Nelson Lima | Universidade do Minho (original) (raw)
Papers by Nelson Lima
Peritoneal dialysis (PD) cathetereassociated infections remain a challenging cause of technique f... more Peritoneal dialysis (PD) cathetereassociated infections remain a challenging cause of technique failure. Patient training and preventive measures are key elements in the management of infection rates. Twenty-seven of the 167 PD catheter transfer sets analyzed (19%) yielded a positive microbial culture (58% gram-negative bacteria). These results show that subclinical contamination, particularly from environmental gram-negative bacteria, is a potential hazard, indicating the need for a protocol for regular transfer set changes.
The main aim of this work is to propose experimental activities for environmental advocacy and ed... more The main aim of this work is to propose experimental activities for environmental advocacy and education within the educational system from Yr1 to Yr9. To achieve this, the work started with a comparative analysis of the textbooks used in Yrs 1 to 9, the National Curriculum and other governamental guidelines in order to find the thematic framework under investigation. The part of the study was carried out using four categories of analysis: (i) cycle of water used, (ii) causes of water pollution, (iii) consequences of water pollution, and (iv) treatments and solutions for water pollution. In chapter 1, we follow step-by-step the environmental perspectives from its genesis to the present day, reviewing the (i) genesis of ecological conscience, (ii) evolution of environmental education, (iii) environmental education in Portugal, (iv) origin of the Portuguese Ministry of the Environment, and (v) mission of the Portuguese Institute of Water. Next, already in chapter 2, a view of the history of water was done from old times to the current delimitation issue. Furthermore, the issue of water is shown from distribution to consumption, passing through pollution, national legislation on the water supplier and quality regulations, water within the politics of the European Community, the cycle of water used and treatment techniques, re-use treatment systems, efficient and sustainable water uses, the conservation of water in Portugal and, eventually, the main world conflicts for water. Chapter 3 presents the methodologies developed and applied in a classroom context to setup the experimental activities related to the cycle of water used and water agro-chemical pollution. This chapter also describes the methodologies used for the assessment of the proposal experimental activities, namely the contents analysis of study 1 (the textbooks and syllabus of the educational system from Yr1 to Yr9), the study of the conceptual changes of pupils about the cycle of water used (study 2) and about water agro-chemical pollution. The study 2 is related with teaching activities proposals which are (1) a Drinking Water Treatment Plant experiment, (2) driking-water distribution network study using a model and, (3) a presentation of a movie about how work a Wastewater Treatment Plant. Study 3, approaches the assessment of the experimental activity proposal which was based on the use of a water chemical analysis kit. This kit was used in an experimental classroom and in other classroom the same content without experiment was teaching theoretically using the oral transmission. This quasi-experimental methodology will allow us compare the learn outcomes of the pupils in different teaching approaches. The results of the three studies are presented in chapter 4 of which study 1 point out the difficulties of relationship of contents and connections as to the 4 parameters in analysis and in studies 2 and 3 to the increase of the students learning outcomes (conceptual changes) as to subjects experimentally worked on. Chapter 5 presents the conclusions, recommendations and perspectives for the future which in brief are: (1) that the experimental teaching in Yrs1 to 4 is an excellent methodology for education in general and in particular for Environmental Education; that the students of Yrs1 to 4 confronted with these new pedagogic proposals of experimental teaching were challenged to develop their critical thinking, the capacity of making decisions and to be able to solve concrete problems. In other words, they were challenged to significantly increase their environmental literacy; (2) as a recommendation we propose that the national curriculum and textbooks from Yr1 to Yr9, incorporate the cycle of water used in a progressive and intricate way; that the problems of water pollution and its solutions should be treated more comprehensibly and persistently, that there is implemented by schools and teachers the use of experimental activities and fieldwork of the cycle of water used and related problems like water degradation; (3) that in the future the proposals presented here should be generalised, as well as expanding the proposals of experimental and observational activities about water.
Revista Ifes Ciência, 2015
O gênero Aspergillus é um dos principais grupos de micro-organismos em importância para a indústr... more O gênero Aspergillus é um dos principais grupos de micro-organismos em importância para a indústria, a agricultura e a saúde pública. A mais importante publicação para a identificação e a classificação desse gênero foi baseada em critérios fenotípicos. Entretanto, devido à variabilidade das características fenotípicas, reinvestigações têm sido realizadas. Dessa forma, este trabalho tem como objetivo apresentar as principais técnicas utilizadas para identificar e classificar espécies do gênero Aspergillus seção Flavi. Nesse sentido, nossa abordagem integrará a Taxonomia Polifásica pautada nas características micro e macromorfológicas, fisiológicas, na produção de metabólitos, dados moleculares e no uso da espectrometria de massas pela técnica de MALDI-TOF MS.
Tomando como objecto de estudo projectos de Compostagem Doméstica (CD) no contexto escolar, este ... more Tomando como objecto de estudo projectos de Compostagem Doméstica (CD) no contexto escolar, este artigo apresenta uma análise do processo de implementaçãoactual de uma prática sustentável milenar. No momento em que a compostagem se expande pelas escolas do país, em especial no 1.º Ciclo do Ensino Básico, tornou-se pertinente observar em profundidade experiências pedagógicas que usam esta metodologia de aproveitamento de resíduos orgânicos como um meio didáctico. Através de uma visão da CD baseada nas vertentes técnica; ambiental; de saúde;pedagógica; social e económica, foi realizado um estudo de casos múltiplos em três contextos educativos. Comparou-se o nível de desenvolvimento daquelas vertentes em escolas com diferentes graus de experiência em compostagem. A compostagem foi igualmente assumida como um "elo" que completa o ciclo da matéria orgânica, com as componentes-chave - "resíduos" e "fertilização do solo". Entre outros aspectos, os resultados d...
Ecology and evolution, 2018
Palm oil is used in various valued commodities and is a large global industry worth over US$ 50 b... more Palm oil is used in various valued commodities and is a large global industry worth over US$ 50 billion annually. Oil palms (OP) are grown commercially in Indonesia and Malaysia and other countries within Latin America and Africa. The large-scale land-use change has high ecological, economic, and social impacts. Tropical countries in particular are affected negatively by climate change (CC) which also has a detrimental impact on OP agronomy, whereas the cultivation of OP increases CC. Amelioration of both is required. The reduced ability to grow OP will reduce CC, which may allow more cultivation tending to increase CC, in a decreasing cycle. OP could be increasingly grown in more suitable regions occurring under CC. Enhancing the soil fauna may compensate for the effect of CC on OP agriculture to some extent. The effect of OP cultivation on CC may be reduced by employing reduced emissions from deforestation and forest degradation plans, for example, by avoiding illegal fire land cl...
International journal of food microbiology, Mar 23, 2018
We read with interest in your journal that Penicillium expansum strains S3, S31 and S87 (Rharmitt... more We read with interest in your journal that Penicillium expansum strains S3, S31 and S87 (Rharmitt et al., 2016) were considered negative for possession of the isoepoxydon dehydrogenase (idh) gene for patulin (PAT) production and positive for PAT production. This led to speculation that an alternative pathway was involved in patulin production. However, the authors did not provide the diode array (DA) UV spectra of the HPLC peaks assigned to PAT, which assist in confirming its identification. UV spectra could usefully be provided in papers when DA analysis has been performed especially for unusual results such as these: At least a statement to say whether the spectra were identical, or not, to the PAT standard is required. One of the current authors (RRMP) reported for the first time the PCR test to assess mycotoxigenic fungi using the idh gene coupled with PAT detection by (a) TLC (Paterson et al., 2000; Paterson et al., 2003) and (b) HPLC UV (Paterson et al., 2003). idh negative and PAT positive strains were not detected. Similarly, Luque et al. (2011) did not detected this combination using micellar electrokinetic capillary electrophoresis, and HPLC-MS for PAT detection. The principle was employed in reverse transcription real-time PCR for idh (De Clercq et al., 2016). The current authors found that a compound which has (a) the same retention time as PAT, but (b) a different UV spectrum using Ultra HPLC DA detection (UHPLC DAD) in a Penicillium strain (Fig. 1), during recent screening work to detect patulin from penicillia isolated from Tunisian apples. Hence, the strain was negative for PAT detection. This was confirmed by the strain being idh negative. Incidentally, the chromatogram for P. expansum (S13) in Rharmitt et al. (2016) had a co-eluting metabolite with PAT as deduced by the peak having a distinct shoulder. The UV spectrum of this sample would probably be different from pure PAT although this was unreported. Perrone et al. (2017) recommended MS and NMR to establish correct ochratoxin A (OTA) production in species not associated conventionally with this mycotoxin. The questionable data were from HPLC-FLD (fluorescence detection) where other fluorescent compounds with the same retention time could be misidentified as OTA. Few laboratories may be able to afford MS and NMR and all methods need assessing on a cost-benefit basis to indicate what is suitable for most laboratories (Paterson et al., 2018). Rharmitt et al. (2016) employed HPLC DAD but the analytical potential of the technique was unfulfilled. Furthermore, Rharmitt et al. (2016) suggested the primers they employed may not have bound to the target DNA hence the negative idh result, which also undermines their premise of a different pathway for PAT. Fig. 1. UHPLC chromatograms and UV spectra for the (i) idh negative and patulin negative Penicillium strain (MUM 17.62) and (ii) patulin (PAT) standard. A, B are the chromatogram and UV spectrum of the PAT standard respectively. C is the false PAT positive chromatogram and D is the PAT negative UV spectrum for the strain.
Food microbiology, 2018
Penicillium and Aspergillus genera, both including mycotoxin producing species, were reported as ... more Penicillium and Aspergillus genera, both including mycotoxin producing species, were reported as associated to cheese and cheese working environment, but never studied in an extensive way in Italian grana cheese (Grana Padano and Parmigiano Reggiano). The aim of this work was to address the identification of Aspergilli and Penicillia associated to grana cheese in order to lay down the basis for risk assessment and safe processing for a high quality production. One hundred and four strains belonging to Aspergillus and Penicillium genera were obtained from cheese crust and from ripening room air (with the latter largely dominant), and identified following a polyphasic approach, strongly required for the identification at the species level. Morphological observation was used along with molecular techniques, RAPD-PCR fingerprinting and calmodulin gene sequencing (CaM), the former aimed to limit as much as possible the latter sequencing effort. Seventy four percent of the strains were as...
International journal of systematic and evolutionary microbiology, Jan 20, 2018
Two similar Penicillium isolates could not be identified as previously described species in a sur... more Two similar Penicillium isolates could not be identified as previously described species in a survey of orchard apples from Tunisia for patulin-producing fungi. These isolates are described as novel species using multilocus DNA sequence analysis of partial β-tubulin, calmodulin and nuclear ribosomal internal transcribed spacer regions; and morphological, physiological and biochemical characteristics. The isolates were considered negative for patulin production since the IDH gene fragment was not detected and the compound detected at the same retention time of patulin (14.9 min) showed a different UV spectrum using U-HPLC/UV-DAD. In terms of phylogeny, the two isolates clustered with Penicillium section Ramosa and are closely related to Penicillium chroogomphum, Penicillium lenticrescens and Penicillium soppii. Furthermore, their macro- and micromorphological traits differed from these species. Hence, the isolates represent a novel species in Penicillium section Ramosa and the name P...
Food research international (Ottawa, Ont.), 2018
Cocoa beans from different geographical and genetic origins show distinct fermentation dynamics w... more Cocoa beans from different geographical and genetic origins show distinct fermentation dynamics which result in different chocolate qualities. In order to understand the effects of genetic improvement of cocoa plants, in this work volatile compounds and proteins profiles of beginning and end of the fermentation from different cocoa hybrids (CEPEC2004, PH15, PS1319, SJ02) were searched. Moreover, sensorial characterization of the produced chocolate from these hybrids was performed. According to the results obtained, different volatile compounds were identified in fermented beans and in the chocolate produced. Chocolate from CEPEC2004 was the most accepted by judges and correlated with sweet and bitter taste which can be explained by the presence of desired flavor compounds, such as 2,3-butanediol and 2-methyl-1-butanol. A higher presence of acids (undesirable compounds) was observed in chocolates samples from PS1319 hybrid, that have resulted in the low acceptance by judges. In addit...
Food research international (Ottawa, Ont.), 2018
Wine is a significant contributor to the economies of many countries. However, the commodity can ... more Wine is a significant contributor to the economies of many countries. However, the commodity can become contaminated with mycotoxins produced by certain fungi. Most information on mycotoxins in wine is from Spain, Italy and France. Grapes can be infected by mycotoxigenic fungi, of which Aspergillus carbonarius producing ochratoxin A (OTA) is of highest concern. Climate is the most important factor in determining contamination once the fungi are established, with high temperatures being a major factor for OTA contamination: OTA in wine is at higher concentrations in warmer southern Europe than northern. Contamination by fumonisins is a particular concern, related to Aspergillus niger producing these compounds and the fungus being isolated frequently from grapes. Aflatoxins can be present in wine, but patulin is seldom detected. Alternaria mycotoxins (e.g. alternariol) have been frequently observed. There are indications that T-2 toxin may be common. Also, the combined effects of myco...
GigaScience, May 22, 2018
Genomic information is essential for taxonomic, phylogenetic and functional studies to comprehens... more Genomic information is essential for taxonomic, phylogenetic and functional studies to comprehensively decipher the characteristics of microorganisms, to explore microbiomes through metagenomics, and to answer fundamental questions of nature and human life. However, large gaps remain in the available genomic sequencing information published for bacterial and archaeal species, and the gaps are even larger for fungal type strains. The Global Catalogue of Microorganisms (GCM) leads an internationally coordinated effort to sequence type strains and close gaps in the genomic maps of microbes. Hence, the GCM aims to promote research by deep-mining genomic data.
Revista iberoamericana de micologia, Jan 29, 2018
No reliable data are available in the province of Buenos Aires regarding the frequency of dermato... more No reliable data are available in the province of Buenos Aires regarding the frequency of dermatophytoses and other fungal diseases. The distribution of the clinical forms and the species involved are also unknown. To present the data collected by the laboratories participating in the Mycology Network of the province of Buenos Aires (MNPBA) from a retrospective epidemiological survey on dermatophytoses. A descriptive and exploratory analysis was performed on the cases of dermatophytoses gathered between 2002 and 2007 by the Mycology Network of the province of Buenos Aires. Of the 3966 dermatophytosis cases reported by 41 laboratories in 31 municipalities, more than a half occurred in three highly populated urban municipalities. The male:female ratio was 1:1.5. The most frequent clinical form was tinea unguium, diagnosed in 904 cases (51.83%), followed by tinea capitis (19.32%), tinea corporis (15.19%), tinea pedis (6.77%), tinea cruris (3.73%), and tinea manuum (2.18%). The species ...
International Journal of Quality & Reliability Management, 2017
Trends in Microbiology, 2017
Journal of Food Protection, 2003
Cheese ripening rooms have an unusual environment, an environment that encourages mold growth. Oz... more Cheese ripening rooms have an unusual environment, an environment that encourages mold growth. Ozone has been applied in various ways in the food industry. One useful advantage of ozone is that it inactivates molds. In this study, a cheese ripening room was ozonated, and the effectiveness of this treatment was evaluated both in air and on surfaces through sampling on a weekly basis over a 3-month period. The results obtained indicate that ozone treatment reduced the viable airborne mold load but did not affect viable mold on surfaces. Only by wiping the surfaces with a commercial sanitizer was it possible to decrease the viable mold load on surfaces. To improve overall hygiene in the ripening room, a combination of cleaning regimes is recommended. The mold genera occurring most frequently in the air of the cheese ripening room were Penicillium, Cladosporium, and Aspergillus, which accounted for 89.9% of the mold isolates. Penicillium and Aspergillus were identified to the species le...
Nucleic acids research, Jan 4, 2017
The World Data Centre for Microorganisms (WDCM) was established 50 years ago as the data center o... more The World Data Centre for Microorganisms (WDCM) was established 50 years ago as the data center of the World Federation for Culture Collections (WFCC)-Microbial Resource Center (MIRCEN). WDCM aims to provide integrated information services using big data technology for microbial resource centers and microbiologists all over the world. Here, we provide an overview of WDCM including all of its integrated services. Culture Collections Information Worldwide (CCINFO) provides metadata information on 708 culture collections from 72 countries and regions. Global Catalogue of Microorganism (GCM) gathers strain catalogue information and provides a data retrieval, analysis, and visualization system of microbial resources. Currently, GCM includes >368 000 strains from 103 culture collections in 43 countries and regions. Analyzer of Bioresource Citation (ABC) is a data mining tool extracting strain related publications, patents, nucleotide sequences and genome information from public data so...
Enfermedades Infecciosas Y Microbiologia Clinica, 2014
Ecologia Dos Fungos, 2002
Vieme Congres National De La Societe Francaise De Microbiologie, 2004
Peritoneal dialysis (PD) cathetereassociated infections remain a challenging cause of technique f... more Peritoneal dialysis (PD) cathetereassociated infections remain a challenging cause of technique failure. Patient training and preventive measures are key elements in the management of infection rates. Twenty-seven of the 167 PD catheter transfer sets analyzed (19%) yielded a positive microbial culture (58% gram-negative bacteria). These results show that subclinical contamination, particularly from environmental gram-negative bacteria, is a potential hazard, indicating the need for a protocol for regular transfer set changes.
The main aim of this work is to propose experimental activities for environmental advocacy and ed... more The main aim of this work is to propose experimental activities for environmental advocacy and education within the educational system from Yr1 to Yr9. To achieve this, the work started with a comparative analysis of the textbooks used in Yrs 1 to 9, the National Curriculum and other governamental guidelines in order to find the thematic framework under investigation. The part of the study was carried out using four categories of analysis: (i) cycle of water used, (ii) causes of water pollution, (iii) consequences of water pollution, and (iv) treatments and solutions for water pollution. In chapter 1, we follow step-by-step the environmental perspectives from its genesis to the present day, reviewing the (i) genesis of ecological conscience, (ii) evolution of environmental education, (iii) environmental education in Portugal, (iv) origin of the Portuguese Ministry of the Environment, and (v) mission of the Portuguese Institute of Water. Next, already in chapter 2, a view of the history of water was done from old times to the current delimitation issue. Furthermore, the issue of water is shown from distribution to consumption, passing through pollution, national legislation on the water supplier and quality regulations, water within the politics of the European Community, the cycle of water used and treatment techniques, re-use treatment systems, efficient and sustainable water uses, the conservation of water in Portugal and, eventually, the main world conflicts for water. Chapter 3 presents the methodologies developed and applied in a classroom context to setup the experimental activities related to the cycle of water used and water agro-chemical pollution. This chapter also describes the methodologies used for the assessment of the proposal experimental activities, namely the contents analysis of study 1 (the textbooks and syllabus of the educational system from Yr1 to Yr9), the study of the conceptual changes of pupils about the cycle of water used (study 2) and about water agro-chemical pollution. The study 2 is related with teaching activities proposals which are (1) a Drinking Water Treatment Plant experiment, (2) driking-water distribution network study using a model and, (3) a presentation of a movie about how work a Wastewater Treatment Plant. Study 3, approaches the assessment of the experimental activity proposal which was based on the use of a water chemical analysis kit. This kit was used in an experimental classroom and in other classroom the same content without experiment was teaching theoretically using the oral transmission. This quasi-experimental methodology will allow us compare the learn outcomes of the pupils in different teaching approaches. The results of the three studies are presented in chapter 4 of which study 1 point out the difficulties of relationship of contents and connections as to the 4 parameters in analysis and in studies 2 and 3 to the increase of the students learning outcomes (conceptual changes) as to subjects experimentally worked on. Chapter 5 presents the conclusions, recommendations and perspectives for the future which in brief are: (1) that the experimental teaching in Yrs1 to 4 is an excellent methodology for education in general and in particular for Environmental Education; that the students of Yrs1 to 4 confronted with these new pedagogic proposals of experimental teaching were challenged to develop their critical thinking, the capacity of making decisions and to be able to solve concrete problems. In other words, they were challenged to significantly increase their environmental literacy; (2) as a recommendation we propose that the national curriculum and textbooks from Yr1 to Yr9, incorporate the cycle of water used in a progressive and intricate way; that the problems of water pollution and its solutions should be treated more comprehensibly and persistently, that there is implemented by schools and teachers the use of experimental activities and fieldwork of the cycle of water used and related problems like water degradation; (3) that in the future the proposals presented here should be generalised, as well as expanding the proposals of experimental and observational activities about water.
Revista Ifes Ciência, 2015
O gênero Aspergillus é um dos principais grupos de micro-organismos em importância para a indústr... more O gênero Aspergillus é um dos principais grupos de micro-organismos em importância para a indústria, a agricultura e a saúde pública. A mais importante publicação para a identificação e a classificação desse gênero foi baseada em critérios fenotípicos. Entretanto, devido à variabilidade das características fenotípicas, reinvestigações têm sido realizadas. Dessa forma, este trabalho tem como objetivo apresentar as principais técnicas utilizadas para identificar e classificar espécies do gênero Aspergillus seção Flavi. Nesse sentido, nossa abordagem integrará a Taxonomia Polifásica pautada nas características micro e macromorfológicas, fisiológicas, na produção de metabólitos, dados moleculares e no uso da espectrometria de massas pela técnica de MALDI-TOF MS.
Tomando como objecto de estudo projectos de Compostagem Doméstica (CD) no contexto escolar, este ... more Tomando como objecto de estudo projectos de Compostagem Doméstica (CD) no contexto escolar, este artigo apresenta uma análise do processo de implementaçãoactual de uma prática sustentável milenar. No momento em que a compostagem se expande pelas escolas do país, em especial no 1.º Ciclo do Ensino Básico, tornou-se pertinente observar em profundidade experiências pedagógicas que usam esta metodologia de aproveitamento de resíduos orgânicos como um meio didáctico. Através de uma visão da CD baseada nas vertentes técnica; ambiental; de saúde;pedagógica; social e económica, foi realizado um estudo de casos múltiplos em três contextos educativos. Comparou-se o nível de desenvolvimento daquelas vertentes em escolas com diferentes graus de experiência em compostagem. A compostagem foi igualmente assumida como um "elo" que completa o ciclo da matéria orgânica, com as componentes-chave - "resíduos" e "fertilização do solo". Entre outros aspectos, os resultados d...
Ecology and evolution, 2018
Palm oil is used in various valued commodities and is a large global industry worth over US$ 50 b... more Palm oil is used in various valued commodities and is a large global industry worth over US$ 50 billion annually. Oil palms (OP) are grown commercially in Indonesia and Malaysia and other countries within Latin America and Africa. The large-scale land-use change has high ecological, economic, and social impacts. Tropical countries in particular are affected negatively by climate change (CC) which also has a detrimental impact on OP agronomy, whereas the cultivation of OP increases CC. Amelioration of both is required. The reduced ability to grow OP will reduce CC, which may allow more cultivation tending to increase CC, in a decreasing cycle. OP could be increasingly grown in more suitable regions occurring under CC. Enhancing the soil fauna may compensate for the effect of CC on OP agriculture to some extent. The effect of OP cultivation on CC may be reduced by employing reduced emissions from deforestation and forest degradation plans, for example, by avoiding illegal fire land cl...
International journal of food microbiology, Mar 23, 2018
We read with interest in your journal that Penicillium expansum strains S3, S31 and S87 (Rharmitt... more We read with interest in your journal that Penicillium expansum strains S3, S31 and S87 (Rharmitt et al., 2016) were considered negative for possession of the isoepoxydon dehydrogenase (idh) gene for patulin (PAT) production and positive for PAT production. This led to speculation that an alternative pathway was involved in patulin production. However, the authors did not provide the diode array (DA) UV spectra of the HPLC peaks assigned to PAT, which assist in confirming its identification. UV spectra could usefully be provided in papers when DA analysis has been performed especially for unusual results such as these: At least a statement to say whether the spectra were identical, or not, to the PAT standard is required. One of the current authors (RRMP) reported for the first time the PCR test to assess mycotoxigenic fungi using the idh gene coupled with PAT detection by (a) TLC (Paterson et al., 2000; Paterson et al., 2003) and (b) HPLC UV (Paterson et al., 2003). idh negative and PAT positive strains were not detected. Similarly, Luque et al. (2011) did not detected this combination using micellar electrokinetic capillary electrophoresis, and HPLC-MS for PAT detection. The principle was employed in reverse transcription real-time PCR for idh (De Clercq et al., 2016). The current authors found that a compound which has (a) the same retention time as PAT, but (b) a different UV spectrum using Ultra HPLC DA detection (UHPLC DAD) in a Penicillium strain (Fig. 1), during recent screening work to detect patulin from penicillia isolated from Tunisian apples. Hence, the strain was negative for PAT detection. This was confirmed by the strain being idh negative. Incidentally, the chromatogram for P. expansum (S13) in Rharmitt et al. (2016) had a co-eluting metabolite with PAT as deduced by the peak having a distinct shoulder. The UV spectrum of this sample would probably be different from pure PAT although this was unreported. Perrone et al. (2017) recommended MS and NMR to establish correct ochratoxin A (OTA) production in species not associated conventionally with this mycotoxin. The questionable data were from HPLC-FLD (fluorescence detection) where other fluorescent compounds with the same retention time could be misidentified as OTA. Few laboratories may be able to afford MS and NMR and all methods need assessing on a cost-benefit basis to indicate what is suitable for most laboratories (Paterson et al., 2018). Rharmitt et al. (2016) employed HPLC DAD but the analytical potential of the technique was unfulfilled. Furthermore, Rharmitt et al. (2016) suggested the primers they employed may not have bound to the target DNA hence the negative idh result, which also undermines their premise of a different pathway for PAT. Fig. 1. UHPLC chromatograms and UV spectra for the (i) idh negative and patulin negative Penicillium strain (MUM 17.62) and (ii) patulin (PAT) standard. A, B are the chromatogram and UV spectrum of the PAT standard respectively. C is the false PAT positive chromatogram and D is the PAT negative UV spectrum for the strain.
Food microbiology, 2018
Penicillium and Aspergillus genera, both including mycotoxin producing species, were reported as ... more Penicillium and Aspergillus genera, both including mycotoxin producing species, were reported as associated to cheese and cheese working environment, but never studied in an extensive way in Italian grana cheese (Grana Padano and Parmigiano Reggiano). The aim of this work was to address the identification of Aspergilli and Penicillia associated to grana cheese in order to lay down the basis for risk assessment and safe processing for a high quality production. One hundred and four strains belonging to Aspergillus and Penicillium genera were obtained from cheese crust and from ripening room air (with the latter largely dominant), and identified following a polyphasic approach, strongly required for the identification at the species level. Morphological observation was used along with molecular techniques, RAPD-PCR fingerprinting and calmodulin gene sequencing (CaM), the former aimed to limit as much as possible the latter sequencing effort. Seventy four percent of the strains were as...
International journal of systematic and evolutionary microbiology, Jan 20, 2018
Two similar Penicillium isolates could not be identified as previously described species in a sur... more Two similar Penicillium isolates could not be identified as previously described species in a survey of orchard apples from Tunisia for patulin-producing fungi. These isolates are described as novel species using multilocus DNA sequence analysis of partial β-tubulin, calmodulin and nuclear ribosomal internal transcribed spacer regions; and morphological, physiological and biochemical characteristics. The isolates were considered negative for patulin production since the IDH gene fragment was not detected and the compound detected at the same retention time of patulin (14.9 min) showed a different UV spectrum using U-HPLC/UV-DAD. In terms of phylogeny, the two isolates clustered with Penicillium section Ramosa and are closely related to Penicillium chroogomphum, Penicillium lenticrescens and Penicillium soppii. Furthermore, their macro- and micromorphological traits differed from these species. Hence, the isolates represent a novel species in Penicillium section Ramosa and the name P...
Food research international (Ottawa, Ont.), 2018
Cocoa beans from different geographical and genetic origins show distinct fermentation dynamics w... more Cocoa beans from different geographical and genetic origins show distinct fermentation dynamics which result in different chocolate qualities. In order to understand the effects of genetic improvement of cocoa plants, in this work volatile compounds and proteins profiles of beginning and end of the fermentation from different cocoa hybrids (CEPEC2004, PH15, PS1319, SJ02) were searched. Moreover, sensorial characterization of the produced chocolate from these hybrids was performed. According to the results obtained, different volatile compounds were identified in fermented beans and in the chocolate produced. Chocolate from CEPEC2004 was the most accepted by judges and correlated with sweet and bitter taste which can be explained by the presence of desired flavor compounds, such as 2,3-butanediol and 2-methyl-1-butanol. A higher presence of acids (undesirable compounds) was observed in chocolates samples from PS1319 hybrid, that have resulted in the low acceptance by judges. In addit...
Food research international (Ottawa, Ont.), 2018
Wine is a significant contributor to the economies of many countries. However, the commodity can ... more Wine is a significant contributor to the economies of many countries. However, the commodity can become contaminated with mycotoxins produced by certain fungi. Most information on mycotoxins in wine is from Spain, Italy and France. Grapes can be infected by mycotoxigenic fungi, of which Aspergillus carbonarius producing ochratoxin A (OTA) is of highest concern. Climate is the most important factor in determining contamination once the fungi are established, with high temperatures being a major factor for OTA contamination: OTA in wine is at higher concentrations in warmer southern Europe than northern. Contamination by fumonisins is a particular concern, related to Aspergillus niger producing these compounds and the fungus being isolated frequently from grapes. Aflatoxins can be present in wine, but patulin is seldom detected. Alternaria mycotoxins (e.g. alternariol) have been frequently observed. There are indications that T-2 toxin may be common. Also, the combined effects of myco...
GigaScience, May 22, 2018
Genomic information is essential for taxonomic, phylogenetic and functional studies to comprehens... more Genomic information is essential for taxonomic, phylogenetic and functional studies to comprehensively decipher the characteristics of microorganisms, to explore microbiomes through metagenomics, and to answer fundamental questions of nature and human life. However, large gaps remain in the available genomic sequencing information published for bacterial and archaeal species, and the gaps are even larger for fungal type strains. The Global Catalogue of Microorganisms (GCM) leads an internationally coordinated effort to sequence type strains and close gaps in the genomic maps of microbes. Hence, the GCM aims to promote research by deep-mining genomic data.
Revista iberoamericana de micologia, Jan 29, 2018
No reliable data are available in the province of Buenos Aires regarding the frequency of dermato... more No reliable data are available in the province of Buenos Aires regarding the frequency of dermatophytoses and other fungal diseases. The distribution of the clinical forms and the species involved are also unknown. To present the data collected by the laboratories participating in the Mycology Network of the province of Buenos Aires (MNPBA) from a retrospective epidemiological survey on dermatophytoses. A descriptive and exploratory analysis was performed on the cases of dermatophytoses gathered between 2002 and 2007 by the Mycology Network of the province of Buenos Aires. Of the 3966 dermatophytosis cases reported by 41 laboratories in 31 municipalities, more than a half occurred in three highly populated urban municipalities. The male:female ratio was 1:1.5. The most frequent clinical form was tinea unguium, diagnosed in 904 cases (51.83%), followed by tinea capitis (19.32%), tinea corporis (15.19%), tinea pedis (6.77%), tinea cruris (3.73%), and tinea manuum (2.18%). The species ...
International Journal of Quality & Reliability Management, 2017
Trends in Microbiology, 2017
Journal of Food Protection, 2003
Cheese ripening rooms have an unusual environment, an environment that encourages mold growth. Oz... more Cheese ripening rooms have an unusual environment, an environment that encourages mold growth. Ozone has been applied in various ways in the food industry. One useful advantage of ozone is that it inactivates molds. In this study, a cheese ripening room was ozonated, and the effectiveness of this treatment was evaluated both in air and on surfaces through sampling on a weekly basis over a 3-month period. The results obtained indicate that ozone treatment reduced the viable airborne mold load but did not affect viable mold on surfaces. Only by wiping the surfaces with a commercial sanitizer was it possible to decrease the viable mold load on surfaces. To improve overall hygiene in the ripening room, a combination of cleaning regimes is recommended. The mold genera occurring most frequently in the air of the cheese ripening room were Penicillium, Cladosporium, and Aspergillus, which accounted for 89.9% of the mold isolates. Penicillium and Aspergillus were identified to the species le...
Nucleic acids research, Jan 4, 2017
The World Data Centre for Microorganisms (WDCM) was established 50 years ago as the data center o... more The World Data Centre for Microorganisms (WDCM) was established 50 years ago as the data center of the World Federation for Culture Collections (WFCC)-Microbial Resource Center (MIRCEN). WDCM aims to provide integrated information services using big data technology for microbial resource centers and microbiologists all over the world. Here, we provide an overview of WDCM including all of its integrated services. Culture Collections Information Worldwide (CCINFO) provides metadata information on 708 culture collections from 72 countries and regions. Global Catalogue of Microorganism (GCM) gathers strain catalogue information and provides a data retrieval, analysis, and visualization system of microbial resources. Currently, GCM includes >368 000 strains from 103 culture collections in 43 countries and regions. Analyzer of Bioresource Citation (ABC) is a data mining tool extracting strain related publications, patents, nucleotide sequences and genome information from public data so...
Enfermedades Infecciosas Y Microbiologia Clinica, 2014
Ecologia Dos Fungos, 2002
Vieme Congres National De La Societe Francaise De Microbiologie, 2004