Publications by authors named "Raffaella Villa"

53 Publications

Achieving drinking water compliance levels for metaldehyde with an acclimated sand bioreactor.

Water Res 2020 Oct 6;184:116084. Epub 2020 Jul 6.

De Montfort University, Leicester, LE1 9HB, UK.

Metaldehyde removal was delivered to below the 0.1 μg L regulatory concentration in a laboratory scale continuous upflow fluidised sand bioreactor that had undergone acclimation through selective enrichment for metaldehyde degradation. This is the first reported case of successful continuous flow biological treatment of metaldehyde from real drinking water sources treating environmentally realistic metaldehyde concentrations. The impact of the acclimation process was impermanent, with the duration of effective treatment directly related to the elevated concentration of metaldehyde used during the enrichment process. The efficacy of the approach was demonstrated in continuous flow columns at both laboratory and pilot scale enabling degradation rates of between 0.1 and 0.2 mg L h. Future work needs to focus on optimisation of the sand bioreactor and the acclimation process to ensure viability and feasibility of the approach at full scale.
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http://dx.doi.org/10.1016/j.watres.2020.116084DOI Listing
October 2020

Two-step mechanism for selective incorporation of lncRNA into a chromatin modifier.

Nucleic Acids Res 2020 07;48(13):7483-7501

Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany.

The MLE DExH helicase and the roX lncRNAs are essential components of the chromatin modifying Dosage Compensation Complex (DCC) in Drosophila. To explore the mechanism of ribonucleoprotein complex assembly, we developed vitRIP, an unbiased, transcriptome-wide in vitro assay that reveals RNA binding specificity. We found that MLE has intrinsic specificity for U-/A-rich sequences and tandem stem-loop structures and binds many RNAs beyond roX in vitro. The selectivity of the helicase for physiological substrates is further enhanced by the core DCC. Unwinding of roX2 by MLE induces a highly selective RNA binding surface in the unstructured C-terminus of the MSL2 subunit and triggers-specific association of MLE and roX2 with the core DCC. The exquisite selectivity of roX2 incorporation into the DCC thus originates from intimate cooperation between the helicase and the core DCC involving two distinct RNA selection principles and their mutual refinement.
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http://dx.doi.org/10.1093/nar/gkaa492DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7528653PMC
July 2020

Assessing the potential of enhanced primary clarification to manage fats, oils and grease (FOG) at wastewater treatment works.

Sci Total Environ 2020 Aug 20;728:138415. Epub 2020 Apr 20.

Cranfield University, Cranfield MK43 0AL, United Kingdom. Electronic address:

Daily, sewage treatment works (STWs) receive large volumes of fats, oils and greases (FOG), by-products of food preparation. To increase FOG removal at STW, conventional primary sedimentation tanks (PSTs) can be enhanced using chemical coagulant or through dissolved air flotation (DAF) techniques. This work aimed to assess the potential benefits of enhanced primary treatment for FOG removal through an energy and costs analysis. To achieve this, a five-year sampling programme was conducted monthly at 15 STWs measuring FOG concentrations in crude and settled sewage (i.e. after primary treatment). In addition, two DAF pilot systems were trialled for four months and their performance, in terms of FOG removal, was assessed and compared to that of a control primary clarifier. Across the 15 STWs, influent FOG concentrations were found at 57 ± 11 mg.L. Chemical coagulants dosed prior to PSTs increased FOG removal rates on average to 71% whilst traditional sedimentation only achieved 50% removal. Effluent FOG concentrations were found between 12-22 mg.L and 19-36 mg.L respectively. By contrast, DAF achieved FOG effluent concentrations on average at 10 ± 4 mg.L corresponding to 74% removal from a relatively low influent concentration of 40 ± 30 mg.L. Thus, enhanced primary treatments have the potential to reduce organic load to secondary treatment and increase energy generation through anaerobic digestion. The overall net energy balance was estimated at 2269 MWh.year for the DAF compared to 3445 MWh.year for the chemically-enhanced PST making it a less financially attractive alternative. Yet, in the case where the works require upgrading to accommodate flow or load increases, DAF appeared as a sensible option over sedimentation offering significantly lower capital costs and footprint. In relation to FOG management, upgrading all STWs is not realistic and will require understanding where the benefits would be the highest.
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http://dx.doi.org/10.1016/j.scitotenv.2020.138415DOI Listing
August 2020

Potential influence of sewer heat recovery on in-sewer processes.

Water Sci Technol 2019 Dec;80(12):2344-2351

Department of Civil and Structural Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, UK.

Heat recovery from combined sewers has a significant potential for practical renewable energy provision as sources of heat demand and sewer pipes are spread across urban areas. Sewers are continuously recharged with relatively hot wastewater, as well as interacting with heat sources from surrounding air and soil. However, the potential effects of modifying sewage temperature on in-sewer processes have received little attention. The deposition of fats, oils and greases (FOGs) and hydrogen sulphide formation are biochemical processes and are thus influenced by temperature. This paper utilises a case study approach to simulate anticipated temperature reductions in a sewer network due to heat recovery. A laboratory investigation into the formation of FOG deposits at temperatures varying between 5 °C and 20 °C provided mixed results, with only a weak temperature influence, highlighting the need for more research to fully understand the influence of the wastewater composition as well as temperature on FOG deposit formation. A separate modelling investigation into the formation of hydrogen sulphide when inflow temperature is varied between 5 °C and 20 °C showed considerable reductions in hydrogen sulphide formation. Hence, heat extraction from sewers could be a promising method for managing some in-sewer processes, combined with traditional methods such as chemical dosing.
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http://dx.doi.org/10.2166/wst.2020.061DOI Listing
December 2019

Characterisation and energy assessment of fats, oils and greases (FOG) waste at catchment level.

Waste Manag 2020 Feb 13;103:399-406. Epub 2020 Jan 13.

Cranfield University, Cranfield, Bedfordshire MK43 0AL, United Kingdom; Cranfield University, Cranfield, Bedfordshire MK43 0AL, UK De Montfort University, Leicester, LE1 9BH, UK. Electronic address:

Several of the waste materials that have a negative impact on the sewer system are produced by fats, oils and greases (FOG) discharged from commercial and domestic kitchens. These materials accumulate at different points in the sewer catchment, from kitchens to pumping stations, sewers and sewage treatment works (STWs), and comprise oily wastewater, floating agglomerates and hard deposits. Despite their detrimental effects, these waste materials have a high calorific content and are an ideal feedstock for energy recovery processes. So far, the overall volume of each type of waste and their physical-chemical properties in relation to their collection point are unknown. However, from a management point of view, knowledge on each feedstock quality and volumes is necessary to develop an economic viable solution for their collection and for energy recovery purposes. In this study, FOG wastes collected from households, food service establishments (FSEs), sewage pumping stations, sewers and STWs, were compared to sewage sludge in terms of organic contents and energy potentials. As expected, FOG recovered at source (households and FSEs) were 'cleaner' and had a higher energy content. Once mixed with wastewater the materials changed in composition and lost some of their energy per unit mass. Our results showed that around 94,730 tonnes.year of these materials could be recovered from the Thames Water Utilities' catchment, one of the most populated in the UK. These materials could produce up to 222 GWh.year as biogas, close to double of what is produced with sewage sludge digestion and around 19% of the company energy needs. Finally, even with over six million households in the catchment, the results showed that most of the FOG waste was produced by FSEs (over 48,000 premises) with an estimated average of 79,810 tonnes.year compared to 14,920 tonnes.year from private households. This is an important outcome as recovery from FSEs will be cheaper and easier if the company decides to implement a collection system for energy recovery.
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http://dx.doi.org/10.1016/j.wasman.2019.12.040DOI Listing
February 2020

Dry anaerobic digestion of organic waste: A review of operational parameters and their impact on process performance.

Bioresour Technol 2020 Mar 24;299:122681. Epub 2019 Dec 24.

Cranfield University, School of Water, Energy and Environment, United Kingdom. Electronic address:

Dry digestion is a suitable technology for treating organic wastes with varying composition such as the organic fraction of municipal solids waste. Yet, there is a need for further research to overcome some of the disadvantages associated with the high total solids content of the process. Optimisation of inoculum to substrate ratio, feedstock composition and size, liquid recirculation, bed compaction and use of bulking agents are some of the parameters that need further investigation in batch dry anaerobic digestion, to limit localised inhibition effects and avoid process instability. In addition, further attention on the relation between feedstock composition, organic loading rate and mixing regimes is required for continuous dry anaerobic digestion systems. This paper highlights all the areas where knowledge is scarce and value can be added to increase dry anaerobic digestion performance and expansion.
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http://dx.doi.org/10.1016/j.biortech.2019.122681DOI Listing
March 2020

From full-scale biofilters to bioreactors: Engineering biological metaldehyde removal.

Sci Total Environ 2019 Oct 21;685:410-418. Epub 2019 May 21.

Cranfield University, Bedfordshire MK43 0AL, UK.

Polar, low molecular weight pesticides such as metaldehyde are challenging and costly to remove from drinking water using conventional treatment methods. Although biological treatments can be effective at treating micropollutants, through biodegradation and sorption processes, only some operational biofilters have shown the ability to remove metaldehyde. As sorption plays a minor role for such polar organic micropollutants, biodegradation is therefore likely to be the main removal pathway. In this work, the biodegradation of metaldehyde was monitored, and assessed, in an operational slow sand filter. Long-term data showed that metaldehyde degradation improved when inlet concentrations increased. A comparison of inactive and active sand batch reactors showed that metaldehyde removal happened mainly through biodegradation and that the removal rates were greater after the biofilm was acclimated through exposure to high metaldehyde concentrations. This suggested that metaldehyde removal was reliant on enrichment and that the process could be engineered to decrease treatment times (from days to hours). Through-flow experiments using fluidised bed reactors, showed the same behaviour following metaldehyde acclimation. A 40% increase in metaldehyde removal was observed in acclimated compared with non-acclimated columns. This increase was sustained for >40 days, achieving an average of 80% removal and compliance (<0.1 μ L) for >20 days. An initial microbial analysis of the acclimated and non-acclimated biofilm from the same filter materials, showed that the microbial community in acclimated sand was significantly different. This work presents a novel conceptual template for a faster, chemical free, low cost, biological treatment of metaldehyde and other polar pollutants in drinking water. In addition, this is the first study to report kinetics of metaldehyde degradation in an active microbial biofilm at a WTW.
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http://dx.doi.org/10.1016/j.scitotenv.2019.05.304DOI Listing
October 2019

Risk assessments for quality-assured, source-segregated composts and anaerobic digestates for a circular bioeconomy in the UK.

Environ Int 2019 06 28;127:253-266. Epub 2019 Mar 28.

Waste and Resources Action Programme, Second Floor, Blenheim Court, 19 George Street, Banbury, Oxfordshire OX16 5BH, United Kingdom.

A circular economy relies on demonstrating the quality and environmental safety of wastes that are recovered and reused as products. Policy-level risk assessments, using generalised exposure scenarios, and informed by stakeholder communities have been used to appraise the acceptability of necessary changes to legislation, allowing wastes to be valued, reused and marketed. Through an extensive risk assessment exercise, summarised in this paper, we explore the burden of proof required to offer safety assurance to consumer and brand-sensitive food sectors in light of attempts to declassify, as wastes, quality-assured, source-segregated compost and anaerobic digestate products in the United Kingdom. We report the residual microbiological and chemical risks estimated for both products in land application scenarios and discuss these in the context of an emerging UK bioeconomy worth £52bn per annum. Using plausible worst case assumptions, as demanded by the quality food sector, risk estimates and hazard quotients were estimated to be low or negligible. For example, the human health risk of E. coli 0157 illness from exposure to microbial residuals in quality-assured composts, through a ready-to-eat vegetable consumption exposure route, was estimated at ~10 per person per annum. For anaerobic digestion residues, 7 × 10cases of E. coli 0157 were estimated per annum, a potential contribution of 0.0007% of total UK cases. Hazard quotients for potential chemical contaminants in both products were insufficient in magnitude to merit detailed quantitative risk assessments. Stakeholder engagement and expert review was also a substantive feature of this study. We conclude that quality-assured, source-segregated products applied to land, under UK quality protocols and waste processing standards, pose negligible risks to human, animal, environmental and crop receptors, providing that risk management controls set within the standards and protocols are adhered to.
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http://dx.doi.org/10.1016/j.envint.2019.03.044DOI Listing
June 2019

Understanding microbial ecology can help improve biogas production in AD.

Sci Total Environ 2018 Nov 17;642:754-763. Epub 2018 Jun 17.

School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, UK. Electronic address:

454-Pyrosequencing and lipid fingerprinting were used to link anaerobic digestion (AD) process parameters (pH, alkalinity, volatile fatty acids (VFAs), biogas production and methane content) with the reactor microbial community structure and composition. AD microbial communities underwent stress conditions after changes in organic loading rate and digestion substrates. 454-Pyrosequencing analysis showed that, irrespectively of the substrate digested, methane content and pH were always significantly, and positively, correlated with community evenness. In AD, microbial communities with more even distributions of diversity are able to use parallel metabolic pathways and have greater functional stability; hence, they are capable of adapting and responding to disturbances. In all reactors, a decrease in methane content to <30% was always correlated with a 50% increase of Firmicutes sequences (particularly in operational taxonomic units (OTUs) related to Ruminococcaceae and Veillonellaceae). Whereas digesters producing higher methane content (above 60%), contained a high number of sequences related to Synergistetes and unidentified bacterial OTUs. Finally, lipid fingerprinting demonstrated that, under stress, the decrease in archaeal biomass was higher than the bacterial one, and that archaeal Phospholipid etherlipids (PLEL) levels were correlated to reactor performances. These results demonstrate that, across a number of parameters such as lipids, alpha and beta diversity, and OTUs, knowledge of the microbial community structure can be used to predict, monitor, or optimise AD performance.
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http://dx.doi.org/10.1016/j.scitotenv.2018.06.007DOI Listing
November 2018

Aged-engineered nanoparticles effect on sludge anaerobic digestion performance and associated microbial communities.

Sci Total Environ 2017 Dec 23;609:232-241. Epub 2017 Jul 23.

Cranfield University, School of Water, Energy and Environment, Cranfield MK43 0AL, UK. Electronic address:

To investigate the potential effect of aged engineered nanoparticles (a-ENPs) on sludge digestion performance, 150L pilot anaerobic digesters (AD) were fed with a blend of primary and waste activated sludge spiked either with a mixture of silver oxide, titanium dioxide and zinc oxide or a mixture of their equivalent bulk metal salts to achieve a target concentration of 250, 2000, and 2800mgkg dry weight, respectively. Volatile fatty acids (VFA) were 1.2 times higher in the spiked digesters and significantly different (p=0.05) from the control conditions. Specifically, isovaleric acid concentration was 2 times lower in the control digester compared to the spiked digesters, whereas hydrogen sulfide was 2 times lower in the ENPs spiked digester indicating inhibitory effect on sulfate reducing microorganisms. Based on the ether-linked isoprenoids concentration, the total abundance of methanogens was 1.4 times lower in the ENPs spiked digester than in the control and metal salt spiked digesters. Pyrosequencing indicated 80% decrease in abundance and diversity of methanogens in ENPs spiked digester compared to the control digester. Methanosarcina acetivorans and Methanosarcina barkeri were identified as nano-tolerant as their relative abundance increased by a factor of 6 and 11, respectively, compared to the other digesters. The results further provide compelling evidence on the resilience of Fusobacteria, Actinobacteria and the Trojan horse-like effect of ENPs which offered a competitive advantage to some organisms while reducing microbial abundance and diversity.
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http://dx.doi.org/10.1016/j.scitotenv.2017.07.178DOI Listing
December 2017

Ubiquitylation of the acetyltransferase MOF in Drosophila melanogaster.

PLoS One 2017 16;12(5):e0177408. Epub 2017 May 16.

Molecular Biology Division, Biomedical Center and Center for integrated Protein Science Ludwig-Maximilians-University, Munich, Germany.

The nuclear acetyltransferase MOF (KAT8 in mammals) is a subunit of at least two multi-component complexes involved in transcription regulation. In the context of complexes of the 'Non-Specific-Lethal' (NSL) type it controls transcription initiation of many nuclear housekeeping genes and of mitochondrial genes. While this function is conserved in metazoans, MOF has an additional, specific function in Drosophila in the context of dosage compensation. As a subunit of the male-specific-lethal dosage compensation complex (MSL-DCC) it contributes to the doubling of transcription output from the single male X chromosome by acetylating histone H4. Proper dosage compensation requires finely tuned levels of MSL-DCC and an appropriate distribution of MOF between the regulatory complexes. The amounts of DCC formed depends directly on the levels of the male-specific MSL2, which orchestrates the assembly of the DCC, including MOF recruitment. We found earlier that MSL2 is an E3 ligase that ubiquitylates most MSL proteins, including MOF, suggesting that ubiquitylation may contribute to a quality control of MOF's overall levels and folding state as well as its partitioning between the complex entities. We now used mass spectrometry to map the lysines in MOF that are ubiquitylated by MSL2 in vitro and identified in vivo ubiquitylation sites of MOF in male and female cells. MSL2-specific ubiquitylation in vivo could not be traced due to the dominance of other, sex-independent ubiquitylation events and conceivably may be rare or transient. Expressing appropriately mutated MOF derivatives we assessed the importance of the ubiquitylated lysines for dosage compensation by monitoring DCC formation and X chromosome targeting in cultured cells, and by genetic complementation of the male-specific-lethal mof2 allele in flies. Our study provides a comprehensive analysis of MOF ubiquitylation as a reference for future studies.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0177408PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5433716PMC
September 2017

Microbial production of succinic acid using crude and purified glycerol from a based biorefinery.

Biotechnol Rep (Amst) 2016 Jun 2;10:84-93. Epub 2016 Apr 2.

Department of Chemical Engineering, Jadavpur University, Kolkata 700032, India.

Microbial conversion of crude and purified glycerol obtained in the process of biorefining is carried out to produce succinic acid using . Batch tests are performed for nine different substrate concentrations of commercial, purified and crude glycerol, in order to observe cell growth and substrate utilization rate. Inhibitory (Halden-Andrew, Aiba-Edward, Tessier type and Andrews) as well as non-inhibitory (Monod, Moser and Tessier) models are fitted to the relationship between specific growth rate and substrate concentration obtained from the growth curves. Considering the inhibition effect, Aiba-Edward model ranked 1 out of 7 in case of two samples and Haldane-Andrew model ranked 1 in case of one sample. Aiba-Edward model gave the best fitment for a large range of concentrations of all the three types of glycerol, crude, purified and laboratory grade. Maximum production of succinic acid is obtained from commercial glycerol at pH 7 and 37.5 °C.
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http://dx.doi.org/10.1016/j.btre.2016.03.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5040874PMC
June 2016

PionX sites mark the X chromosome for dosage compensation.

Nature 2016 09 31;537(7619):244-248. Epub 2016 Aug 31.

Division of Molecular Biology, Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany.

The rules defining which small fraction of related DNA sequences can be selectively bound by a transcription factor are poorly understood. One of the most challenging tasks in DNA recognition is posed by dosage compensation systems that require the distinction between sex chromosomes and autosomes. In Drosophila melanogaster, the male-specific lethal dosage compensation complex (MSL-DCC) doubles the level of transcription from the single male X chromosome, but the nature of this selectivity is not known. Previous efforts to identify X-chromosome-specific target sequences were unsuccessful as the identified MSL recognition elements lacked discriminative power. Therefore, additional determinants such as co-factors, chromatin features, RNA and chromosome conformation have been proposed to refine targeting further. Here, using an in vitro genome-wide DNA binding assay, we show that recognition of the X chromosome is an intrinsic feature of the MSL-DCC. MSL2, the male-specific organizer of the complex, uses two distinct DNA interaction surfaces-the CXC and proline/basic-residue-rich domains-to identify complex DNA elements on the X chromosome. Specificity is provided by the CXC domain, which binds a novel motif defined by DNA sequence and shape. This motif characterizes a subclass of MSL2-binding sites, which we name PionX (pioneering sites on the X) as they appeared early during the recent evolution of an X chromosome in D. miranda and are the first chromosomal sites to be bound during de novo MSL-DCC assembly. Our data provide the first, to our knowledge, documented molecular mechanism through which the dosage compensation machinery distinguishes the X chromosome from an autosome. They highlight fundamental principles in the recognition of complex DNA elements by protein that will have a strong impact on many aspects of chromosome biology.
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http://dx.doi.org/10.1038/nature19338DOI Listing
September 2016

Anaplastic lymphoma kinase aberrations correlate with metastatic features in pediatric rhabdomyosarcoma.

Oncotarget 2016 09;7(37):58903-58914

Department of Pediatric Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.

Rhabdomyosarcoma (RMS) is the most frequent soft tissue tumor in childhood and arises from immature mesenchymal cells committed to skeletal muscle differentiation. Anaplastic Lymphoma Kinase (ALK) is a receptor tyrosine kinase aberrantly expressed in several cancers. Moreover, ALK full-length receptor protein has been observed in RMS, although its clinical and functional significance is yet controversial. The role of ALK and its clinical relevance were investigated in a selected cohort of 74 FFPE pediatric RMS and a panel of RMS cell lines, evaluating its gene and protein status, utilizing Fluorescent In Situ Hybridization (FISH), immunohistochemistry (IHC) and Western blot approaches. Moreover, to get insight into its possible therapeutic relevance, effects of ALK silencing on cell proliferation, invasion and apoptosis were studied in RMS cells. ALK IHC positivity was significantly correlated with gene copy number gain, the alveolar subtype, PAX3/7-FOXO1 rearrangements, the presence of metastasis at diagnosis and a worse overall outcome. Furthermore, EML4-ALK fusion gene associated with higher protein expression was identified in an embryonal RMS. ALK silencing in RH30 ALK positive cells strongly inhibited invasion capability. Overall, our data suggest a potential role of ALK in pediatric RMS.
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http://dx.doi.org/10.18632/oncotarget.10368DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5312284PMC
September 2016

Organic loading rate: A promising microbial management tool in anaerobic digestion.

Water Res 2016 09 6;100:348-356. Epub 2016 May 6.

Cranfield University, School of Water, Energy and Environment, Cranfield, MK43 0AL, UK. Electronic address:

This study investigated the effect of changes in organic loading rate (OLR) and feedstock on the volatile fatty acids (VFAs) production and their potential use as a bioengineering management tool to improve stability of anaerobic digesters. Digesters were exposed to one or two changes in OLR using the same or different co-substrates (Fat Oil and Grease waste (FOG) and/or glycerol). Although all the OLR fluctuations produced a decrease in biogas and methane production, the digesters exposed twice to glycerol showed faster recovery towards stable conditions after the second OLR change. This was correlated with the composition of the VFAs produced and their mode of production, from parallel to sequential, resulting in a more efficient recovery from inhibition of methanogenesis. The change in acids processing after the first OLR increase induced a shift in the microbial community responsible of the process optimisation when the digesters were exposed to a subsequent OLR increase with the same feedstock. When the digesters were exposed to an OLR change with a different feedstock (FOG), the recovery took 7d longer than with the same one (glycerol). However, the microbial community showed functional resilience and was able to perform similarly to pre-exposure conditions. Thus, changes in operational conditions can be used to influence microbial community structure for anaerobic digestion (AD) optimisation. Finally, shorter recovery times and increased resilience of digesters were linked to higher numbers of Clostridia incertae sedis XV, suggesting that this group may be a good candidate for AD bioaugmentation to speed up recovery after process instability or OLR increase.
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http://dx.doi.org/10.1016/j.watres.2016.05.009DOI Listing
September 2016

Influence of microalgal N and P composition on wastewater nutrient remediation.

Water Res 2016 Mar 4;91:371-8. Epub 2016 Jan 4.

Cranfield University, Cranfield, MK43 0AL, UK. Electronic address:

Microalgae have demonstrated the ability to remediate wastewater nutrients efficiently, with methods to further enhance performance through species selection and biomass concentration. This work evaluates a freshwater species remediation characteristics through analysis of internal biomass N:P (nitrogen:phosphorus) and presents a relationship between composition and nutrient uptake ability to assist in species selection. Findings are then translated to an optimal biomass concentration, achieved through immobilisation enabling biomass intensification by modifying bead concentration, for wastewaters of differing nutrient concentrations at hydraulic retention times (HRT) from 3 h to 10 d. A HRT <20 h was found suitable for the remediation of secondary effluent by immobilised Scenedesmus obliquus and Chlorella vulgaris at bead concentrations as low as 3.2 and 4.4 bead·mL(-1). Increasing bead concentrations were required for shorter HRTs with 3 h possible at influent concentrations <5 mgP L(-1).
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http://dx.doi.org/10.1016/j.watres.2015.12.054DOI Listing
March 2016

Insights into the effect of mixed engineered nanoparticles on activated sludge performance.

FEMS Microbiol Ecol 2015 Jul 16;91(7). Epub 2015 Jul 16.

School of Energy, Environment and Agrifood, Cranfield University, College Road, Cranfield, Bedfordshire MK43 0AL, UK

In this study, the effects, fate and transport of ENPs in wastewater treatment plants (WWTP) were investigated using three parallel pilot WWTPs operated under identical conditions. The WWTPs were spiked with (i) an ENP mixture consisting of silver oxide, titanium dioxide and zinc oxide, and (ii) bulk metal salts. The third plant served as control (unspiked). ENP effects were evaluated for (i) bulk contaminant removal, (ii) activated sludge (AS) process performance, (iii) microbial community structure and dynamics and (iv) microbial inhibition. ENPs showed a strong affinity for biosolids and induced a specific oxygen uptake rate two times higher than the control. The heterotrophic biomass retained its ability to nitrify and degrade organic matter. However, non-recovery of ammonia- and nitrite-oxidizing bacteria such as Nitrosomonas, Nitrobacter or Nitrospira in the ENP spiked reactors suggests selective inhibitory effects. The results further suggest that ENPs and metal salts have antimicrobial properties which can reduce synthesis of extracellular polymeric substances and therefore floc formation. Scanning electron microscopy evidenced selective damage to some microbes, whereas lipid fingerprinting and 454 pyrosequencing indicated a temporal shift in the microbial community structure and diversity. Acidovorax, Rhodoferax, Comamonas and Methanosarcina were identified as nano-tolerant species. Competitive growth advantage of the nano-tolerant species influenced the removal processes and unlike other xenobiotic compounds, ENPs can hasten the natural selection of microbial species in AS.
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http://dx.doi.org/10.1093/femsec/fiv082DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4629872PMC
July 2015

Lack of activation of telomere maintenance mechanisms in human adipose stromal cells derived from fatty portion of lipoaspirates.

Plast Reconstr Surg 2015 Jan;135(1):114e-123e

Milan and Catania, Italy From the Department of Surgery, Plastic and Reconstructive Surgery Unit, and the Department of Experimental Oncology and Molecular Medicine, Biomarkers Unit, Fondazione IRCCS Istituto Nazionale dei Tumori Milano; the Multidisciplinary Breast Unit, Azienda Ospedaliera Cannizzaro; and the Scuola di Oncologia Chirurgica Ricostruttiva.

Background: Significant improvement in the understanding of mesenchymal stem cell biology paved the way to their clinical use. Human lipoaspirates derived from mesenchymal stem cells (adipose-derived stem cells) continue to draw the attention of researchers in the field of basic and applied research due to their regenerative, reparative, angiogenic, antiapoptotic, and immunosuppressive properties, all of which collectively point out their therapeutic potential. There is still, however, a need for further investigation to improve the knowledge of stem cell biology, to broaden their field of use, and to enhance their therapeutic effectiveness.

Methods: The authors characterized human adipose-derived stem cells at different in vitro culture time points in terms of immunophenotype, multilineage differentiation, long-term survival with self-renewal capacity, and presence of telomere maintenance mechanisms (telomerase activity and alternative lengthening of telomere) for excluding their eventual susceptibility to malignant transformation.

Results: Adipose-derived stem cells were isolated from the abdomen and peritrochanteric region of 31 female donors, propagated, and monitored in vitro for several passages. The outgrown cells shared the biological properties of mesenchymal stem cells, with adherence to plastic, expression of the typical surface markers, and induction of adipogenic, osteogenic, and chondrogenic differentiation. Telomerase activity and alternative lengthening of telomere mechanisms at different passages of cultures were not evidenced.

Conclusion: The results support the concept that in vitro expanded adipose-derived stem cells obtained from fat tissue are not susceptible to developing one of the hallmarks of malignant transformation and can be considered amenable for cell therapy approaches.
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http://dx.doi.org/10.1097/PRS.0000000000001008DOI Listing
January 2015

Structural basis of X chromosome DNA recognition by the MSL2 CXC domain during Drosophila dosage compensation.

Genes Dev 2014 Dec;28(23):2652-62

National Institute of Biological Sciences, Beijing 102206, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China

The male-specific lethal dosage compensation complex (MSL-DCC) selectively assembles on the X chromosome in Drosophila males and activates gene transcription by twofold through histone acetylation. An MSL recognition element (MRE) sequence motif nucleates the initial MSL association, but how it is recognized remains unknown. Here, we identified the CXC domain of MSL2 specifically recognizing the MRE motif and determined its crystal structure bound to specific and nonspecific DNAs. The CXC domain primarily contacts one strand of DNA duplex and employs a single arginine to directly read out dinucleotide sequences from the minor groove. The arginine is flexible when bound to nonspecific sequences. The core region of the MRE motif harbors two binding sites on opposite strands that can cooperatively recruit a CXC dimer. Specific DNA-binding mutants of MSL2 are impaired in MRE binding and X chromosome localization in vivo. Our results reveal multiple dynamic DNA-binding modes of the CXC domain that target the MSL-DCC to X chromosomes.
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http://dx.doi.org/10.1101/gad.250936.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4248295PMC
December 2014

Impacts of microalgae pre-treatments for improved anaerobic digestion: thermal treatment, thermal hydrolysis, ultrasound and enzymatic hydrolysis.

Water Res 2014 Nov 6;65:350-61. Epub 2014 Aug 6.

Cranfield University, Bedfordshire, UK. Electronic address:

Anaerobic digestion (AD) of microalgae is primarily inhibited by the chemical composition of their cell walls containing biopolymers able to resist bacterial degradation. Adoption of pre-treatments such as thermal, thermal hydrolysis, ultrasound and enzymatic hydrolysis have the potential to remove these inhibitory compounds and enhance biogas yields by degrading the cell wall, and releasing the intracellular algogenic organic matter (AOM). This work investigated the effect of four pre-treatments on three microalgae species, and their impact on the quantity of soluble biomass released in the media and thus on the digestion process yields. The analysis of the composition of the soluble COD released and of the TEM images of the cells showed two main degradation actions associated with the processes: (1) cell wall damage with the release of intracellular AOM (thermal, thermal hydrolysis and ultrasound) and (2) degradation of the cell wall constituents with the release of intracellular AOM and the solubilisation of the cell wall biopolymers (enzymatic hydrolysis). As a result of this, enzymatic hydrolysis showed the greatest biogas yield increments (>270%) followed by thermal hydrolysis (60-100%) and ultrasounds (30-60%).
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http://dx.doi.org/10.1016/j.watres.2014.07.040DOI Listing
November 2014

Role of UTX in retinoic acid receptor-mediated gene regulation in leukemia.

Mol Cell Biol 2014 Oct 28;34(19):3765-75. Epub 2014 Jul 28.

Center for Genomic Regulation, Barcelona, Spain Universitat Pompeu Fabra, Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain

Human UTX, a member of the Jumonji C family of proteins, associates with mixed-lineage leukemia 3/4 complexes. Stimulation with retinoic acid leads to the recruitment of UTX-containing complexes to HOX genes, which results in demethylation of histone H3 lysine 27 and concomitant methylation of histone H3 lysine 4. Here, we show that UTX interacts with the retinoic acid receptor α (RARα) and that this interaction is essential for proper differentiation of leukemic U937 cells in response to retinoic acid. UTX occupies the promoters of several RAR target genes and regulates their transcriptional output by modulating ASH2L complex recruitment. Overexpression of UTX in promyelocytic NB4 cells results in enhanced cellular differentiation upon retinoic acid treatment. Our results show that UTX is important for RAR-mediated transcription and provide insight into the critical role of cross talk between histone H3 lysine 4 methylation and histone H3 lysine 27 demethylation during cellular differentiation.
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http://dx.doi.org/10.1128/MCB.00839-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4187727PMC
October 2014

The impacts of replacing air bubbles with microspheres for the clarification of algae from low cell-density culture.

Water Res 2014 Apr 24;53:168-79. Epub 2014 Jan 24.

Cranfield University, Cranfield, United Kingdom. Electronic address:

Dissolved Air Flotation (DAF) is a well-known coagulation-flotation system applied at large scale for microalgae harvesting. Compared to conventional harvesting technologies DAF allows high cell recovery at lower energy demand. By replacing microbubbles with microspheres, the innovative Ballasted Dissolved Air Flotation (BDAF) technique has been reported to achieve the same algae cell removal efficiency, while saving up to 80% of the energy required for the conventional DAF unit. Using three different algae cultures (Scenedesmus obliquus, Chlorella vulgaris and Arthrospira maxima), the present work investigated the practical, economic and environmental advantages of the BDAF system compared to the DAF system. 99% cells separation was achieved with both systems, nevertheless, the BDAF technology allowed up to 95% coagulant reduction depending on the algae species and the pH conditions adopted. In terms of floc structure and strength, the inclusion of microspheres in the algae floc generated a looser aggregate, showing a more compact structure within single cell alga, than large and filamentous cells. Overall, BDAF appeared to be a more reliable and sustainable harvesting system than DAF, as it allowed equal cells recovery reducing energy inputs, coagulant demand and carbon emissions.
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http://dx.doi.org/10.1016/j.watres.2014.01.012DOI Listing
April 2014

Targeted doxorubicin delivery by chitosan-galactosylated modified polymer microbubbles to hepatocarcinoma cells.

Colloids Surf B Biointerfaces 2013 Oct 13;110:434-42. Epub 2013 May 13.

Dipartimento di Oncologia Sperimentale e Medicina Molecolare, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milano, Italy.

Targeted drug delivery is a main issue in cancer treatment. Taking advantage of recently developed polyvinyl alcohol (PVA)-based microbubbles, which are characterized by chemical versatility of the polymeric surface thereby allowing coating with different ligands, we set up a strategy for the targeted delivery of the anticancer agent doxorubicin to hepatocarcinoma cells. Such microbubbles are exceptionally efficient ultrasound scatterers and thus represent also an option as potential ultrasound contrast agents. Moreover, the oscillation of microbubbles induced by ultrasound could contribute to favor the release of drugs allocated on shell. Specifically, PVA-based microbubbles were reacted with a galactosylated chitosan complex and loaded with doxorubicin to enable the localization and drug delivery to HepG2 hepatocarcinoma cells overexpressing asialoglycoprotein receptors. We demonstrated selectivity and greater bioadhesive properties of the functionalized microbubbles for tumor cells than to normal fibroblasts, which were influenced by the degree of galactosylation. The presence of galactosylated chitosan did not modify the rate of doxorubicin release from microbubbles, whichwas almost complete within 48h. Cellular uptake of doxorubicin loaded on functionalized microbubbles was higher in HepG2 than in normal fibroblasts, which do not over express the asialoglycoprotein receptors. In addition, doxorubicin loaded onto functionalized microbubbles fully retained its cytotoxic activity. Cells were also irradiated with ultrasound, immediately after exposure to microbubbles. An early enhancement of doxorubicin release and cellular drug uptake associated to a concomitant increase in cytotoxicity was observed in HepG2 cells. Overall, results of the study indicate that galactosylated chitosan microbubbles represent promising devices for the targeted delivery of antitumor agents to liver cancer cells.
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http://dx.doi.org/10.1016/j.colsurfb.2013.04.022DOI Listing
October 2013

MSL2 combines sensor and effector functions in homeostatic control of the Drosophila dosage compensation machinery.

Mol Cell 2012 Nov 18;48(4):647-54. Epub 2012 Oct 18.

Molecular Biology Unit, Adolf Butenandt Institute and Center for Integrated Protein Science, Ludwig Maximilians University, 80336 Munich, Germany.

The process of dosage compensation (DC) in Drosophila counterbalances the monosomy of the X chromosome in male flies by increasing the transcription from this unique chromosome in the two-fold range. Upon exclusive expression of male-specific lethal 2 (MSL2) in males, the dosage compensation machinery assembles on active X-chromosomal genes. Overexpression of MSL proteins leads to aberrant binding of complex components to autosomes. Accordingly, MSL levels have to be carefully regulated. Here we describe a new mechanism through which MSL2 can fulfill its role as the central regulator of the faithful biogenesis and functionality of the DC machinery. MSL2 is an E3 ligase that ubiquitylates itself and the other associated components when their stoichiometry is unbalanced, uncovering proteasome-dependent degradation as an additional layer of homeostatic control of MSL levels. Furthermore, systematic mapping of modification sites by mass spectrometry and chromatin interaction studies on the target protein MSL1 suggest that the role of MSL2-mediated ubiquitylation goes beyond proteolysis.
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http://dx.doi.org/10.1016/j.molcel.2012.09.012DOI Listing
November 2012

Temporal and spatial changes in the microbial bioaerosol communities in green-waste composting.

FEMS Microbiol Ecol 2012 Jan;79(1):229-39

Department of Environmental Science and Technology, School of Applied Sciences, Cranfield University, Cranfield, Bedfordshire, UK.

In this study, the microbial community within compost, emitted into the airstream, downwind and upwind from a composting facility was characterized and compared through phospholipid fatty acid analysis and 16S rRNA gene analysis using denaturing gradient gel electrophoresis and bar-coded pyrosequencing techniques. All methods used suggested that green-waste composting had a significant impact upon bioaerosol community composition. Daily variations of the on-site airborne community showed how specific site parameters such as compost process activity and meteorological conditions affect bioaerosol communities, although more data are required to qualify and quantify the causes for these variations. A notable feature was the dominance of Pseudomonas in downwind samples, suggesting that this genus can disperse downwind in elevated abundances. Thirty-nine phylotypes were homologous to plant or human phylotypes containing pathogens and were found within compost, on-site and downwind microbial communities. Although the significance of this finding in terms of potential health impact was beyond the scope of this study, it clearly illustrated the potential of molecular techniques to improve our understanding of the impact that green-waste composting emissions may have on the human health.
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http://dx.doi.org/10.1111/j.1574-6941.2011.01210.xDOI Listing
January 2012

Feasibility and safety of adoptive immunotherapy with ex vivo-generated autologous, cytotoxic T lymphocytes in patients with solid tumor.

Cytotherapy 2012 Jan 23;14(1):80-90. Epub 2011 Sep 23.

Dipartimento di Scienze Pediatriche, Università di Pavia, Italy.

Background Aims: Adoptive T-cell therapy with tumor-specific T cells has emerged as a potentially useful approach for treating patients with advanced malignancies. We have demonstrated previously the feasibility of obtaining large numbers of autologous anti-tumor-specific cytotoxic T lymphocytes (CTL) generated by stimulation of patients' peripheral blood mononuclear cells with dendritic cells pulsed with apoptotic tumor cells. Methods. Six patients with progressing metastatic solid tumors (one renal cell carcinoma, two ovarian cancers, two extraosseous peripheral neuroectodermal tumors, one soft tissue sarcoma) not eligible for conventional therapies were treated with adoptive immunotherapy. Anti-tumor CTL, proven to be reactive in vitro against patient tumor cells, but not against normal cells, were infused following lymphodepleting chemotherapy administered to favor T-cell proliferation in vivo.

Results: Patients received a median of nine CTL infusions (range 2-19). The median number of CTL administered per infusion was 11 × 10(8) (range 1-55 × 10(8)). No patient experienced acute or late adverse events related to CTL infusion, even when large numbers of cells were given. Post-infusion laboratory investigations demonstrated an increase in the frequency of circulating anti-tumor T-cells and, in patients with a longer follow-up receiving two CTL infusions/year, a stabilization of these values.

Conclusions: Our study demonstrates that autologous ex vivo-generated anti-tumor CTL can be administered safely in patients with advanced solid tumors and can improve the immunologic reactivity of recipients against tumor. These preliminary results provide a rationale for evaluating the clinical efficacy of this immunotherapeutic approach in phase I/II studies.
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http://dx.doi.org/10.3109/14653249.2011.610303DOI Listing
January 2012

Experience with peritoneal mesothelioma at the Milan National Cancer Institute.

World J Gastrointest Oncol 2010 Feb;2(2):76-84

Marcello Deraco, Dario Baratti, Maria Rosaria Balestra, Shigeki Kusamura, Barbara Laterza, Department of Surgery, National Cancer Institute, 20133 Milan, Italy.

Diffuse malignant peritoneal mesothelioma (DMPM) is an uncommon and rapidly fatal tumor. Therapeutic options have traditionally been limited and ineffective. The biologic and molecular events correlated with poor responsiveness to therapy are still poorly understood. In recent years, an innovative treatment approach involving aggressive cytoreductive surgery (CRS) and perioperative intraperitoneal chemotherapy has reportedly resulted in improved outcome, as compared to historical controls. Since 1995, at the National Cancer Institute (NCI) of Milan (Italy), patients with DMPM have been treated with CRS and hyperthermic intra-peritoneal chemotherapy (HIPEC). In the present paper, clinical experiences and basic science investigations on DMPM at Milan NCI are reviewed. Peri-operative and long-term outcome results with CRS and HIPEC are presented. Clinico-pathological prognostic factors were investigated by multivariate analysis. The pathologic features and immunohistochemical markers related to DMPM biologic behavior were assessed in a large case-series uniformly treated at our institution. The prevalence and prognostic role of telomere maintenance mechanisms, which account for the limitless cell replicative potential of many malignancies, were studied. The dysregulation of the apoptotic pathways may play a role in the relative chemo-resistance of DMPM and a better understanding of apoptosis-related mechanisms could result in novel targeted therapeutic strategies. On this basis, the expression of survivin and other IAP family members (IAP-1, IAP-2, and X-IAP), the pro-apoptotic protein Smac/DIABLO, and antigens associated with cell proliferation (Ki-67) and apoptosis (caspase-cleaved cytokeratin-18) were analyzed. Finally, analyses of EGFR, PDGFRA and PDGFRB were performed to ascertain if deregulation of RTK could offer useful alternative therapeutic targets.
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http://dx.doi.org/10.4251/wjgo.v2.i2.76DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2999160PMC
February 2010

Pathophysiology and biology of peritoneal carcinomatosis.

World J Gastrointest Oncol 2010 Jan;2(1):12-8

Shigeki Kusamura, Dario Baratti, Barbara Laterza, Maria Rosaria Balestra, Marcello Deraco, Department of Surgery, National Cancer Institute of Milan, Via Venezian 1, 20133 Milano, Italy.

Peritoneal carcinomatosis represents a devastating form of cancer progression with a very poor prognosis. Its complex pathogenesis is represented by a dynamic process comprising several steps. To the best of our knowledge pathogenesis can be partly explained by 3 major molecular pathways: (1) dissemination from the primary tumor; (2) primary tumor of peritoneum; and (3) independent origins of the primary tumor and peritoneal implants. These are not mutually exclusive and combinations of different mechanisms could occur inside a single case. There are still several aspects which need explanation by future studies. A comprehensive understanding of molecular events involved in peritoneal carcinomatosis is of paramount importance and should be systematically pursued not only to identify novel strategies for the prevention of the condition, but also to obtain therapeutic advances, through the identification of surrogate markers of prognosis and development of future molecular targeted therapies.
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http://dx.doi.org/10.4251/wjgo.v2.i1.12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2999153PMC
January 2010

Multimedia fate of petroleum hydrocarbons in the soil: oil matrix of constructed biopiles.

Chemosphere 2010 Dec 18;81(11):1454-62. Epub 2010 Sep 18.

Cranfield University, Sustainable Systems Department, School of Applied Sciences, Cranfield MK43 0AL, UK.

A dynamic multimedia fugacity model was used to evaluate the partitioning and fate of petroleum hydrocarbon fractions and aromatic indicator compounds within the soil: oil matrix of three biopiles. Each biopile was characterised by four compartments: air, water, soil solids and non-aqueous phase liquid (NAPL). Equilibrium partitioning in biopile A and B suggested that most fractions resided in the NAPL, with the exception of the aromatic fraction with an equivalent carbon number from 5 to 7 (EC(5-7)). In Biopile C, which had the highest soil organic carbon content (13%), the soil solids were the most important compartment for both light aliphatic fractions (EC(5-6) and EC(6-8)) and aromatic fractions, excluding the EC(16-21) and EC(21-35). Our starting hypothesis was that hydrocarbons do not degrade within the NAPL. This was supported by the agreement between predicted and measured hydrocarbon concentrations in Biopile B when the degradation rate constant in NAPL was set to zero. In all scenarios, biodegradation in soil was predicted as the dominant removal process for all fractions, except for the aliphatic EC(5-6) which was predominantly lost via volatilization. The absence of an explicit NAPL phase in the model yielded a similar prediction of total petroleum hydrocarbon (TPH) behaviour; however the predicted concentrations in the air and water phases were significantly increased with consequent changes in potential mobility. Further comparisons between predictions and measured data, particularly concentrations in the soil mobile phases, are required to ascertain the true value of including an explicit NAPL in models of this kind.
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http://dx.doi.org/10.1016/j.chemosphere.2010.08.057DOI Listing
December 2010

Generation of mesenchymal stromal cells in the presence of platelet lysate: a phenotypic and functional comparison of umbilical cord blood- and bone marrow-derived progenitors.

Haematologica 2009 Dec 22;94(12):1649-60. Epub 2009 Sep 22.

Oncoematologia Pediatrica, Fondazione IRCCS Policlinico San Matteo, Università di Pavia, Pavia, Italy.

Background: Mesenchymal stromal cells are employed in various different clinical settings in order to modulate immune response. However, relatively little is known about the mechanisms responsible for their immunomodulatory effects, which could be influenced by both the cell source and culture conditions.

Design And Methods: We tested the ability of a 5% platelet lysate-supplemented medium to support isolation and ex vivo expansion of mesenchymal stromal cells from full-term umbilical-cord blood. We also investigated the biological/functional properties of umbilical cord blood mesenchymal stromal cells, in comparison with platelet lysate-expanded bone marrow mesenchymal stromal cells.

Results: The success rate of isolation of mesenchymal stromal cells from umbilical cord blood was in the order of 20%. These cells exhibited typical morphology, immunophenotype and differentiation capacity. Although they have a low clonogenic efficiency, umbilical cord blood mesenchymal stromal cells may possess high proliferative potential. The genetic stability of these cells from umbilical cord blood was demonstrated by a normal molecular karyotype; in addition, these cells do not express hTERT and telomerase activity, do express p16(ink4a) protein and do not show anchorage-independent cell growth. Concerning alloantigen-specific immune responses, umbilical cord blood mesenchymal stromal cells were able to: (i) suppress T- and NK-lymphocyte proliferation, (ii) decrease cytotoxic activity and (iii) only slightly increase interleukin-10, while decreasing interferon-gamma secretion, in mixed lymphocyte culture supernatants. While an indoleamine 2,3-dioxygenase-specific inhibitor did not reverse mesenchymal stromal cell-induced suppressive effects, a prostaglandin E(2)-specific inhibitor hampered the suppressive effect of both umbilical cord blood- and bone marrow-mesenchymal stromal cells on alloantigen-induced cytotoxic activity. Mesenchymal stromal cells from both sources expressed HLA-G.

Conclusions: Umbilical cord blood- and bone marrow-mesenchymal stromal cells may differ in terms of clonogenic efficiency, proliferative capacity and immunomodulatory properties; these differences may be relevant for clinical applications.
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http://dx.doi.org/10.3324/haematol.2009.006171DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2791945PMC
December 2009