Alexander Neef | Universitat Jaume I de Castelló (original) (raw)
Papers by Alexander Neef
Scientific Reports, 2020
Nearly 50% of patients with de novo acute myeloid leukemia (AML) harbor an apparently normal kary... more Nearly 50% of patients with de novo acute myeloid leukemia (AML) harbor an apparently normal karyotype (NK) by conventional cytogenetic techniques showing a very heterogeneous prognosis. This could be related to the presence of cryptic cytogenetic abnormalities (CCA) not detectable by conventional methods. The study of copy number alterations (CNA) and loss of heterozygozity (LOH) in hematological malignancies is possible using a high resolution SNP-array. Recently, in clinical practice the karyotype study has been complemented with the identification of point mutations in an increasing number of genes. We analyzed 252 de novo NK-AML patients from Hospital La Fe (n = 44) and from previously reported cohorts (n = 208) to identify CCA by SNP-array, and to integrate the analysis of CCA with molecular alterations detected by Next-Generation-sequencing. CCA were detected in 58% of patients. In addition, 49% of them harbored CNA or LOH and point mutations, simultaneously. Patients were gr...
Myelodysplastic Syndromes (MDS) are a heterogeneous group of diseases, characterized by the clona... more Myelodysplastic Syndromes (MDS) are a heterogeneous group of diseases, characterized by the clonal acquisition of somatic point mutations and chromosomal alterations. Conventional karyotyping remains one of the most important tools for MDS diagnosis because several cytogenetics abnormalities can be used to stratify patients into subtypes with different prognoses. However, a non-informative cytogenetics due to normal or unsuccessful karyotype could lead to an erroneous estimation of the prognostic risk. To overcome this drawback, we assessed the reliability of a single Next-Generation Sequencing (NGS) assay to simultaneously detect Single Nucleotide Variations (SNVs), including small indels, as well as Copy Number Alterations (CNAs) and copy-neutral Loss of Heterozygosity (cnLOH) for diagnostic application. We combined a custom panel, targeting 40 genes frequently implicated in myeloid neoplasms, with a target enrichment design (OneSeq, Agilent®), having a genome-wide backbone resolu...
Food Research International
Food microbiology, 2017
Diversity and dynamics of yeasts associated with the fermentation of Argentinian maize-based beve... more Diversity and dynamics of yeasts associated with the fermentation of Argentinian maize-based beverage chicha was investigated. Samples taken at different stages from two chicha productions were analyzed by culture-dependent and culture-independent methods. Five hundred and ninety six yeasts were isolated by classical microbiological methods and 16 species identified by RFLPs and sequencing of D1/D2 26S rRNA gene. Genetic typing of isolates from the dominant species, Saccharomyces cerevisiae, by PCR of delta elements revealed up to 42 different patterns. High-throughput sequencing (HTS) of D1/D2 26S rRNA gene amplicons from chicha samples detected more than one hundred yeast species and almost fifty filamentous fungi taxa. Analysis of the data revealed that yeasts dominated the fermentation, although, a significant percentage of filamentous fungi appeared in the first step of the process. Statistical analysis of results showed that very few taxa were represented by more than 1% of th...
Molecular Microbial Ecology of the Soil, 1998
Ribosomal ribonucleic acids are excellent marker molecules for the elucidation of bacterial phylo... more Ribosomal ribonucleic acids are excellent marker molecules for the elucidation of bacterial phylogeny; they also provide useful target sites for identification and detection with nucleic acid probes. Based on the currently available 16S rRNA sequence data, bacteria of the rhizobial phenotype (plant nodulation, nitrogen fixation) are members of three moderately related phylogenetic subgroups of the α-subclass of the Proteobacteria: i.e. the rhizobia group, the bradyrhizobia group, and the azorhizobia group. All rhizobia, azo-, brady-, meso-and sinorhizobia are closely related to and in some cases phylogenetically intermixed with, non-symbiotic and/or non-nitrogen-fixing bacteria. Especially in the case of Bradyrhizobium japonicum strains, the 16S rRNA sequence data indicate substantial heterogeneity. Specific probe design and evaluation are discussed. A multiprobe concept for resolving specificity problems with group specific probes is presented. In situ identification with group specific probes of rhizobia in cultures as well as rhizobia and cyanobacteria within plant material is shown.
Systematic and Applied Microbiology, 1995
Non-radioactive hybridization methods were c,•aluated for the identification of microorganisms in... more Non-radioactive hybridization methods were c,•aluated for the identification of microorganisms in mixed bioacrosols. A cultivation-dependent method, colony hybridization, was compared to a direct, cultivationindependent approach, whole cell hybridization with fluorescently labeled oligonucleotides. After sampling of the aerosols by filtration, special processing of filters (cells) preceded hybridization with fluorescent-Iy, digoxigenin-or enzyme-labeled oligonuculeotide probes. Group, genus, or species affiliation of collected cells was analyzed with rRNA-targeted probes. Using nucleic acid probes directed against the multiple cloning site, plasmid bearing Escherichia coli colonies could be differentiated from wild-type colonies. The microbial composition of aerosols ranging from less than one to greater than 10 9 cells/m 3 air could be analyzed with appropriate hybridization formats: whole cell hybridization was only applicable to dense aerosols, colony hybridization yielded best results with lower concentrations. After a shorr incubation period (several hours), a combination of both formats could be used to rapidly determine the fraction of culrurable cells within a bioaerosol. When applying these techniques for the monitoring of aerosols generated by standard microbiological laboratory procedures, low concentrations of airborne Escherichia coli cells (1-450 m,3) could be detected. Compared to conventional air monitoring techniques, hybridization with nucleic acid probes should allow more rapid and reliable detection of airborne microorganisms induding genetic engineered microorganisms.
Journal of Industrial Microbiology and Biotechnology, 1999
Nova Acta Leopoldina NF, 2010
A model to explain the evolutionary history of animalbacteria obligatory mutualistic symbiosis is... more A model to explain the evolutionary history of animalbacteria obligatory mutualistic symbiosis is presented. Dis pensability of genes and adaptability to the host are key factors in the reduction process of these bacterial genomes. Major steps in such genome reductive evolution, leading towards primary endosymbiosis, and the possibility of complementation or replacement by a secondary symbiont are also indicated. Yet, we need to understand what hap pens at the beginning of the adaptive process towards an obligate mutualistic ...
Gefahrstoffe Reinhaltung der Luft, 1999
Résumé/Abstract The statement presented in this paper gives an overview and assessment of the pro... more Résumé/Abstract The statement presented in this paper gives an overview and assessment of the procedures and concepts used currently for the collection and determination of airborne, culturable microorganisms at sources of emission within composting plants and in near vicinity. The paper focuses on classical methods, which involve cultivation as an intermediate step for the determination of viable, airborne microorganisms. The theoretical and practical requirements on such methods are discussed. Results and experiences from ...
PLOS ONE, 2015
The role of intestinal dysbiosis in obesity-associated systemic inflammation via the cross-talk w... more The role of intestinal dysbiosis in obesity-associated systemic inflammation via the cross-talk with peripheral tissues is under debate. Our objective was to decipher the mechanisms by which intervention in the gut ecosystem with a specific Bifidobacterium strain reduces systemic inflammation and improves metabolic dysfunction in obese high-fat diet (HFD) fed mice. Adult male wild-type C57BL-6 mice were fed either a standard or HFD, supplemented with placebo or Bifidobacterium pseudocatenulatum CECT 7765, for 14 weeks. Lymphocytes, macrophages and cytokine/chemokine concentrations were quantified in blood, gut, liver and adipose tissue using bead-based multiplex assays. Biochemical parameters in serum were determined by ELISA and enzymatic assays. Histology was assessed by hematoxylin-eosin staining. Microbiota was analyzed by 16S rRNA gene pyrosequencing and quantitative PCR. B. pseudocatenulatum CECT 7765 reduced obesity-associated systemic inflammation by restoring the balance between regulatory T cells (Tregs) and B lymphocytes and reducing pro-inflammatory cytokines of adaptive (IL-17A) and innate (TNF-α) immunity and endotoxemia. In the gut, the bifidobacterial administration partially restored the HFD-induced alterations in microbiota, reducing abundances of Firmicutes and of LPS-producing Proteobacteria, paralleled to reductions in B cells, macrophages, and cytokines (IL-6, MCP-1, TNF-α, IL-17A), which could contribute to systemic effects. In adipose tissue, bifidobacterial administration reduced B cells whereas in liver the treatment increased Tregs and shifted different cytokines (MCP-1 plus ILP-10 in adipose tissue and INF-γ plus IL-1β in liver). In both tissues, the bifidobacteria reduced pro-inflammatory macrophages and, TNF-α and IL-17A concentrations. These effects were accompanied by reductions in body weight gain and in serum cholesterol, triglyceride, glucose and insulin levels and improved oral glucose tolerance and insulin sensitivity in obese mice. Here, we provide evidence of the immune cellular mechanisms by which the inflammatory cascade associated with diet-induced obesity is attenuated by the administration of a specific Bifidobacterium strain and that these effects are associated with modulation of gut microbiota structure.
Gut, 2015
Intestinal dysbiosis has been associated with coeliac disease (CD), but whether the alterations a... more Intestinal dysbiosis has been associated with coeliac disease (CD), but whether the alterations are cause or consequence of the disease is unknown. This study investigated whether the human leukocyte antigen (HLA)-DQ2 genotype is an independent factor influencing the early gut microbiota composition of healthy infants at family risk of CD. As part of a larger prospective study, a subset (n=22) of exclusively breastfed and vaginally delivered infants with either high genetic risk (HLA-DQ2 carriers) or low genetic risk (non-HLA-DQ2/8 carriers) of developing CD were selected from a cohort of healthy infants with at least one first-degree relative with CD. Infant faecal microbiota was analysed by 16S rRNA gene pyrosequencing and real time quantitative PCR. Infants with a high genetic risk had significantly higher proportions of Firmicutes and Proteobacteria and lower proportions of Actinobacteria compared with low-risk infants. At genus level, high-risk infants had significantly less Bi...
Schriftenreihe des Vereins für Wasser-, Boden- und Lufthygiene, 1999
Emission concentrations of culturable microorganisms were determined in the vicinity of three ope... more Emission concentrations of culturable microorganisms were determined in the vicinity of three open or partly encapsulated composting facilities. Sampling was performed during so-called worst case situations which should promote aerial transport of emissions. Suitability of thermophilic organisms to detect an emitting influence of the plant was confirmed. Generally, concentrations decreased significantly with increasing distances from the plant at all three locations. At one plant 10(6) CFU m-3 thermophilic actinomycetes were found in a distance of 200 m. Partly increased concentrations could be determined even in distances above 500 m. Concentrations could vary within one hour to more than ten times.
Schriftenreihe des Vereins für Wasser-, Boden- und Lufthygiene, 1999
The detection of airborne microorganisms including selected cell constituents (e.g. allergens or ... more The detection of airborne microorganisms including selected cell constituents (e.g. allergens or endotoxins) depends on suitable methods and instruments for their collection. Furthermore, microbiological methods are necessary for their quantification and qualification. In the past these methods were largely based on the classical cultivation dependent approach. Modern molecular methods, e.g. direct staining procedures, hybridization assays with nucleic acids including the PCR-technology or immunological assays are promising new tools for a more sophisticated detection of bioaerosols. They allow a better detection rate, a more precise identification of certain members of the aerosol including cell constituents. With respect to speed and lower costs they are an important alternative to established detection methods.
Schriftenreihe des Vereins für Wasser-, Boden- und Lufthygiene, 1999
Either your web browser doesn't support Javascript or it is currently turned off. In... more Either your web browser doesn't support Javascript or it is currently turned off. In the latter case, please turn on Javascript support in your web browser and reload this page. ... Find all citations by this author (default). ... Find all citations by this author (default). ... Find all citations by this author (default). ... Find all citations by this author (default). ... Find all citations by this author (default). ... Find all citations by this author (default). ... Find all citations by this author (default). ... Find all citations by this author (default). ... Find all citations by this author ( ...
Scientific Reports, 2020
Nearly 50% of patients with de novo acute myeloid leukemia (AML) harbor an apparently normal kary... more Nearly 50% of patients with de novo acute myeloid leukemia (AML) harbor an apparently normal karyotype (NK) by conventional cytogenetic techniques showing a very heterogeneous prognosis. This could be related to the presence of cryptic cytogenetic abnormalities (CCA) not detectable by conventional methods. The study of copy number alterations (CNA) and loss of heterozygozity (LOH) in hematological malignancies is possible using a high resolution SNP-array. Recently, in clinical practice the karyotype study has been complemented with the identification of point mutations in an increasing number of genes. We analyzed 252 de novo NK-AML patients from Hospital La Fe (n = 44) and from previously reported cohorts (n = 208) to identify CCA by SNP-array, and to integrate the analysis of CCA with molecular alterations detected by Next-Generation-sequencing. CCA were detected in 58% of patients. In addition, 49% of them harbored CNA or LOH and point mutations, simultaneously. Patients were gr...
Myelodysplastic Syndromes (MDS) are a heterogeneous group of diseases, characterized by the clona... more Myelodysplastic Syndromes (MDS) are a heterogeneous group of diseases, characterized by the clonal acquisition of somatic point mutations and chromosomal alterations. Conventional karyotyping remains one of the most important tools for MDS diagnosis because several cytogenetics abnormalities can be used to stratify patients into subtypes with different prognoses. However, a non-informative cytogenetics due to normal or unsuccessful karyotype could lead to an erroneous estimation of the prognostic risk. To overcome this drawback, we assessed the reliability of a single Next-Generation Sequencing (NGS) assay to simultaneously detect Single Nucleotide Variations (SNVs), including small indels, as well as Copy Number Alterations (CNAs) and copy-neutral Loss of Heterozygosity (cnLOH) for diagnostic application. We combined a custom panel, targeting 40 genes frequently implicated in myeloid neoplasms, with a target enrichment design (OneSeq, Agilent®), having a genome-wide backbone resolu...
Food Research International
Food microbiology, 2017
Diversity and dynamics of yeasts associated with the fermentation of Argentinian maize-based beve... more Diversity and dynamics of yeasts associated with the fermentation of Argentinian maize-based beverage chicha was investigated. Samples taken at different stages from two chicha productions were analyzed by culture-dependent and culture-independent methods. Five hundred and ninety six yeasts were isolated by classical microbiological methods and 16 species identified by RFLPs and sequencing of D1/D2 26S rRNA gene. Genetic typing of isolates from the dominant species, Saccharomyces cerevisiae, by PCR of delta elements revealed up to 42 different patterns. High-throughput sequencing (HTS) of D1/D2 26S rRNA gene amplicons from chicha samples detected more than one hundred yeast species and almost fifty filamentous fungi taxa. Analysis of the data revealed that yeasts dominated the fermentation, although, a significant percentage of filamentous fungi appeared in the first step of the process. Statistical analysis of results showed that very few taxa were represented by more than 1% of th...
Molecular Microbial Ecology of the Soil, 1998
Ribosomal ribonucleic acids are excellent marker molecules for the elucidation of bacterial phylo... more Ribosomal ribonucleic acids are excellent marker molecules for the elucidation of bacterial phylogeny; they also provide useful target sites for identification and detection with nucleic acid probes. Based on the currently available 16S rRNA sequence data, bacteria of the rhizobial phenotype (plant nodulation, nitrogen fixation) are members of three moderately related phylogenetic subgroups of the α-subclass of the Proteobacteria: i.e. the rhizobia group, the bradyrhizobia group, and the azorhizobia group. All rhizobia, azo-, brady-, meso-and sinorhizobia are closely related to and in some cases phylogenetically intermixed with, non-symbiotic and/or non-nitrogen-fixing bacteria. Especially in the case of Bradyrhizobium japonicum strains, the 16S rRNA sequence data indicate substantial heterogeneity. Specific probe design and evaluation are discussed. A multiprobe concept for resolving specificity problems with group specific probes is presented. In situ identification with group specific probes of rhizobia in cultures as well as rhizobia and cyanobacteria within plant material is shown.
Systematic and Applied Microbiology, 1995
Non-radioactive hybridization methods were c,•aluated for the identification of microorganisms in... more Non-radioactive hybridization methods were c,•aluated for the identification of microorganisms in mixed bioacrosols. A cultivation-dependent method, colony hybridization, was compared to a direct, cultivationindependent approach, whole cell hybridization with fluorescently labeled oligonucleotides. After sampling of the aerosols by filtration, special processing of filters (cells) preceded hybridization with fluorescent-Iy, digoxigenin-or enzyme-labeled oligonuculeotide probes. Group, genus, or species affiliation of collected cells was analyzed with rRNA-targeted probes. Using nucleic acid probes directed against the multiple cloning site, plasmid bearing Escherichia coli colonies could be differentiated from wild-type colonies. The microbial composition of aerosols ranging from less than one to greater than 10 9 cells/m 3 air could be analyzed with appropriate hybridization formats: whole cell hybridization was only applicable to dense aerosols, colony hybridization yielded best results with lower concentrations. After a shorr incubation period (several hours), a combination of both formats could be used to rapidly determine the fraction of culrurable cells within a bioaerosol. When applying these techniques for the monitoring of aerosols generated by standard microbiological laboratory procedures, low concentrations of airborne Escherichia coli cells (1-450 m,3) could be detected. Compared to conventional air monitoring techniques, hybridization with nucleic acid probes should allow more rapid and reliable detection of airborne microorganisms induding genetic engineered microorganisms.
Journal of Industrial Microbiology and Biotechnology, 1999
Nova Acta Leopoldina NF, 2010
A model to explain the evolutionary history of animalbacteria obligatory mutualistic symbiosis is... more A model to explain the evolutionary history of animalbacteria obligatory mutualistic symbiosis is presented. Dis pensability of genes and adaptability to the host are key factors in the reduction process of these bacterial genomes. Major steps in such genome reductive evolution, leading towards primary endosymbiosis, and the possibility of complementation or replacement by a secondary symbiont are also indicated. Yet, we need to understand what hap pens at the beginning of the adaptive process towards an obligate mutualistic ...
Gefahrstoffe Reinhaltung der Luft, 1999
Résumé/Abstract The statement presented in this paper gives an overview and assessment of the pro... more Résumé/Abstract The statement presented in this paper gives an overview and assessment of the procedures and concepts used currently for the collection and determination of airborne, culturable microorganisms at sources of emission within composting plants and in near vicinity. The paper focuses on classical methods, which involve cultivation as an intermediate step for the determination of viable, airborne microorganisms. The theoretical and practical requirements on such methods are discussed. Results and experiences from ...
PLOS ONE, 2015
The role of intestinal dysbiosis in obesity-associated systemic inflammation via the cross-talk w... more The role of intestinal dysbiosis in obesity-associated systemic inflammation via the cross-talk with peripheral tissues is under debate. Our objective was to decipher the mechanisms by which intervention in the gut ecosystem with a specific Bifidobacterium strain reduces systemic inflammation and improves metabolic dysfunction in obese high-fat diet (HFD) fed mice. Adult male wild-type C57BL-6 mice were fed either a standard or HFD, supplemented with placebo or Bifidobacterium pseudocatenulatum CECT 7765, for 14 weeks. Lymphocytes, macrophages and cytokine/chemokine concentrations were quantified in blood, gut, liver and adipose tissue using bead-based multiplex assays. Biochemical parameters in serum were determined by ELISA and enzymatic assays. Histology was assessed by hematoxylin-eosin staining. Microbiota was analyzed by 16S rRNA gene pyrosequencing and quantitative PCR. B. pseudocatenulatum CECT 7765 reduced obesity-associated systemic inflammation by restoring the balance between regulatory T cells (Tregs) and B lymphocytes and reducing pro-inflammatory cytokines of adaptive (IL-17A) and innate (TNF-α) immunity and endotoxemia. In the gut, the bifidobacterial administration partially restored the HFD-induced alterations in microbiota, reducing abundances of Firmicutes and of LPS-producing Proteobacteria, paralleled to reductions in B cells, macrophages, and cytokines (IL-6, MCP-1, TNF-α, IL-17A), which could contribute to systemic effects. In adipose tissue, bifidobacterial administration reduced B cells whereas in liver the treatment increased Tregs and shifted different cytokines (MCP-1 plus ILP-10 in adipose tissue and INF-γ plus IL-1β in liver). In both tissues, the bifidobacteria reduced pro-inflammatory macrophages and, TNF-α and IL-17A concentrations. These effects were accompanied by reductions in body weight gain and in serum cholesterol, triglyceride, glucose and insulin levels and improved oral glucose tolerance and insulin sensitivity in obese mice. Here, we provide evidence of the immune cellular mechanisms by which the inflammatory cascade associated with diet-induced obesity is attenuated by the administration of a specific Bifidobacterium strain and that these effects are associated with modulation of gut microbiota structure.
Gut, 2015
Intestinal dysbiosis has been associated with coeliac disease (CD), but whether the alterations a... more Intestinal dysbiosis has been associated with coeliac disease (CD), but whether the alterations are cause or consequence of the disease is unknown. This study investigated whether the human leukocyte antigen (HLA)-DQ2 genotype is an independent factor influencing the early gut microbiota composition of healthy infants at family risk of CD. As part of a larger prospective study, a subset (n=22) of exclusively breastfed and vaginally delivered infants with either high genetic risk (HLA-DQ2 carriers) or low genetic risk (non-HLA-DQ2/8 carriers) of developing CD were selected from a cohort of healthy infants with at least one first-degree relative with CD. Infant faecal microbiota was analysed by 16S rRNA gene pyrosequencing and real time quantitative PCR. Infants with a high genetic risk had significantly higher proportions of Firmicutes and Proteobacteria and lower proportions of Actinobacteria compared with low-risk infants. At genus level, high-risk infants had significantly less Bi...
Schriftenreihe des Vereins für Wasser-, Boden- und Lufthygiene, 1999
Emission concentrations of culturable microorganisms were determined in the vicinity of three ope... more Emission concentrations of culturable microorganisms were determined in the vicinity of three open or partly encapsulated composting facilities. Sampling was performed during so-called worst case situations which should promote aerial transport of emissions. Suitability of thermophilic organisms to detect an emitting influence of the plant was confirmed. Generally, concentrations decreased significantly with increasing distances from the plant at all three locations. At one plant 10(6) CFU m-3 thermophilic actinomycetes were found in a distance of 200 m. Partly increased concentrations could be determined even in distances above 500 m. Concentrations could vary within one hour to more than ten times.
Schriftenreihe des Vereins für Wasser-, Boden- und Lufthygiene, 1999
The detection of airborne microorganisms including selected cell constituents (e.g. allergens or ... more The detection of airborne microorganisms including selected cell constituents (e.g. allergens or endotoxins) depends on suitable methods and instruments for their collection. Furthermore, microbiological methods are necessary for their quantification and qualification. In the past these methods were largely based on the classical cultivation dependent approach. Modern molecular methods, e.g. direct staining procedures, hybridization assays with nucleic acids including the PCR-technology or immunological assays are promising new tools for a more sophisticated detection of bioaerosols. They allow a better detection rate, a more precise identification of certain members of the aerosol including cell constituents. With respect to speed and lower costs they are an important alternative to established detection methods.
Schriftenreihe des Vereins für Wasser-, Boden- und Lufthygiene, 1999
Either your web browser doesn't support Javascript or it is currently turned off. In... more Either your web browser doesn't support Javascript or it is currently turned off. In the latter case, please turn on Javascript support in your web browser and reload this page. ... Find all citations by this author (default). ... Find all citations by this author (default). ... Find all citations by this author (default). ... Find all citations by this author (default). ... Find all citations by this author (default). ... Find all citations by this author (default). ... Find all citations by this author (default). ... Find all citations by this author (default). ... Find all citations by this author ( ...