vrn-A1 gene at 575 Mb and its homeologs on chr5D, were strongly associated with multiple yield-related traits and flowering time under salinity stress conditions. The diversity panel was screened with more than 68 kompetitive allele-specific PCR (KASP) markers of functional genes in wheat, and the pleiotropic effects of superior alleles of Rht-1, TaGASR-A1, and TaCwi-A1 were revealed under salinity stress. To effectively utilize the extensive genetic information obtained from the GWAS analysis, a genetic interaction network was constructed to reveal correlations among the investigated traits. The genetic network data combined with GWAS, selective sweeps, and the functional gene survey provided a quantitative genetic framework for identifying differentially retained loci associated with salinity tolerance in wheat.
  • Natural carbon fixation and advances in synthetic engineering for redesigning and creating new fixation pathways

    Santos Correa, Sulamita; Schultz, Junia; Lauersen, Kyle J.; Soares Rosado, Alexandre (Journal of advanced research, Elsevier BV, 2022-07-30) [Article]
    Background: Autotrophic carbon fixation is the primary route through which organic carbon enters the biosphere, and it is a key step in the biogeochemical carbon cycle. The Calvin–Benson–Bassham pathway, which is predominantly found in plants, algae, and some bacteria (mainly cyanobacteria), was previously considered to be the sole carbon-fixation pathway. However, the discovery of a new carbon-fixation pathway in sulfurous green bacteria almost two decades ago encouraged further research on previously overlooked ancient carbon-fixation pathways in taxonomically and phylogenetically distinct microorganisms. Aim of Review: In this review, we summarize the six known natural carbon-fixation pathways and outline the newly proposed additions to this list. We also discuss the recent achievements in synthetic carbon fixation and the importance of the metabolism of thermophilic microorganisms in this field. Key Scientific Concepts of Review: Currently, at least six carbon-fixation routes have been confirmed in Bacteria and Archaea. Other possible candidate routes have also been suggested on the basis of emerging “omics” data analyses, expanding our knowledge and stimulating discussions on the importance of these pathways in the way organisms acquire carbon. Notably, the currently known natural fixation routes cannot balance the excessive anthropogenic carbon emissions in a highly unbalanced global carbon cycle. Therefore, significant efforts have also been made to improve the existing carbon-fixation pathways and/or design new efficient in vitro and in vivo synthetic pathways.
  • Nickel-Coated ceramic hollow fiber cathode for fast enrichment of chemolithoautotrophs and efficient reduction of CO2 in microbial electrosynthesis

    Bian, Bin; Singh, Yogesh Balwant; Rabaey, Korneel; Saikaly, Pascal (Chemical Engineering Journal, Elsevier BV, 2022-07-30) [Article]
    Microbial electrosynthesis (MES) explores the potential of chemolithoautotrophs for the production of value-added products from CO2. However, the enrichment of chemolithoautotrophs on a cathode is relatively slow and the separation of the products is energy intensive. In this study, a novel and multifunctional cathode configuration, enabling the simultaneous enrichment of chemolithoautotrophs and separation of acetate from MES, was developed through one-step electroless nickel plating on ceramic hollow fiber (CHF) membrane. A thick layer of chemolithoautotrophs with 5.2 times higher cell density, which was dominated by Sporomusa (68 % of the total sequence reads in biocathode), was enriched on the membrane cathode surface through suspended biomass microfiltration compared to MES reactors operated without filtration. Simultaneously, >87 % of acetate (31 mM) per batch could be harvested after catholyte microfiltration. The Ni content was > 80 % on the CHF surface after long-term operation in the two-chamber MES system, which exhibited 78 % lower charge transfer resistance compared to three-chamber MES system (∼110 vs 510 Ω) for acetate separation/extraction. The ease of product separation in two-chamber MES systems and the fast establishment of chemolithoautotrophs on the cathode are a step forward in realizing MES systems as a promising platform for CO2 reduction and biochemical production in a circular carbon bioeconomy.
  • Are commercial polyamide seawater and brackish water membranes effectively charged?

    Blankert, Bastiaan; Huisman, Kees Theo; Martinez, Fernan David; Vrouwenvelder, Johannes Simon; Picioreanu, Cristian (Journal of Membrane Science Letters, Elsevier BV, 2022-07-30) [Article]
    New developments in modeling solute transport in reverse osmosis (RO) membranes are based on the mechanistic description of solution friction and electromigration. In these models, the membrane charge significantly impacts the separation that occurs in the membrane through Donnan partitioning. One implication of membrane charge is that the salt permeability strongly depends on the ion concentration in the feedwater. In this study, we experimentally evaluate the effect of salinity, varied over almost two orders of magnitude (ca. 10–650mM), on four commercially available polyamide seawater RO and brackish water RO membranes. We found no significant effect of feed concentration on observed salt permeability, while the membrane performance closely resembled the specification by the manufacturers. We also demonstrate that a minor leak in the membrane provides a plausible alternative explanation to trend between concentration and salt permeability reported in other studies. The standard solution diffusion model provides a satisfactory description of our data for the membranes and feedwater conditions that we tested.
  • The Gardenia Carotenoid Cleavage Dioxygenase 4a is an efficient tool for biotechnological production of crocins in green and non-green plant tissues

    Zheng, Xiongjie; Mi, Jianing; Balakrishna, Aparna; Liew, Kit Xi; Ablazov, Abdugaffor; Sougrat, Rachid; Al-Babili, Salim (Plant Biotechnology Journal, Wiley, 2022-07-29) [Article]
    Crocins are beneficial antioxidants and potential chemotherapeutics that give raise, together with picrocrocin, to the color and taste of saffron, the most expensive spice, respectively. Crocins are formed from crocetin dialdehyde that is produced in Crocus sativus from zeaxanthin by the Carotenoid Cleavage Dioxygenase 2L (CsCCD2L), while GjCCD4a from Gardenia jasminoides, another major source of crocins, converted different carotenoids, including zeaxanthin, into crocetin dialdehyde in bacterio. To establish a biotechnological platform for sustainable production of crocins, we investigated the enzymatic activity of GjCCD4a, in comparison to CsCCD2L, in citrus callus engineered by Agrobacterium-mediated super-transformation of multi genes and in transiently transformed Nicotiana benthamiana leaves. We demonstrate that co-expression of GjCCD4a with phytoene synthase and β-carotene hydroxylase genes is an optimal combination for heterologous production of crocetin, crocins and picrocrocin in citrus callus. By profiling apocarotenoids and using in vitro assays, we show that GjCCD4a cleaved β-carotene, in planta, and produced crocetin dialdehyde via C30 β-apocarotenoid intermediate. GjCCD4a also cleaved C27 β-apocarotenoids, providing a new route for C17-dialdehyde biosynthesis. Callus lines overexpressing GjCCD4a contained higher number of plastoglobuli in chromoplast-like plastids and increased contents in phytoene, C17:0 fatty acid (FA), and C18:1 cis-9 and C22:0 FA esters. GjCCD4a showed a wider substrate specificity and higher efficiency in Nicotiana leaves, leading to the accumulation of up to 1.6 mg/g dry weight crocins. In summary, we established a system for investigating CCD enzymatic activity in planta and an efficient biotechnological platform for crocins production in green and non-green crop tissues/organs.
  • Peptide nanogels as a scaffold for fabricating dermal grafts and 3D vascularized skin models

    Arab, Wafaa; Susapto, Hepi Hari; Alhattab, Dana Majed; Hauser, Charlotte (Journal of Tissue Engineering, SAGE Publications, 2022-07-29) [Article]
    Millions of people worldwide suffer from skin injuries, which create significant problems in their lives and are costly to cure. Tissue engineering is a promising approach that aims to fabricate functional organs using biocompatible scaffolds. We designed ultrashort tetrameric peptides with promising properties required for skin tissue engineering. Our work aimed to test the efficacy of these scaffolds for the fabrication of dermal grafts and 3D vascularized skin tissue models. We found that the direct contact of keratinocytes and fibroblasts enhanced the proliferation of the keratinocytes. Moreover, the expression levels of TGF-β1, b-FGF, IL-6, and IL-1α is correlated with the growth of the fibroblasts and keratinocytes in the co-culture. Furthermore, we successfully produced a 3D vascularized skin co-culture model using these peptide scaffolds. We believe that the described results represent an advancement in the fabrication of skin tissue equivalent, thereby providing the opportunity to rebuild missing, failing, or damaged parts.
  • Synergistic Practicing of Rhizobacteria and Silicon Improve Salt Tolerance: Implications from Boosted Oxidative Metabolism, Nutrient Uptake, Growth and Grain Yield in Mung Bean

    Mahmood, Sajid; Daur, Ihsanullah; Yasir, Muhammad; Waqas, Muhammad; Hirt, Heribert (Plants, MDPI AG, 2022-07-29) [Article]
    Plant growth promoting rhizobacteria (PGPR) and silicon (Si) are known for alleviating abiotic stresses in crop plants. In this study, Bacillus drentensis and Enterobacter cloacae strains of PGPR and foliar application of Si were tested for regulating the antioxidant metabolism and nutrient uptake on grain yield of mung bean under irrigation of saline water (3.12 and 7.81 dS m−1). Bacterial inoculation and supplemental Si (1 and 2 kg ha−1) reduced salinity-induced oxidative stress in mung bean leaves. The improved salt stress tolerance was achieved by enhancing the activities of catalase (45%), peroxidase (43%) and ascorbate peroxidase (48%), while decreasing malondialdehyde levels (57%). Enhanced nutrient uptake of magnesium 1.85 mg g−1, iron 7 mg kg−1, zinc 49.66 mg kg−1 and copper 12.92 mg kg−1 in mung bean seeds was observed with foliar application of Si and PGPR inoculation. Biomass (7.75 t ha−1), number of pods per plant (16.02) and 1000 seed weight (60.95 g) of plants treated with 2 kg Si ha−1 and B. drentensis clearly outperformed treatments with Si or PGPR alone. In conclusion, application of Si and PGPR enhances mung bean productivity under saline conditions, thereby helping exploitation of agriculture in low productive areas.
  • Modular safe-harbor transgene insertion (MosTI) for targeted single-copy and extrachromosomal array integration in C. elegans

    El Mouridi, Sonia; Alkhaldi, Faisal; Frøkjær-Jensen, Christian (G3 Genes|Genomes|Genetics, Oxford University Press (OUP), 2022-07-28) [Article]
    Efficient and reproducible transgenesis facilitates and accelerates research using genetic model organisms. Here we describe a modular safe harbor transgene insertion (MosTI) for use in C. elegans which improves targeted insertion of single-copy transgenes by homology directed repair and targeted integration of extrachromosomal arrays by non-homologous end-joining. MosTI allows easy conversion between selection markers at insertion site and a collection of universal targeting vectors with commonly used promoters and fluorophores. Insertions are targeted at three permissive safe-harbor intergenic locations and transgenes are reproducibly expressed in somatic and germ cells. Chromosomal integration is mediated by CRISPR/Cas9, and positive selection is based on a set of split markers (unc-119, hygroR, and gfp) where only animals with chromosomal insertions are rescued, resistant to antibiotics, or fluorescent, respectively. Single-copy insertion is efficient using either constitutive or heat-shock inducible Cas9 expression (25 - 75%) and insertions can be generated from a multiplexed injection mix. Extrachromosomal array integration is also efficient (7 - 44%) at MosTI landing sites or at the endogenous unc-119 locus. We use short-read sequencing to estimate the plasmid copy numbers for eight integrated arrays (6 to 37 copies) and long-read Nanopore sequencing to determine the structure and size (5.4 Mb) of one array. Using universal targeting vectors, standardized insertion strains, and optimized protocols, it is possible to construct complex transgenic strains which should facilitate the study of increasingly complex biological problems in C. elegans.
  • Increased incompatibility of heterologous algal symbionts under thermal stress in the cnidarian-dinoflagellate model Aiptasia

    Cziesielski, Maha Joana; Liew, Yi Jin; Cui, Guoxin; Aranda, Manuel (Communications Biology, Springer Science and Business Media LLC, 2022-07-28) [Article]
    Rising ocean temperatures are increasing the rate and intensity of coral mass bleaching events, leading to the collapse of coral reef ecosystems. To better understand the dynamics of coral-algae symbioses, it is critical to decipher the role each partner plays in the holobiont’s thermotolerance. Here, we investigated the role of the symbiont by comparing transcriptional heat stress responses of anemones from two thermally distinct locations, Florida (CC7) and Hawaii (H2) as well as a heterologous host-symbiont combination composed of CC7 host anemones inoculated with the symbiont Breviolum minutum (SSB01) from H2 anemones (CC7-B01). We find that oxidative stress and apoptosis responses are strongly influenced by symbiont type, as further confirmed by caspase-3 activation assays, but that the overall response to heat stress is dictated by the compatibility of both partners. Expression of genes essential to symbiosis revealed a shift from a nitrogen- to a carbon-limited state only in the heterologous combination CC7-B01, suggesting a bioenergetic disruption of symbiosis during stress. Our results indicate that symbiosis is highly fine-tuned towards particular partner combinations and that heterologous host-symbiont combinations are metabolically less compatible under stress. These results are essential for future strategies aiming at increasing coral resilience using heterologous thermotolerant symbionts.
  • Unraveling the role of feed temperature and cross-flow velocity on organic fouling in membrane distillation using response surface methodology

    Ricceri, Francesco; Blankert, Bastiaan; Ghaffour, NorEddine; Vrouwenvelder, Johannes S.; Tiraferri, Alberto; Fortunato, Luca (Desalination, Elsevier BV, 2022-07-28) [Article]
    Understanding the role of operating condition on fouling development in membrane distillation (MD) is critical for the further optimization of MD technology. In this study, organic fouling development in MD was investigated varying the feed inlet temperature from 35 to 65 °C and the cross-flow velocity from 0.21 to 0.42 m/s. The fouling layer thickness was estimated at the end of each experiment non-invasively with optical coherence tomography. The set of experiments was mined to model the initial flux decline, the near-stable flux, and the final foulant thickness responses by central composite design, a useful response surface methodology (RSM) tool. The results indicated a linear increment of the fouling thickness by increasing the feed inlet temperatures. Overall, the feed inlet temperature governed both the initial flux decline and the fouling deposition. The benefits in water productivity obtained by increasing the feed temperature were always offset by higher fouling deposition. Higher cross-flow velocities showed a positive effect on the initial flux, which however translated in larger values of the initial flux decline rate. On the other hand, the higher shear stress contributed to a decrease of the final steady-state fouling layer thickness. The proposed approach was proven to be a valuable tool to assess the role of the operating conditions on fouling and process performance in MD.
  • Pollution and edaphic factors shape bacterial community structure and functionality in historically contaminated soils

    Mapelli, Francesca; Vergani, Lorenzo; Terzaghi, Elisa; Zecchin, Sarah; Raspa, Giuseppe; Marasco, Ramona; Rolli, Eleonora; Zanardini, Elisabetta; Morosini, Cristiana; Anelli, Simone; Nastasio, Paolo; Sale, Vanna Maria; Armiraglio, Stefano; Di Guardo, Antonio; Borin, Sara (Microbiological research, Elsevier BV, 2022-07-28) [Article]
    Studies about biodegradation potential in soils often refer to artificially contaminated and simplified systems, overlooking the complexity associated with contaminated sites in a real context. This work aims to provide a holistic view on microbiome assembly and functional diversity in the model site SIN Brescia-Caffaro (Italy), characterized by historical and uneven contamination by organic and inorganic compounds. Here, physical and chemical analyses and microbiota characterization were applied on one-hundred-twenty-seven soil samples to unravel the environmental factors driving bacterial community assembly and biodegradation potential in three former agricultural fields. Chemical analyses showed a patchy distribution of metals, metalloids and polychlorinated biphenyls (PCB) and allowed soil categorization according to depth and area of collections. Likewise, the bacterial community structure, described by molecular fingerprinting and 16S rRNA gene analyses, was significantly different according to collection site and depth. Pollutant concentrations (i.e., hexachloro-biphenyls, arsenic and mercury), nitrogen content and parameters related to soil texture were identified as main drivers of microbiota assembly, being significantly correlated to bacterial community composition. Moreover, bacteria putatively involved in the aerobic degradation of PCBs were enriched over the total bacterial community in topsoils, where the highest activity was recorded using fluorescein hydrolysis as proxy. Metataxonomic analyses revealed the presence of bacteria having metabolic pathways related to PCB degradation and tolerance to heavy metals and metalloids in the topsoil samples collected in all areas. Overall, the provided dissection of soil microbiota structure and its degradation potential in the SIN Brescia-Caffaro can contribute to target specific areas for rhizoremediation implementation. Metagenomics studies could be implemented in the future to understand if specific degradative pathways are present in historically polluted sites characterized by the co-occurrence of multiple classes of contaminants.
  • Establishment of 3D culture protocols for the maintenance and expansion of human pluripotent stem cell aggregates in a low scale platform and in the DASbox® Mini-Bioreactor System

    Hernandez-Bautista, Carlos Alberto (2022-07-27) [Thesis]
    Advisor: Adamo, Antonio
    Committee members: Merzaban, Jasmeen; Ibrahim, Leena Ali
    The human Embryonic Stem Cells (hESCs) and human induced Pluripotent Stem Cells (hiPSCs) have offered numerous advantages including but not limited to model diseases, high-throughput drug screening, and regenerative purposes. However, the employment of monolayer cultures has not been sufficient to mimic the in vivo stem cells niche. Thus, three-dimensional suspension cultures have helped us to advance our knowledge and ease the development of the human organs’ counterparts, commonly referred as organoids. Currently, the challenge is the generation of homogenous and reproducible human Pluripotent Stem Cell (hPSC) aggregates, the basic cellular unit to derive organoids. To date, the Ultra-Low Attachment (ULA) 6-well plates have been routinary used for the hPSC aggregates formation, which mainly relies on the inhibition of the Rho-associated kinase (ROCK) pathway resulting in the enhancement of cell survival coming from cryopreserved stocks or when passaging. However, little is known in this regard when analyzing the aggregate formation of hPSCs with two widely used compounds: RevitaCellTM Supplement and Y27632. Importantly, due to the high demand required from the regenerative medicine, I aimed to upscale the hPSC aggregates production in the DASbox® Mini-Bioreactor System. In this thesis, I established protocols for the hPSC aggregates formation by using two different types of media in two platforms being the ULA 6-well plates and the DASbox® Mini-Bioreactor System. In addition, I demonstrated that monolayer confluence cultures before single cell inoculations are paramount for the formation of bona fide hPSC aggregates in healthy and X aneuploid hiPSCs, precisely two hESCs and five hiPSCs.
  • A new approach to broaden the range of eye colour identifiable by IrisPlex in DNA phenotyping

    Paparazzo, Ersilia; Gozalishvili, Anzor; Lagani, Vincenzo; Geracitano, Silvana; Bauleo, Alessia; Falcone, Elena; Passarino, Giuseppe; Montesanto, Alberto (Scientific reports, Springer Science and Business Media LLC, 2022-07-27) [Article]
    IrisPlex system represents the most popular model for eye colour prediction. Based on six polymorphisms this model provides very accurate predictions that strongly depend on the definition of eye colour phenotypes. The aim of the present study was to introduce a new approach to improve eye colour prediction using the well-validated IrisPlex system. A sample of 238 individuals from a Southern Italian population was collected and for each of them a high-resolution image of eye was obtained. By quantifying eye colour variation into CIELAB space several clustering algorithms were applied for eye colour classification. Predictions with the IrisPlex model were obtained using eye colour categories defined by both visual inspection and clustering algorithms. IrisPlex system predicted blue and brown eye colour with high accuracy while it was inefficient in the prediction of intermediate eye colour. Clustering-based eye colour resulted in a significantly increased accuracy of the model especially for brown eyes. Our results confirm the validity of the IrisPlex system for forensic purposes. Although the quantitative approach here proposed for eye colour definition slightly improves its prediction accuracy, further research is still required to improve the model particularly for the intermediate eye colour prediction.
  • Formation of Organic Acids and Carbonyl Compounds in n-Butane Oxidation via γ-Ketohydroperoxide Decomposition

    Popolan-Vaida, Denisia Maria; Eskola, Arkke J.; Rotavera, Brandon; Lockyear, Jessica F.; Wang, Zhandong; Sarathy, Mani; Caravan, Rebecca L.; Zádor, Judit; Sheps, Leonid; Lucassen, Arnas; Moshammer, Kai; Dagaut, Philippe; Osborn, David L.; Hansen, Nils; Leone, Stephen R.; Taatjes, Craig A. (Angewandte Chemie, Wiley, 2022-07-27) [Article]
    A crucial chain-branching step in autoignition is the decomposition of ketohydroperoxides (KHP) to form an oxy radical and OH. Other pathways compete with chain-branching, such as “Korcek” dissociation of γ-KHP to a carbonyl and an acid. Here we characterize the formation of a γ-KHP and its decomposition to formic acid + acetone products from observations of n ‑butane oxidation in two complementary experiments. In jet-stirred reactor measurements, KHP is observed above 590 K. The KHP concentration decreases with increasing temperature, whereas formic acid and acetone products increase. Observation of characteristic isotopologs acetone‑ d 3 and formic acid- d 0 in the oxidation of CH 3 CD 2 CD 2 CH 3 is consistent with a Korcek mechanism. In laser-initiated oxidation experiments of n -butane, formic acid and acetone are produced on the timescale of KHP removal. Modelling the time-resolved production of formic acid provides an estimated upper limit of 2 s ‑1 for the rate coefficient of KHP decomposition to formic acid + acetone.

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