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1.
Lisa Rizzetto Gloria Giovannini Michael Bromley Paul Bowyer Luigina Romani Duccio Cavalieri 《PloS one》2013,8(2)
For over a century microbiologists and immunologist have categorized microorganisms as pathogenic or non-pathogenic species or genera. This definition, clearly relevant at the strain and species level for most bacteria, where differences in virulence between strains of a particular species are well known, has never been probed at the strain level in fungal species. Here, we tested the immune reactivity and the pathogenic potential of a collection of strains from Aspergillus spp, a fungus that is generally considered pathogenic in immuno-compromised hosts. Our results show a wide strain-dependent variation of the immune response elicited indicating that different isolates possess diverse virulence and infectivity. Thus, the definition of markers of inflammation or pathogenicity cannot be generalized. The profound understanding of the molecular mechanisms subtending the different immune responses will result solely from the comparative study of strains with extremely diverse properties. 相似文献
2.
Duccio Malinverni Simone Marsili Alessandro Barducci Paolo De Los Rios 《PLoS computational biology》2015,11(6)
Hsp70s are a class of ubiquitous and highly conserved molecular chaperones playing a central role in the regulation of proteostasis in the cell. Hsp70s assist a myriad of cellular processes by binding unfolded or misfolded substrates during a complex biochemical cycle involving large-scale structural rearrangements. Here we show that an analysis of coevolution at the residue level fully captures the characteristic large-scale conformational transitions of this protein family, and predicts an evolutionary conserved–and thus functional–homo-dimeric arrangement. Furthermore, we highlight that the features encoding the Hsp70 dimer are more conserved in bacterial than in eukaryotic sequences, suggesting that the known Hsp70/Hsp110 hetero-dimer is a eukaryotic specialization built on a pre-existing template. 相似文献
3.
Sheila Unger Maria?W. Górna Antony Le?Béchec Sonia Do?Vale-Pereira Maria?Francesca Bedeschi Stefan Geiberger Giedre Grigelioniene Eva Horemuzova Faustina Lalatta Ekkehart Lausch Cinzia Magnani Sheela Nampoothiri Gen Nishimura Duccio Petrella Francisca Rojas-Ringeling Akari Utsunomiya Bernhard Zabel Sylvain Pradervand Keith Harshman Belinda Campos-Xavier Luisa Bonafé Giulio Superti-Furga Brian Stevenson Andrea Superti-Furga 《American journal of human genetics》2013,92(6):990-995
Kenny-Caffey syndrome (KCS) and the similar but more severe osteocraniostenosis (OCS) are genetic conditions characterized by impaired skeletal development with small and dense bones, short stature, and primary hypoparathyroidism with hypocalcemia. We studied five individuals with KCS and five with OCS and found that all of them had heterozygous mutations in FAM111A. One mutation was identified in four unrelated individuals with KCS, and another one was identified in two unrelated individuals with OCS; all occurred de novo. Thus, OCS and KCS are allelic disorders of different severity. FAM111A codes for a 611 amino acid protein with homology to trypsin-like peptidases. Although FAM111A has been found to bind to the large T-antigen of SV40 and restrict viral replication, its native function is unknown. Molecular modeling of FAM111A shows that residues affected by KCS and OCS mutations do not map close to the active site but are clustered on a segment of the protein and are at, or close to, its outer surface, suggesting that the pathogenesis involves the interaction with as yet unidentified partner proteins rather than impaired catalysis. FAM111A appears to be crucial to a pathway that governs parathyroid hormone production, calcium homeostasis, and skeletal development and growth. 相似文献
4.
Dynamic changes in microbiota and mycobiota during spontaneous ‘Vino Santo Trentino’ fermentation
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Irene Stefanini Davide Albanese Agostino Cavazza Elena Franciosi Carlotta De Filippo Claudio Donati Duccio Cavalieri 《Microbial biotechnology》2016,9(2):195-208
Vino Santo is a sweet wine produced from late harvesting and pressing of Nosiola grapes in a small, well‐defined geographical area in the Italian Alps. We used metagenomics to characterize the dynamics of microbial communities in the products of three wineries, resulting from spontaneous fermentation with almost the same timing and procedure. Comparing fermentation dynamics and grape microbial composition, we show a rapid increase in a small number of wine yeast species, with a parallel decrease in complexity. Despite the application of similar protocols, slight changes in the procedures led to significant differences in the microbiota in the three cases of fermentation: (i) fungal content of the must varied significantly in the different wineries, (ii) Pichia membranifaciens persisted in only one of the wineries, (iii) one fermentation was characterized by the balanced presence of Saccharomyces cerevisiae and Hanseniaspora osmophila during the later phases. We suggest the existence of a highly winery‐specific ‘microbial‐terroir’ contributing significantly to the final product rather than a regional ‘terroir’. Analysis of changes in abundance during fermentation showed evident correlations between different species, suggesting that fermentation is the result of a continuum of interaction between different species and physical–chemical parameters. 相似文献
5.
Cavalieri D McGovern PE Hartl DL Mortimer R Polsinelli M 《Journal of molecular evolution》2003,57(Z1):S226-S232
Saccharomyces cerevisiae is the principal yeast used in modern fermentation processes, including winemaking, breadmaking, and brewing. From residue present inside one of the earliest known wine jars from Egypt, we have extracted, amplified, and sequenced ribosomal DNA from S. cerevisiae. These results indicate that this organism was probably responsible for wine fermentation by at least 3150 B.C. This inference has major implications for the evolution of bread and beer yeasts, since it suggests that S. cerevisiae yeast, which occurs naturally on the surface bloom of grapes, was also used as an inoculum to ferment cereal products. 相似文献
6.
Cryptosporidium,Giardia, and Cyclospora in ancient Peruvians 总被引:2,自引:0,他引:2
Twenty-two coprolites of human origin, collected from excavations along the north-central coast of Peru, were examined using fluorescent microscopy for the presence of fecal parasites, with emphasis on Cryptosporidium sp., Giardia sp., and Cyclospora sp. Three samples were positive. One coprolite dated between ca. 2,375 and 1,525 BC contained Giardia sp. cysts. This coprolite corresponded to the Peruvian preceramic period. Another positive coprolite ca. AD 770-830 corresponded to Epoch 3 of the Middle Horizon and contained Cryptosporidium sp. oocysts. The third positive coprolite (corresponding to the Middle Horizon. ca. AD 500-900) contained Giardia sp. cysts. This report demonstrates that Giardia sp. and Cryptosporidium sp. were present in Peruvian coastal populations for at least 4,300 and 1,100 BP. 相似文献
7.
Population genetic variation in genome-wide gene expression 总被引:21,自引:0,他引:21
Evolutionary biologists seek to understand which traits display variation, are heritable, and influence differential reproduction, because such traits respond to natural selection and underlie organic evolution. Selection acts upon individual differences within a population. Whether individual differences within a natural population include variation in gene expression levels has not yet been addressed on a genome-wide scale. Here we use DNA microarray technology for measuring comparative gene expression and a refined statistical analysis for the purpose of comparing gene expression levels in natural isolates of the wine yeast Saccharomyces cerevisiae. A method for the Bayesian analysis of gene expression levels is used to compare four natural isolates of S. cerevisiae from Montalcino, Italy. Widespread variation in amino acid metabolism, sulfur assimilation and processing, and protein degradation-primarily consisting of differences in expression level smaller than a factor of 2-is demonstrated. Genetic variation in gene expression among isolates from a natural population is present on a genomic scale. It remains to be determined what role differential gene expression may play in adaptation to new or changing environments. 相似文献
8.
Duccio Rocchini Niko Balkenhol Gregory A. Carter Giles M. Foody Thomas W. Gillespie Kate S. He Salit Kark Noam Levin Kelly Lucas Miska Luoto Harini Nagendra Jens Oldeland Carlo Ricotta Jane Southworth Markus Neteler 《Ecological Informatics》2010,5(5):318-329
Environmental heterogeneity is considered to be one of the main factors associated with biodiversity given that areas with highly heterogeneous environments can host more species due to their higher number of available niches. In this view, spatial variability extracted from remotely sensed images has been used as a proxy of species diversity, as these data provide an inexpensive means of deriving environmental information for large areas in a consistent and regular manner. The aim of this review is to provide an overview of the state of the art in the use of spectral heterogeneity for estimating species diversity. We will examine a number of issues related to this theme, dealing with: i) the main sensors used for biodiversity monitoring, ii) scale matching problems between remotely sensed and field diversity data, iii) spectral heterogeneity measurement techniques, iv) types of species taxonomic diversity measures and how they influence the relationship between spectral and species diversity, v) spectral versus genetic diversity, and vi) modeling procedures for relating spectral and species diversity. Our review suggests that remotely sensed spectral heterogeneity information provides a crucial baseline for rapid estimation or prediction of biodiversity attributes and hotspots in space and time. 相似文献
9.
Fabio Rizzolo Chiara Testa Duccio Lambardi Michael Chorev Mario Chelli Paolo Rovero Anna Maria Papini 《Journal of peptide science》2011,17(10):708-714
Attracted by the possibility to optimize time and yield of the synthesis of difficult peptide sequences by MW irradiation, we compared Fmoc/tBu MW‐assisted SPPS of 1–34 N‐terminal fragment of parathyroid hormone‐related peptide (PTHrP) with its conventional SPPS carried out at RT. MWs were applied in both coupling and deprotection steps of SPPS protocol. During the stepwise elongation of the resin‐bound peptide, monitoring was conducted by performing MW‐assisted mini‐cleavages and analyzing them by UPLC‐ESI‐MS. Identification of some deletion sequences was helpful to recognize critical couplings and as such helped to guide the introduction of MW irradiations to these stages. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd. 相似文献
10.
Extremely low-frequency electromagnetic fields do not affect DNA damage and gene expression profiles of yeast and human lymphocytes 总被引:3,自引:0,他引:3
Luceri C De Filippo C Giovannelli L Blangiardo M Cavalieri D Aglietti F Pampaloni M Andreuccetti D Pieri L Bambi F Biggeri A Dolara P 《Radiation research》2005,164(3):277-285
We studied the effects of extremely low-frequency (50 Hz) electromagnetic fields (EMFs) on peripheral human blood lymphocytes and DBY747 Saccharomyces cerevisiae. Graded exposure to 50 Hz magnetic flux density was obtained with a Helmholtz coil system set at 1, 10 or 100 microT for 18 h. The effects of EMFs on DNA damage were studied with the single-cell gel electrophoresis assay (comet assay) in lymphocytes. Gene expression profiles of EMF-exposed human and yeast cells were evaluated with DNA microarrays containing 13,971 and 6,212 oligonucleotides, respectively. After exposure to the EMF, we did not observe an increase in the amount of strand breaks or oxidated DNA bases relative to controls or a variation in gene expression profiles. The results suggest that extremely low-frequency EMFs do not induce DNA damage or affect gene expression in these two different eukaryotic cell systems. 相似文献