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  • 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
  • Bacteria
  • Frontiers Media SA  (14)
  • Lagos (Nigeria)  (6)
  • Istituto Nazionale di Geofisica e Vulcanologia  (5)
  • Massachusetts Institute of Technology and Woods Hole Oceanographic Institution  (5)
  • American Chemical Society
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  • 1
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    Microbial load on smoked fish sold in Ibadan, Oyo State (2021)
    FISON | Lagos (Nigeria)
    In:  http://aquaticcommons.org/id/eprint/24208 | 19325 | 2018-05-19 06:39:34 | 24208 | Fisheries Society of Nigeria
    Details
    Publication Date: 2021-07-15
    Description: The microbial load of four different fish species from five different market locations in Ibadan metropolis were determined using standard microbiological procedures. The bacteria count of fish sampled from Ojo market was the highest while the bacteria count of the fish sample from Bodija market was the lowest. There was no significant difference (p〈0.05) in the microbial load of the fish sampled from various market locations in Ibadan metropolis. Similarly, there was no significant difference (p〉0.05) in the microbial load on various fish species sold in Ibadan metropolis. The isolated bacteria from the study were: E. coli, Salmonella spp, Klebsiella spp, Staphylococcus aureus, Aerosomonas spp, Pseudomonas spp, Vibrio spp, Serratia spp, Chromobacterium spp, Enterobacteria spp and Shigella spp. The fungi count of fish sampled from Omi markets was the highest while the fungi count of the fish sampled from Ojo market was the lowest. The following fungi were however isolated from the study: Aspergillus flavus, Penicillium spp, Fusarium oxysporum, Trrichoderma spp and Ceotrichium albidium. The study shows that reheating may be necessary to destroy or inactivate micro-organisms in smoked fish before consumption.
    Description: Includes: 2 tables and 2 figures.;Also includes: 17 refernces.
    Keywords: Fisheries ; Nigeria ; Ibadan ; Bacteria ; Fungi ; Market ; Fish species ; freshwater environment ; Microbial contamination ; Microorganisms ; Bacteria ; Freshwater fish ; Cured products ; Sample contamination ; Fungi ; Public health ; Quality assurance ; Disinfection
    Repository Name: AquaDocs
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    Format: 223-227
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  • 2
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    Isolation, identification and characterization of Lactobacillus species from fermented locust bean (Parkia biglobosa) for use as probiotics in the aquaculture industry (2021)
    FISON | Lagos (Nigeria)
    In:  http://aquaticcommons.org/id/eprint/24166 | 19325 | 2018-05-13 18:40:22 | 24166 | Fisheries Society of Nigeria
    Details
    Publication Date: 2021-07-15
    Description: Probiotics are a promising feed additive to stimulate animal growth and secure a low disease response in aquaculture industry where there are high stocking densities in shrimp and fish production. Fermented locust beans (Parkia biglobosa) are known to be rich in protein and used as food condiment. Probiotic bacteria were isolated from this locally available food material. Culture and characterizations of isolates were carried out. Sugar fermentation patterns were determined by using an API 50 CHL system and incubation were performed anaerobically at 37~'C. MRS broth culture grown at 37~'C overnight was added to 9ml of MRS Agar and the bacteria were incubated at 37~'C for 24 and 48 hrs. Discrete and single colony of lactobacillus was isolated using colony morphology and biochemical tests. The most significant viable taxa isolated was Lactobacillus fermentum at a pH range of (3.0-8.0), while the least viable taxa isolated was Leuconostoc mesenteroides ssp. Microscopically they were Grampositive, rod shaped, non- motile, catalase negative and absence of Endospore.
    Description: Includes: 2 tables and 2 plates.;Also includes: 15 references.
    Keywords: Aquaculture ; Nigeria ; Lagos ; Locust bean ; Probiotics ; Lactobacillus ; Probiotics ; freshwater environment ; Feed ; Additives ; Aquaculture ; Microorganisms ; Bacteria ; Disease resistance ; Fermented products ; Fish culture ; Shrimp culture
    Repository Name: AquaDocs
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    Format: 60-63
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  • 3
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    Microbiological status of water and fish samples from Jabi Lake, Abuja (2021)
    FISON | Lagos (Nigeria)
    In:  http://aquaticcommons.org/id/eprint/24224 | 19325 | 2018-05-19 07:11:26 | 24224 | Fisheries Society of Nigeria
    Details
    Publication Date: 2021-07-15
    Description: Jabi Lake is a natural water body in Abuja Federal Capital Territory (FCT). It was expanded for commercial fishing following relocation of Nigeria's headquarters to Abuja in 1993. Quantitative analysis of microbiological status of water and fish from the Lake was carried out. Samples were collected from the dam site, open water, middle lake and inlet. Result reveal that total coliform count which are indicators of pollution are high (2.0 x 103 cfu/ml, 1.1 x 103 cfu/ml, 1.0 x 103 cfu/ml and 1.1 x 103 cfu/ml for dam site, open water, middle lake, and inlet respectively). Total viable count too is high (9.2 x 103 cfu/ml, 4.9 x 103 cfu/ml, 4.6 x 103 cfu/ml and 4.9 x 103 cfu/ml for dam site, open water, middle lake and inlet respectively). There are no coliform bacteria in the muscle of the fish. High bacterial load is an indication of biological pollution and these calls for restraint on the side of those who are using the lake as site for refuse dump.
    Description: Includes: 10 references.
    Keywords: Fisheries ; Pollution ; Nigeria ; Jabi Lake ; Jabi lake ; Water ; Fish ; Bacteria ; freshwater environment ; Microbiology ; Fish ; Pollution ; Water pollution ; Lake fisheries ; Fishery surveys ; Bacteria ; Baseline studies ; Water sampling ; Microbial contamination ; Muscles ; Freshwater fish ; Pollution surveys ; Water analysis ; Freshwater pollution
    Repository Name: AquaDocs
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    Format: 284-286
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  • 4
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    Bacteriological assessment of smoked fish (Clarias Sp.) around Shiroro Lake area of Niger State, Nigeria (2021)
    FISON | Lagos (Nigeria)
    In:  http://aquaticcommons.org/id/eprint/24185 | 19325 | 2018-05-16 14:41:02 | 24185 | Fisheries Society of Nigeria
    Details
    Publication Date: 2021-07-15
    Description: Bacteria has been implicated in food poisoning, and smoked fish is not an exception.Generally, fish is highly susceptible to spoilage; therefore this study evaluated the bacteria load in smoked fish from three major locations in Shiroro area of Niger State namely; Gwada, Kuta and Zumba.The smoked fish samples collected from these locations were smeared at both the gills and head regions of the fishes. The bacteria samples identified were Escherichia coli, Bacillus subtilis, Staphylococcus aureus, Staphylococcus epidermis, Pseudomonas aeruginosa, and Samonella typhi, which were common to all the three locations sampled, while only Streptococcus feacaliswas only was found to be present in both Kuta and Zumba location.The frequency of occurrence of these 68 bacteria samples isolated ranges from 8 - 20%, with Bacillius subtilis having the highest occurrence and Pseudomonas aeruginosa have the least occurrence. Out of the total 68 samples, 14 skin samples (20.6%) and 5 gills samples (7.4%) exceeded the acceptable limits of total mesophilic aerobic counts which were 10〈sup〉6〈/sup〉 - 10〈sup〉7〈/sup〉 cfu/g. In the case of total coliform counts, 12 skin samples (17.6%) and 7 gills samples (10.3%) exceeded the acceptable limit which is 4.0 x 102, while in the case of Staphylococcus aureus, 4 skin samples (5.9%) and 2 gills samples (2.9%) exceeded the acceptable limit which is 103 cfu/g. Similarly 3 skin samples (4.4%) and 1 gill sample (1.5%) exceeded the acceptable limit of Salmonella typhi which is 104 cfu/g.
    Description: Includes: 4 tables.;Also includes: 21 references.
    Keywords: Fisheries ; Health ; Escherichia coli ; Bacillus subtilis ; Staphylococcus aureus ; Staphylococcus epidermis ; Pseeudomonas aeruginosa ; Nigeria ; Shiroro L. ; Bacteria ; Smoked (Clarias spp) fish ; Location and recommended values ; brackishwater environment ; freshwater environment ; marine environment ; Bacteria ; Food poisoning ; Cured products ; Fish ; Fish spoilage ; Acceptability ; Lake fisheries ; Gills ; Brain ; Evaluation
    Repository Name: AquaDocs
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    Format: 140-144
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  • 5
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    Microbiological quality of fresh tilapia raised in ponds fertilized with raw and sterilized cow dung manures (2021)
    FISON | Lagos (Nigeria)
    In:  http://aquaticcommons.org/id/eprint/24222 | 19325 | 2018-05-19 07:06:04 | 24222 | Fisheries Society of Nigeria
    Details
    Publication Date: 2021-07-15
    Description: A total of 2,800 tilapia (Oreochromis niloticus) were stocked in seven duplicates 5 by 4 m2 earthen ponds in NIFFR Integrated Farm, New-Bussa, Niger-State. Raw and sterilized poultry manure of 0.13 to 0.52 kg/m3 concentrations were used to fertilize the ponds with the unfertilized ponds serving as control. The following bacteria were isolated from the cow dung manure; Escherichia coli, E. co1iOl57:H7, Aeromonas hydrophila,Salmonella typhi, Shigella dysenteriae and Staphylococcus aureus. The fish samples from the 0.13 and 0.26 kg/m3 sterilized manure fertilized ponds had zero count in the muscles while samples from other ponds had pathogens in their fish muscles. The study revealed that fish samples from sterilized manures were better in terms of microbial safety for fish productions hence sterilized manure are recommended for use in fish production to ensure the microbial safety of the fish, handlers and that of the consumers.
    Description: includes: 13 references.
    Keywords: Aquaculture ; Oreochromis niloticus ; Escherichia coli ; Aeromonas hydrophila ; Samonela typhi ; Shigella dysenteriae ; Staphylococcus aureus ; Nigeria ; Niger State ; Catfish ; Pathogens ; Microbial quality ; Raw and sterilized manue ; freshwater environment ; Bacteria ; Freshwater fish ; Fish culture ; Fish ponds ; Manure ; Microorganisms ; Freshwater aquaculture ; Aquaculture products ; Food fish ; Quality assurance ; Muscles ; Microbial contamination
    Repository Name: AquaDocs
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    Format: 278-280
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  • 6
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    Comparative study of bacterial isolates associated with the skin of catfish (Clarias anguillaris and Heterobranchus bidorsalis) in Kainji Lake area (2021)
    FISON | Lagos (Nigeria)
    In:  http://aquaticcommons.org/id/eprint/24596 | 19325 | 2018-05-20 16:13:09 | 24596 | Fisheries Society of Nigeria
    Details
    Publication Date: 2021-07-15
    Description: Sixty apparently healthy Heterobranchus bidorsalis and Clarias anguillaris from NIFFR were cultured and 30 each from Monai and wara villages as wild environments were obtained for the studies. The total bacterial load varied from 2.2 x l05 to 1.08 x l08 and 2.27 x 105 to 6.3 x l08 CFU/g of the skin of C. anguillaris and H.bidorsalis in the culture respectively, while the load varied from 1.77 x 105 to 1.17 x l08 and 2.27 x 105 to 9.0 x l07 CFU/g in the wild respectively. Eleven bacterial general species were identified which include: Bacillus species B.firmus, Pseudomonas species, P. aeruginosa, Escherichia coli, Klebsiella aerogenes, K. ozaenae, Staphylococcus aureus, Streptococcus species, S.faecalis, and Aeromonas species. The aims of this investigation is to compare the type and the load of bacteria isolates on the skin of catfish in both culture and wild environment.
    Description: Includes: 7 references.
    Keywords: Aquaculture ; Fisheries ; Clarias anguillaris ; Heterobranchus bidorsalis ; Nigeria ; Kainji L. ; Comparative study ; Bacteria ; Skin ; Clarias ; Heterobranchus ; Kainji Lake ; freshwater environment ; automation
    Repository Name: AquaDocs
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    Format: 119-122
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  • 7
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    Production of two highly abundant 2-methyl-branched fatty acids by blooms of the globally significant marine cyanobacteria Trichodesmium erythraeum (2021)
    American Chemical Society
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gosselin, K. M., Nelson, R. K., Spivak, A. C., Sylva, S. P., Van Mooy, B. A. S., Aeppli, C., Sharpless, C. M., O’Neil, G. W., Arrington, E. C., Reddy, C. M., & Valentine, D. L. Production of two highly abundant 2-methyl-branched fatty acids by blooms of the globally significant marine cyanobacteria Trichodesmium erythraeum. ACS Omega, 6(35), (2021): 22803–22810, https://doi.org/10.1021/acsomega.1c03196.
    Description: The bloom-forming cyanobacteria Trichodesmium contribute up to 30% to the total fixed nitrogen in the global oceans and thereby drive substantial productivity. On an expedition in the Gulf of Mexico, we observed and sampled surface slicks, some of which included dense blooms of Trichodesmium erythraeum. These bloom samples contained abundant and atypical free fatty acids, identified here as 2-methyldecanoic acid and 2-methyldodecanoic acid. The high abundance and unusual branching pattern of these compounds suggest that they may play a specific role in this globally important organism.
    Description: This work was funded with grants from the National Science Foundation grants OCE-1333148, OCE-1333162, and OCE-1756254 and the Woods Hole Oceanographic Institution (IR&D). GCxGC analysis made possible by WHOI’s Investment in Science Fund.
    Keywords: Lipids ; Alkyls ; Bacteria ; Genetics ; Chromatography
    Repository Name: Woods Hole Open Access Server
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  • 8
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    The metabolic pathways and environmental controls of hydrocarbon biodegradation in marine ecosystems (2021)
    Frontiers Media SA
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    Publication Date: 2022-01-31
    Description: Biodegradation mediated by indigenous microbial communities is the ultimate fate of the majority of oil hydrocarbon that enters the marine environment. The aim of this Research Topic is to highlight recent advances in our knowledge of the pathways and controls of microbially-catalyzed hydrocarbon degradation in marine ecosystems, with emphasis on the response of microbial communities to the Deepwater Horizon oil spill in the Gulf of Mexico. In this Research Topic, we encouraged original research and reviews on the ecology of hydrocarbon-degrading bacteria, the rates and mechanisms of biodegradation, and the bioremediation of discharged oil under situ as well as near in situ conditions.
    Keywords: GC1-1581 ; QR1-502 ; Q1-390 ; Biodegradation ; Metagenomics ; oil spill ; metatran ; bacterioplankton ; Bacteria ; Gulf of Mexico ; microbial communities ; hydrocarbon ; Deepwater Horizon
    Language: English
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  • 9
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    Bacterial Secretion Systems (2021)
    Frontiers Media SA
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    Publication Date: 2024-04-04
    Description: This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact
    Keywords: Bacteria ; Secretion ; Membrane ; Transport ; Protein Complex ; Pathogen ; thema EDItEUR::P Mathematics and Science::PD Science: general issues ; thema EDItEUR::M Medicine and Nursing::MK Medical specialties, branches of medicine::MKF Pathology::MKFM Medical microbiology and virology ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSG Microbiology (non-medical)
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  • 10
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    Microbiota of Grapes: Positive and Negative Role on Wine Quality (2021)
    Frontiers Media SA
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    Publication Date: 2024-04-05
    Description: During spontaneous food/beverage fermentations, the microbiota associated with the raw material has a considerable importance: this microbial consortium evolves in reason of the nutrient content and of the physical, chemical, and biological determinants present in the food matrix, shaping fermentation dynamics with significant impacts on the ‘qualities’ of final productions. The selection from the indigenous micro-biodiversity of ‘virtuous’ ecotypes that coupled pro-technological and biotechnological aptitudes provide the basis for the formulation of ‘tailored’ starter cultures. In the fermenting food and beverage arena, the wine sector is generally characterized by the generation of a high added value. Together with a pronounced seasonality, this feature strongly contributes to the selection of a large group of starter cultures. In the last years, several studies contributed to describe the complexity of grapevine-associated microbiota using both culture-dependent and culture-independent approaches. The grape-associated microbial communities continuously change during the wine-making process, with different dominances that correspond to the main biotechnological steps that take place in wine. In order to simplify, following a time trend, four major dominances can be mainly considered: non-Saccharomyces, Saccharomyces, lactic acid bacteria (LAB), and spoilage microbes. The first two dominances come in succession during the alcoholic fermentation: the impact of Saccharomyces (that are responsible of key enological step of ethanol production) can be complemented/integrated by the contributions of compatible non-Saccharomyces strains. Lactic acid bacteria constitute the malolactic consortium responsible of malolactic fermentation, a microbial bioconversion often desired in wine (especially in red wine production). Finally, the fourth dominance, the undesired microbiota, represents a panel of microorganisms that, coupling spoilage potential to the resistance to the harsh conditions typical of wine environment, can cause important economic losses. In each of these four dominances a complex microbial biodiversity has been described. The studies on the enological significance of the micro-biodiversity connected with each of the four dominances highlighted the presence of a dichotomy: in each consortia there are species/strains that, in reason of their metabolisms, are able to improve wine ‘qualities’ (resource of interest in starter cultures design), and species/strains that with their metabolism are responsible of depreciation of wine. Articles describing new oenological impacts of yeasts and bacteria belonging to the four main categories above mentioned (non-Saccharomyces, Saccharomycetes, lactic acid bacteria, and spoilage microbes) are welcome. Moreover, in this Research Topic, we encourage mini-review submissions on topics of immediate interest in wine microbiology that link microbial biodiversity with positive/negative effects in wine.
    Keywords: QR1-502 ; Q1-390 ; Wine ; Yeasts ; Microbial Diversity ; Bacteria ; Safety ; alcoholic fermentation ; malolactic fermentation ; grapes ; quality ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSG Microbiology (non-medical)
    Language: English
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  • 11
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    LuxR Solos are Becoming Major Players in Cell-Cell Communication in Bacteria (2021)
    Frontiers Media SA
    Details
    Publication Date: 2024-04-05
    Description: The most common quorum sensing (QS) system in Gram-negative bacteria occurs via N-acyl homoserine lactone (AHLs) signals. An archetypical system consists of a LuxI-family protein synthesizing the AHL signal which binds at quorum concentrations to the cognate LuxR-family transcription factors which then control gene expression by binding to specific sequences in target gene promoters. QS LuxR-family proteins are approximately 250 amino acids long and made up of two domains; at the N-terminus there is an autoinducer-binding domain whereas the C-terminus contains a DNA-binding helix-turn-helix (HTH) domain. QS LuxRs display surprisingly low similarities (18-25%) even if they respond to structurally similar AHLs. 95% of LuxRs share 9 highly conserved amino acid residues; six of these are hydrophobic or aromatic and form the cavity of the AHL-binding domain and the remaining three are in the HTH domain. With only very few exceptions, the luxI/R cognate genes of AHL QS systems are located adjacent to each other. The sequencing of many bacterial genomes has revealed that many proteobacteria also possess LuxRs that do not have a cognate LuxI protein associated with them. These LuxRs have been called orphans and more recently solos. LuxR solos are widespread in proteobacterial species that possess a canonical complete AHL QS system as well as in species that do not. In many cases more than one LuxR solo is present in a bacterial genome. Scientists are beginning to investigate these solos. Are solos responding to AHL signals? If present in a bacterium which possesses a canonical AHL QS system are solos an integral part of the regulatory circuit? Are LuxR solos eavesdropping on AHLs produced by neighboring bacteria? Have they evolved to respond to different signals instead of AHLs, and are these signals endogenously produced or exogenously provided? Are they involved in interkingdom signaling by responding to eukaryotic signals? Recent studies have revealed that LuxR solos are involved in several mechanisms of cell-cell communication in bacteria implicating them in bacterial intraspecies and interspecies communication as well as in interkingdom signaling by responding to molecules produced by eukaryotes. LuxR solos are likely to become major players in signaling since they are widespread among proteobacterial genomes and because initial studies highlight their different roles in bacterial communication. This Research Topic allows scientists studying or interested in LuxR solos to report their data and/or express their hypotheses and thoughts on this important and currently understudied family of signaling proteins.
    Keywords: QH301-705.5 ; Q1-390 ; LuxR solos ; Quorum Sensing ; signaling ; AHL ; Bacteria ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences
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  • 12
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    Protein Solubility and Aggregation in Bacteria (2021)
    Frontiers Media SA
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    Publication Date: 2024-04-05
    Description: Proteins suffer many conformational changes and interactions through their life, from their synthesis at ribosomes to their controlled degradation. Only folded and soluble proteins are functional. Thus, protein folding and solubility are controlled genetically, transcriptionally, and at the protein sequence level. In addition, a well-conserved cellular machinery assists the folding of polypeptides to avoid misfolding and ensure the attainment of soluble and functional structures. When these redundant protective strategies are overcome, misfolded proteins are recruited into aggregates. Recombinant protein production is an essential tool for the biotechnology industry and also supports expanding areas of basic and biomedical research, including structural genomics and proteomics. Although bacteria still represent a convenient production system, many recombinant polypeptides produced in prokaryotic hosts undergo irregular or incomplete folding processes that usually result in their accumulation as insoluble aggregates, narrowing thus the spectrum of protein-based drugs that are available in the biotechnology market. In fact, the solubility of bacterially produced proteins is of major concern in production processes, and many orthogonal strategies have been exploited to try to increase soluble protein yields. Importantly, contrary to the usual assumption that the bacterial aggregates formed during protein production are totally inactive, the presence of a fraction of molecules in a native-like structure in these assemblies endorse them with a certain degree of biological activity, a property that is allowing the use of bacteria as factories to produce new functional materials and catalysts. The protein embedded in intracellular bacterial deposits might display different conformations, but they are usually enriched in beta-sheet-rich assemblies resembling the amyloid fibrils characteristic of several human neurodegenerative diseases. This makes bacterial cells simple, but biologically relevant model systems to address the mechanisms behind amyloid formation and the cellular impact of protein aggregates. Interestingly, bacteria also exploit the structural principles behind amyloid formation for functional purposes such as adhesion or cytotoxicity. In the present research topic we collect papers addressing all the issues mentioned above from both the experimental and computational point of view.
    Keywords: QR1-502 ; Q1-390 ; protein aggregation ; bacterial chaperones ; Bacteria ; Functional amyloids ; protein expression ; Protein Folding ; Prion-like proteins ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSG Microbiology (non-medical)
    Language: English
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    Proteomics of Microbial Human Pathogens (2021)
    Frontiers Media SA
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    Publication Date: 2024-04-05
    Description: According to the World Health Organization (WHO), in 2012 infectious diseases and related conditions account for more than 70% of premature deaths across 22 African countries and estimated 450 000 people worldwide developed multi-drug resistant tuberculosis. This alarming situation, of great public health concern, calls for the urgent development of novel and efficient responding strategies. The employment of important research platforms, such as genomics and proteomics, has contributed significant insight into the mechanisms underlying microbial infection and microbe-host interaction. In this Frontiers Research Topic, we aim to produce a timely and pertinent discussion regarding the current status of “Proteomics of microbial Human pathogens” and the role of proteomics in combating the challenges posed by microbial infection and indeed acquired anti-microbial resistance. As the field of proteomics progressed from 2-DE gel based approaches to modern LC-MS/MS based workflows, remarkable advances have been reported in terms of data quantity and quality. Given the immediate and enormous advantages that high resolution and accurate mass spectrometers have brought to the field, proteomics has now evolved into a robust platform capable of generating large amounts of comprehensive data comparable to that reported previously in genomics studies. For example, detection of the complete yeast proteome has been reported and other small proteomes, such as those of bacteria, are within reach. Mass spectrometry-based proteomics has become an essential tool for biologists and biochemists, and is now considered by many as an essential component of modern structural biology. Additionally, the introduction of high-resolution mass spectrometers has driven the development of various different strategies aimed at accurate quantification of absolute and relative amount of protein(s) of interest. Emerging targeted mass spectrometry methodologies such as; Selected Reaction Monitoring (SRM), Parallel Reaction Monitoring (PRM) and SWATH, are perhaps the latest breakthrough within the proteomics community. Indeed, through a label free approach, targeted mass spectrometry offers an unequalled capability to characterize and quantify a specific set of proteins reproducibility, in any biological sample. Usefully, Aebersold and colleagues have recently generated and validated a number of assays to quantify 97% of the 4,012 annotated Mycobacterium tuberculosis (Mtb) proteins by SRM. As such, the Mtb Proteome library represents a valuable experimental resource that will undoubtedly bring new insight to the complex life cycle of Mtb. Finally, as reviewed recently in Frontiers Research Topic, mass spectrometry-based proteomics has had a tremendous impact on our current understanding of post translational modification (PTM) in bacteria including the key role of PTMs during interaction of pathogenic bacteria and host interactions. We believe that our understanding of microbial Human pathogens has benefited enormously from both 2-DE gel and modern LC-MS/MS based proteomics. It is our wish to produce an integrated discussion surrounding this topic to highlight the existing synergy between these research fields. We envisage this Research Topic as a window to expert opinions and perspectives on the realistic practicalities of proteomics as an important tool to address healthcare problems caused by microbial pathogens.
    Keywords: QR1-502 ; Q1-390 ; Mass Spectrometry ; Proteomics ; infectious diseases ; Bacteria ; pathogen ; Microbes ; Protein posttranslational modifications ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSG Microbiology (non-medical)
    Language: English
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  • 14
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    An Infectious Origin of Alzheimer’s Disease: An End for This Devastating Disorder? (2021)
    Frontiers Media SA
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    Publication Date: 2024-04-04
    Description: This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact
    Keywords: Alzheimer's disease ; Amyloid ; Bacteria ; Infection ; Spirochetes ; Dementia ; Pathogens ; Biofilm ; Senile plaque ; Beta amyloid ; Tau ; Inflammation ; Bacterial amyloid ; HSV1 ; Virus ; thema EDItEUR::P Mathematics and Science::PD Science: general issues ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAN Neurosciences
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  • 15
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    Evolutionary Feedbacks Between Population Biology and Genome Architecture (2021)
    Frontiers Media SA
    Details
    Publication Date: 2024-04-05
    Description: This eBook presents all 10 articles published under the Frontiers Research Topic "Evolutionary Feedbacks Between Population Biology and Genome Architecture", edited by Scott V. Edwards and Tariq Ezaz. With the rise of rapid genome sequencing across the Tree of Life, challenges arise in understanding the major evolutionary forces influencing the structure of microbial and eukaryotic genomes, in particular the prevalence of natural selection versus genetic drift in shaping those genomes. Additional complexities in understanding genome architecture arise with the increasing incidence of interspecific hybridization as a force for shaping genotypes and phenotypes. A key paradigm shift facilitating a more nuanced interpretation of genomes came with the rise of the nearly neutral theory in the 1970s, followed by a greater appreciation for the contribution of nonadaptive forces such as genetic drift to genome structure in the 1990s and 2000s. The articles published in this eBook grapple with these issues and provide an update as to the ways in which modern population genetics and genome informatics deepen our understanding of the subtle interplay between these myriad forces. From intraspecific to macroevolutionary studies, population biology and population genetics are now major tools for understanding the broad landscape of how genomes evolve across the Tree of Life. This volume is a celebration across diverse taxa of the contributions of population genetics thinking to genome studies. We hope it spurs additional research and clarity in the ongoing search for rules governing the evolution of genomes.
    Keywords: QK1-989 ; Q1-390 ; Genetic Drift ; intron ; natural selection ; gene ; plant ; vertebrate ; Bacteria ; Sex Chromosomes ; Genome ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PST Botany and plant sciences
    Language: English
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    Use of Saliva in Diagnosis of Periodontitis: Cumulative Use of Bacterial and Host-Derived Biomarkers (2021)
    Frontiers Media SA
    Details
    Publication Date: 2023-12-20
    Description: Periodontitis is an infection-induced inflammatory disease of the tooth supporting tissues. Treatment of periodontal diseases and regeneration of the effected tissues can be possible only in the early diagnosis of the disease. If left undiagnosed or untreated, periodontitis leads to irreversible soft and hard tissue destruction and finally to tooth loss. Saliva is known to contain inflammatory mediators, host tissue and cell degradation products as well as microbial metabolites and enzymes, reflecting the health status of the oral cavity. In this topic, in collaboration with the well-known scientists working on the field of salivary diagnostics, we demonstrate evidence on monitoring periodontitis by salivary analysis.
    Keywords: Q1-390 ; RC109-216 ; host response ; Chair-side ; diagnostics ; Periodontal disease ; Salivary ; Bacteria ; bic Book Industry Communication::G Reference, information & interdisciplinary subjects::GP Research & information: general
    Language: English
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    Microbial and Environmental Factors in Autoimmune and Inflammatory Diseases (2021)
    Frontiers Media SA
    Details
    Publication Date: 2023-12-21
    Description: In recent years there has been a substantial increase in the number of diseases with the inflammatory component such as such as allergy, asthma, rheumatoid arthritis, inflammatory bowl disease (IBD, which includes ulcerative colitis and Crohn's disease), chronic sinusitis, and many other conditions. The majority of these diseases are multifactorial, with the contribution of genetic and environmental factors. Among the latter, the role of certain microorganisms and viruses in triggering or sustaining the inflammatory process is most controversial. In rheumatoid arthritis, for example, the following bacteria and viruses have been implicated in triggering the disease: Mycoplasma spp., Proteus mirabilis, Escherichia coli, Staphylococcus spp., Bordetella spp., Acinetobacter spp., the parvoviruses, Epstein-Barr virus, and retroviruses. The list of putative microbial triggers of rheumatoid arthritis is still growing, and it becomes essentially impossible to make a causation link between certain infectious agents and the disease. In the light of these disappointing results there are calls for even larger studies with the use of more advanced and large-scale technologies. The primary function of the immune system is the maintenance of body homeostasis and protection against any threats to it via several lines of elaborate and complex immune defense. Given even higher complexity that involves the microbiota and the corresponding host-microbe interaction, the conditions for this equilibrium become even more challenging. In the absence of a defined pathogen, for example, the spectrum of microorganisms involved in triggering inappropriate immune responses may include polymicrobial communities or the cumulative effect of several microbial/viral factors. Under the normal circumstances there is a fine-tuned balance between commensal microbiota and the host’s immune responses. However, when this balance is compromised, for example in IBD, a massive immune response is launched against commensal microbiota resulting in chronic inflammation. Besides the microbial/viral factors, the balance of the immune system can be compromised by other causes. Given, for example, the close and inclusive interaction of the immune, nervous and endocrine systems, the list of these provoking factors can expand even more. For instance, it has been demonstrated that even mild sleep deprivation may increase the production of interleukin-6 and C-reactive protein. Understanding the complex role of microbial and environmental factors in inflammatory and autoimmune diseases, therefore, is the main subject of this topic.
    Keywords: R5-920 ; RC581-607 ; QR1-502 ; Q1-390 ; environment ; Autoimmune ecology ; Silica exposure ; Rheumatoid arthritis ; Viruses ; Bacteria ; bic Book Industry Communication::M Medicine
    Language: English
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    Regulatory potential of post-translational modifications in bacteria (2021)
    Frontiers Media SA
    Details
    Publication Date: 2024-04-05
    Description: Post-translational modifications (PTMs) are widely employed by all living organisms to control the enzymatic activity, localization or stability of proteins on a much shorter time scale than the transcriptional control. In eukarya, global analyses consistently reveal that proteins are very extensively phosphorylated, acetylated and ubiquitylated. Glycosylation and methylation are also very common, and myriad other PTMs, most with a proven regulatory potential, are being discovered continuously. The emergent picture is that PTM sites on a single protein are not independent; modification of one residue often affects (positively or negatively) modification of other sites on the same protein. The best example of this complex behavior is the histone “bar-code” with very extensive cross-talk between phosphorylation, acetylation and methylation sites. Traditionally it was believed that large networks of PTMs exist only in complex eukaryal cells, which exploit them for coordination and fine-tuning of various cellular functions. PTMs have also been detected in bacteria, but the early examples focused on a few important regulatory events, based mainly on protein phosphorylation. The global importance (and abundance) of PTMs in bacterial physiology was systematically underestimated. In recent years, global studies have reported large datasets of phosphorylated, acetylated and glycosylated proteins in bacteria. Other modifications of bacterial proteins have been recently described: pupylation, methylation, sirtuin acetylation, lipidation, carboxylation and bacillithiolation. As the landscape of PTMs in bacterial cells is rapidly expanding, primarily due to advances of detection methods in mass spectrometry, our research field is adapting to comprehend the potential impact of these modifications on the cellular physiology. The field of protein phosphorylation, especially of the Ser/Thr/Tyr type, has been profoundly transformed. We have become aware that bacterial kinases phosphorylate many protein substrates and thus constitute regulatory nodes with potential for signal integration. They also engage in cross-talk and eukaryal-like mutual activation cascades. The regulatory potential of protein acetylation and glycosylation in bacteria is also rapidly emerging, and the cross-talk between acetylation and phosphorylation has been documented. This topic deals with the complexity of the PTM landscape in bacteria, and focus in particular on the physiological roles that PTMs play and methods to study them. The topic is associated to the 1st International Conference on Post-Translational Modifications in Bacteria (September 9-10, 2014, Göttingen, Germany).
    Keywords: QR1-502 ; Q1-390 ; Infection ; Phosphorylation ; Hydroxylation ; Protein Kinases ; S-thiolation ; Proteomics ; Bacteria ; Dehydration ; N-glycosylation ; antimicrobial peptides ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSG Microbiology (non-medical)
    Language: English
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    DNA Replication Origins in Microbial Genomes (2021)
    Frontiers Media SA
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    Publication Date: 2024-04-05
    Description: DNA replication, a central event for cell proliferation, is the basis of biological inheritance. Complete and accurate DNA replication is integral to the maintenance of the genetic integrity of organisms. In all three domains of life, DNA replication begins at replication origins. In bacteria, replication typically initiates from a single replication origin (oriC), which contains several DnaA boxes and the AT-rich DNA unwinding element (DUE). In eukaryotic genomes, replication initiates from significantly more replication origins, activated simultaneously at a specific time. For eukaryotic organisms, replication origins are best characterized in the unicellular eukaryote budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. The budding yeast origins contain an essential sequence element called the ARS (autonomously replicating sequence), while the fission yeast origins consist of AT-rich sequences. Within the archaeal domain, the multiple replication origins have been identified by a predict-and-verify approach in the hyperthermophilic archaeon Sulfolobus. The basic structure of replication origins is conserved among archaea, typically including an AT-rich unwinding region flanked by several short repetitive DNA sequences, known as origin recognition boxes (ORBs). It appears that archaea have a simplified version of the eukaryotic replication apparatus, which has led to considerable interest in the archaeal machinery as a model of that in eukaryotes. The research on replication origins is important not only in providing insights into the structure and function of the replication origins but also in understanding the regulatory mechanisms of the initiation step in DNA replication. Therefore, intensive studies have been carried out in the last two decades. The pioneer work to identify bacterial oriCs in silico is the GC-skew analysis. Later, a method of cumulative GC skew without sliding windows was proposed to give better resolution. Meanwhile, an oligomer-skew method was also proposed to predict oriC regions in bacterial genomes. As a unique representation of a DNA sequence, the Z-curve method has been proved to be an accurate and effective approach to predict bacterial and archaeal replication origins. Budding yeast origins have been predicted by Oriscan using similarity to the characterized ones, while the fission yeast origins have been identified initially from AT content calculation. In comparison with the in silico analysis, the experimental methods are time-consuming and labor-intensive, but convincing and reliable. To identify microbial replication origins in vivo or in vitro, a number of experimental methods have been used including construction of replicative oriC plasmids, microarray-based or high-throughput sequencing-based marker frequency analysis, two-dimensional gel electrophoresis analysis and replication initiation point mapping (RIP mapping). The recent genome-wide approaches to identify and characterize replication origin locations have boosted the number of mapped yeast replication origins. In addition, the availability of increasing complete microbial genomes and emerging approaches has created challenges and opportunities for identification of their replication origins in silico, as well as in vivo and in vitro. The Frontiers in Microbiology Research Topic on DNA replication origins in microbial genomes is devoted to address the issues mentioned above, and aims to provide a comprehensive overview of current research in this field.
    Keywords: QR1-502 ; Q1-390 ; orisome ; Replication Origin ; Cell-cycle ; Archaea ; origin recognition complex (ORC) ; Bacteria ; DNA Replication ; Replication regulation ; yeast ; Regulatory proteins ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSG Microbiology (non-medical)
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    NLR-protein functions in immunity (2021)
    Frontiers Media SA
    Details
    Publication Date: 2023-12-21
    Description: The Nod-like receptor (NLR) family of proteins are evolutionary conserved molecules that in plants and mammals have been implicated in innate immune sensing of microbes and infection-associated physiological changes, contributing to immune protection of the challenged host organism through the instruction of inflammatory responses, antimicrobial defense and adaptive immunity. Recent data however suggests that the biological roles of NLR go beyond the function of classical pattern recognition molecules (PRM) as they have been implicated in essential cellular processes including autophagy, apoptosis, modification of signal transduction and gene transcription as well as reproductive biology. In this research topic, we aim to provide a comprehensive state-of the art overview of the emerging functions of NLR in plant and mammalian immunity, cell biology and reproductive biology. Potential topics may include, but are not limited to the following areas: • Functions of NLRs as PRMs in infection • Cross-talk of NLRs with other PRMs • Signal transduction pathways of NLRs • New functions of NLRs other than pattern recognition • Structural aspects of NLR activation • Mechanisms of NLRs in cell biological processes • Aspects of NLRs in reproductive biology • Functions of NLRs in plant immune responses
    Keywords: R5-920 ; RC581-607 ; Adaptive Immunity ; PAMP ; pathogens ; MAMP ; innate immunity ; Bacteria ; Sensing ; virus ; LRR ; DAMP ; bic Book Industry Communication::M Medicine
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    Bioprospecting and Biotechnology of Extremophiles (2021)
    Frontiers Media SA
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    Publication Date: 2024-04-11
    Description: This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact
    Keywords: Airborne ; Andean highland ; Bacteria ; fish ; hydrothermal vent ; hot spring ; microorganisms ; Plants ; thema EDItEUR::T Technology, Engineering, Agriculture, Industrial processes::TN Civil engineering, surveying and building ; thema EDItEUR::T Technology, Engineering, Agriculture, Industrial processes::TC Biochemical engineering::TCB Biotechnology
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    Observing microbial processes at the microscale with in situ technology (2019)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-05-25
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Oceanographic Engineering at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2019.
    Description: Marine microbes are key drivers of biogeochemical transformations within the world’s oceans. Although seawater appears uniform at scales that humans often interact with and sample, the world that marine microbes inhabit can be highly heterogeneous, with numerous biological and physical processes giving rise to resource hotspots where nutrient concentrations exceed background levels by orders of magnitude. While the impact of this microscale heterogeneity has been investigated in the laboratory with microbial isolates and theoretical models, microbial ecologists have lacked adequate tools to interrogate microscale processes directly in the natural environment. Within this thesis I introduce three new technologies that enable interrogation of microbial processes at the microscale in natural marine communities. The IFCB-Sorter acquires images and sorts individual phytoplankton cells, directly from seawater, allowing studies exploring connections between the diversity of forms present in the plankton and genetic variability at the single-cell level. The In Situ Chemotaxis Assay (ISCA) is a field-going microfluidic device designed to probe the distribution and role of motility behavior among microbes in aquatic environments. By creating microscale hotspots that simulate naturally occurring ones, the ISCA makes it possible to examine the role of microbial chemotaxis in resource acquisition, phytoplankton-bacteria interactions, and host-symbiont systems. Finally, the Millifluidic In Situ Enrichment (MISE) is an instrument that enables the study of rapid shifts in gene expression that permit microbial communities to exploit chemical hotspots in the ocean. The MISE subjects natural microbial communities to a chemical amendment and preserves their RNA in a minute-scale time series. Leveraging an array of milliliter-volume wells, the MISE allows comparison of community gene expression in response to a chemical stimulus to that of a control, enabling elucidation of the strategies employed by marine microbes to survive and thrive in fluctuating environments. Together, this suite of instruments enables culture-independent examination of microbial life at the microscale and will empower microbial ecologists to develop a more holistic understanding of how interactions at the scale of individual microbes impact processes in marine ecosystems at a global scale.
    Description: I’d like to thank the Gordon and Betty Moore Foundation, the National Science Foundation, and NSERC for funding portions of my research.
    Description: I’d like to thank the Gordon and Betty Moore Foundation, the National Science Foundation, and NSERC for funding portions of my research.
    Keywords: Microorganisms ; Bacteria ; Marine ecology ; Scientific apparatus and instruments ; Plankton ; Plankton--Growth ; Phytoplankton ; Chemical oceanography ; Antarctic Ocean
    Repository Name: Woods Hole Open Access Server
    Type: Thesis
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    Demographics of lytic viral infection of coastal ocean Vibrio (2014)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-05-26
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2014
    Description: Viral predation on bacteria in the ocean liberates carbon from the particulate fraction, where it is accessible to higher trophic levels, and redirects it to the dissolved fraction, where it supports microbial growth. Although viruses are highly abundant in the ocean little is known about how their interactions with bacteria are structured. This challenge arises because the diversity of both bacteria and viruses is exceedingly high and interactions between them are mediated by specific molecular interactions. This thesis uses heterotrophic bacteria of the genus Vibrio as a model to quantify virus-host interactions in light of host population structure and ecology. The methods developed in this thesis include streamlining of standard bacteriophage protocols, such as the agar overlay, and facilitate higher throughput in the isolation and characterization of novel environmental virus-host systems. Here, 〉1300 newly isolated Vibrio are assayed for infection by viral predators and susceptibility is found to be common, though total concentrations of predators are highly skewed, with most present at low abundance. The largest phylogenetically-resolved host range cross test available to date is conducted, using 260 viruses and 277 bacterial strains, and highly-specific viruses are found to be prevalent, with nearly half infecting only a single host in the panel. Observations of blocks of multiple viruses with nearly identical infection profiles infecting sets of highly-similar hosts suggest that increases in abundance of particular lineages of bacteria may be important in supporting the replication of highly specific viruses. The identification of highly similar virus genomes deriving from different sampling time points also suggests that interactions for some groups of viruses and hosts may be stable and persisting. Genome sequencing reveals that members of the largest broad host-range viral group recovered in the collection have sequence homology to non-tailed viruses, which have been shown to be dominant in the surface oceans but are underrepresented in culture collections. By integrating host population structure with sequencing of over 250 viral genomes it is found that viral groups are genomically cohesive and that closely-related and co-occurring populations of bacteria are subject to distinct regimes of viral predation.
    Description: I also gratefully acknowledge the WHOI Ocean Ventures Fund, which provided funding for the sequencing of over 250 viral genomes of the Nahant Collection and thereby contributed immensely to the impact of the thesis work presented here. Work presented in this thesis was also made possible by support from National Science Foundation grant DEB 0821391, National Institute of Environmental Health Sciences grant P30- ES002109, the Moore Foundation and the Broad Institute’s SPARC program.
    Keywords: Host-virus relationships ; Bacteria ; Ecology
    Repository Name: Woods Hole Open Access Server
    Type: Thesis
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    Foreword and Acknowledgements (2012)
    Istituto Nazionale di Geofisica e Vulcanologia
    Details
    Publication Date: 2017-04-04
    Description: This is the first volume of an international scientific journal that is dedicated to issues of geoethics and geological culture. Its goal is to inform the Italian and international scientific communities about what emerged at the GeoItalia 2011 conference, attended by not only Italian geoscientists. At this conference, the geoscientists questioned their role in society and the responsibilities that they have to assume as scholars of the planet Earth and experts of the territory. They highlighted the need for rediscovery of the cultural values of geology as a science that can contribute to the construction of correct social knowledge, and the need to be aware that geoethics cannot exist without a real awareness among geoscientists of the cultural value of the Earth sciences.
    Description: Published
    Description: 331
    Description: 5.9. Formazione e informazione
    Description: JCR Journal
    Description: open
    Keywords: Geoethics ; Geoetica ; Geological Culture ; Earth Sciences ; Philosophy ; Education ; 05. General::05.03. Educational, History of Science, Public Issues::05.03.99. General or miscellaneous ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
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    Ethical and cultural value of the Earth sciences. Interview with Prof. Giulio Giorello (2012)
    Istituto Nazionale di Geofisica e Vulcanologia
    Details
    Publication Date: 2017-04-04
    Description: Prof. Giulio Giorello is amongst the most prominent philosophers of science in Italy and in the world. He is currently Professor of the Philosophy of Science at the University of Milan, Director of the Series ‘Science and Ideas’ (Raffaele Cortina Books Editor), and Literary Journalist of the cultural pages of the Corriere della Sera, one of the most important of the Italian newspapers. In this keynote presentation, in interview form, he talks about the value that the Earth sciences have had through history, framing this group of disciplines in ethical and epistemological terms, and highlighting some important elements that have to be considered in geological activities.
    Description: Published
    Description: 343-346
    Description: 5.9. Formazione e informazione
    Description: JCR Journal
    Description: open
    Keywords: Geoethics ; Geological Culture ; Geoetica ; Giulio Giorello ; Earth Sciences ; Interview ; Philosophy ; Epistemology ; 05. General::05.03. Educational, History of Science, Public Issues::05.03.99. General or miscellaneous ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
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    Geoethics and geological culture: awareness, responsibility and challenges (2012)
    Istituto Nazionale di Geofisica e Vulcanologia
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    Publication Date: 2017-04-04
    Description: The international debate in the field of geoethics focuses on some of the most important environmental emergencies, while highlighting the great responsibilities of geoscientists, whatever field they work in, and the important social, cultural and economic repercussions that their choices can have on society. The GeoItalia 2009 and 2011 conferences that were held in Rimini and Turin, respectively, and were organized by the Italian Federation of Earth Science, were two important moments for the promotion of geoethics in Italy. They were devoted to the highlighting of how, and with what tools and contents, can the geosciences contribute to the cultural renewal of society. They also covered the active roles of geoscientists in the dissemination of scientific information, contributing in this way to the correct construction of social knowledge. Geology is culture, and as such it can help to dispel misconceptions and cultural stereotypes that concern natural phenomena, disasters, resources, and land management. Geological culture consists of methods, goals, values, history, ways of thinking about nature, and specific sensitivity for approaching problems and their solutions. So geology has to fix referenced values, as indispensable prerequisites for geoethics. Together, geological culture and geoethics can strengthen the bond that joins people to their territory, and can help to find solutions and answers to some important challenges in the coming years regarding natural risks, resources, and climate change. Starting from these considerations, we stress the importance of establishing an ethical criterion for Earth scientists, to focus attention on the issue of the responsibility of geoscientists, and the need to more clearly define their scientific identity and the value of their specificities.
    Description: Published
    Description: 335-341
    Description: 5.9. Formazione e informazione
    Description: JCR Journal
    Description: open
    Keywords: Geoethics ; Education ; History of science ; Public issues ; General (Philosophy of Earth sciences) ; 04. Solid Earth::04.04. Geology::04.04.99. General or miscellaneous ; 05. General::05.03. Educational, History of Science, Public Issues::05.03.99. General or miscellaneous ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
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    Social aspects of the Earth sciences. Interview with Prof. Franco Ferrarotti (2012)
    Istituto Nazionale di Geofisica e Vulcanologia
    Details
    Publication Date: 2017-04-04
    Description: Franco Ferrarotti, Professor emeritus at ‘La Sapienza’ University of Rome; since winning the first Chair in this discipline in Italy in 1961, he has been considered the Father of Italian Sociology. An independent Member of Italian Parliament in the third government (1958-1963), a member of the New York Academy of Sciences, and a ‘visiting Professor’ at many universities in Europe, North America, Russia, Japan and Latin America. Franco Ferrarotti has taught and still teaches in Europe and America, and he has received many awards throughout his career. In this interview, he talks about the social aspects and consequences of Earth sciences studies.
    Description: Published
    Description: 347-348
    Description: 5.9. Formazione e informazione
    Description: JCR Journal
    Description: open
    Keywords: Geoethics ; Geological Culture ; Geoetica ; Social aspects ; Geologists activity ; Scientific information ; Society ; 05. General::05.03. Educational, History of Science, Public Issues::05.03.99. General or miscellaneous ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
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    A Hippocratic Oath for geologists? (2012)
    Istituto Nazionale di Geofisica e Vulcanologia
    Details
    Publication Date: 2017-04-04
    Description: We argue here that the introduction of an ethical code of conduct that follows the example of the Hippocratic Oath of physicians will help geologists to acquire binding awareness of their professional and social responsibilities. The ethical behavior and obligations of modern geologists involve, but are not limited to, the following issues: correct land/ environment use and management; respect of truth and science; and protection of the Earth systems, on both the local and global scales, and therefore, of our well-being. We believe that for geoligists, the explicit acceptance of an ethical code will help to promote: (i) an awareness of their social role, expertise and sense of belonging to a professional community; (ii) an understanding of the expectations of citizens and society; and (iii) cultural growth, with better use of research and implementation of scientific and professional skills. All this should enhance the public recognition of the social mission of geologists, which is essential for the well-being of society. Therefore, we suggest that like in the majority of medical schools, ethical training should be a part of the university curriculum for students in geology.
    Description: Published
    Description: 365-369
    Description: 5.9. Formazione e informazione
    Description: JCR Journal
    Description: open
    Keywords: Geoethics ; Geological Culture ; Geoetica ; Hippocratic Oath ; Geologists ; Social responsibility ; 05. General::05.03. Educational, History of Science, Public Issues::05.03.99. General or miscellaneous ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
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    The role of heterotrophic microflagellates in plankton communities (2010)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-05-25
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 1984
    Description: The distribution and feeding behavior of bacterivorous micro flagellates (2-20 μm protozoa) and their ingestion by copepods were examined in an attempt to assess the importance of these protozoa as a trophic link between planktonic bacteria and zooplankton. The abundance of microflagellates relative to other picoplankton (0.2-2.0 μm) and nanoplankton (2-20 μm) populations in water samples in the North Atlantic and in Lake Ontario and on macroaggregates in the North Atlantic was determined using direct microscopical and culture estimation techniques. Seasonal, vertical and geographical changes in the density of microflagellates were generally not greater than one order of magnitude. Microscopical counts of heterotrophic nanoplankton (presumably microflagellates) typically ranged from a few hundred to a few thousand m1-1 for a variety of planktonic environments. They constituted approximately 1/3 to 1/2 of the nanoplankton in the euphotic zone and dominated the nanoplankton in the aphotic zone. Most Probable Number (MPN) estimation of the density of bacterivorous protozoa indicated that microflagellates were, on average, an order of magnitude more abundant than bacterivorous ciliates and amoebae. MPN and direct microscopical counts of microflagellates differed by as much as 104. This discrepancy was smaller in eutrophic environments (e.g. Continental Shelf and Lake Ontario) and on macroscopic detrital aggregates. All microbial populations enumerated were highly concentrated on macroscopic detrital aggregates relative to their abundance in the water surrounding the aggregates. Enrichment factors (the ratio of abundance of a population on a macroaggregate to its abundance in the surrounding water) increased along a eutrophic-to-oligotrophic gradient because of the combined effects of an increased abundance of microorganisms on macroaggregates in oligotrophic environments and a decreased abundance in the surrounding water in these same environments. Average enrichment factors for direct microscopical counts of heterotrophic nanoplankton (range = 17-114) were not as large as enrichment factors observed for MPN estimates of the number of bacterivorous microflagellates (range = 273-18400). Microflagellates numerically dominated the bacterivorous protozoa cultured from macroaggregates by one to two orders of magnitude, but ciliates and amoebae were also highly enriched on macroaggregates. Microenvironments are therefore a potentially important aspect for the ecology of planktonic microorganisms. Observations on the microbial colonization of mucus sloughed by ctenophores and discarded appendicularian houses suggest that these materials may be important sources of macroaggregates. Batch and continuous culture experiments were conducted with clonal cultures of microflagellates to test their ability to grow on various types and densities of bacteria. The doubling time of Monas sp. 1 ranged from 43 hr (when fed the cyanobacterium Synechococcus Strain WH 8101) to 6.9 hr (when fed the heterotrophic bacterium Serratia marinorubra). Cell yields (i.e. the conversion of bacterial biomass into protozoan biomass) of Monas sp. 1 fed two species of heterotrophic bacteria were greater than yields for the microflagellate fed two species chroococcoid cyanobacteria (range = 7-68%). Cell yields of two other species of microflagellates (Monas sp. 2 and Cryptobia maris) were 48% and 61%, respectively, on the bacterium Pseudomonas halodurans. Microflagellates grew in continuous culture at concentrations of bacteria which were lower than bacterial densities required for the growth of ciliates as shown by other investigations. Therefore, microflagellates appear to be well-adapted for grazing bacterioplankton. Microflagellates were also investigated for their ability to graze bacteria attached to particles. Bodo nanorensis and Rhynchomonas nasuta both showed a marked ability to graze attached bacteria and a limited ability to graze unattached cells. These results suggest that microflagellates may also be important consumers of bacteria attached to particles in the plankton and may explain the highly elevated densities of microflagellates on macroaggregates. Grazing experiments performed with the copepod Acartia tonsa indicated that heterotrophic microflagellates were ingested by the copepods at rates comparable to the ingestion of phytoplankton of similar size. The presence of heterotrophic microflagellates did not depress filtration rates of the copepods, and one species (Cryptobia maris) appeared to be selectively grazed. Survival of A. tonsa on a diet of heterotrophic microflagellates was similar to survival on a diet of phytoplankton and was significantly longer than survival of starved Controls or copepods fed only bacteria. Due to their ability to grow at in-situ densities of planktonic bacteria, their relatively high cell yields, and their acceptability as food for zooplankton, it is concluded that bacterivorous microflagellates may constitute an important trophic link between bacteria and zooplankton. This link may provide a mechanism whereby organic material and energy from the detrital food chain can be returned to the classical phytoplankton-copepod-fish food chain.
    Description: This research was supported by National Science Foundation grants OCE80-2444l and OCE82-l4928 and Ocean Industry Program grant 4473 awarded to Dr. Laurence P. Madin, NSF Doctoral Dissertation grant OCE8l-l299l, the Woods Hole Oceanographic Institution Education Program and the Wood Hole Oceanographic Institution Biology Department.
    Keywords: Plankton populations ; Bacteria ; Oceanus (Ship : 1975-) Cruise OC136 ; Oceanus (Ship : 1975-) Cruise OC137 ; Oceanus (Ship : 1975-) Cruise OC115 ; Atlantis II (Ship : 1963-) Cruise AII109 ; Knorr (Ship : 1970-) Cruise KN94 ; Columbus Iselin (Ship) Cruise CI83
    Repository Name: Woods Hole Open Access Server
    Type: Thesis
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  • 30
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    Diversity of the marine cyanobacterium Trichodesmium : characterization of the Woods Hole culture collection and quantification of field populations (2009)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-05-25
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2009
    Description: Trichodesmium is a colonial, N2-fixing cyanobacterium found in tropical oceans. Species of Trichodesmium are genetically similar but several species exist together in the same waters. In order to coexist, Trichodesmium spp. may occupy different niche spaces through differential utilization of resources such as nutrients and light, and through responses to physical characteristics such as temperature and turbulence. To investigate niche differentiation in Trichodesmium, I characterized cultured strains of Trichodesmium, identified and enumerated Trichodesmium clades in the field, and investigated P stress and N2 fixation in field populations. Species of Trichodesmium grouped into two clades based on sequences from 16S rDNA, the internal transcribed spacer (ITS), and the heterocyst differentiation gene hetR. Clade I contained Trichodesmium erythraeum and Trichodesmium contortum, and clade II contained Trichodesmium thiebautii, Trichodesmium tenue, Trichodesmium hildebrandtii, and Trichodesmium pelagicum. Each clade was morphologically diverse, but species within each clade had similar pigmentation. I developed a quantitative polymerase chain reaction (qPCR) method to distinguish between these two clades. In field populations of the Atlantic and Pacific Oceans, the qPCR method revealed that clade II Trichodesmium spp. were more prominent than clade I in the open ocean. Concentrations of Trichodesmium did not correlate with nutrient concentrations, but clade I had wider temperature and depth distributions than clade II. Temperature and light are physical characteristics that may define niche spaces for species of Trichodesmium. Clade I and II concentrations correlated with each other in the Pacific but not in the Atlantic, indicating that the two clades were limited by the same factors in the Pacific while different factors were limiting the abundance of the two clades in the Atlantic. Trichodesmium populations in the North Atlantic were more P stressed and had higher N2 fixation rates than populations in the western Pacific. While nutrient concentrations didn’t directly correlate with Trichodesmium concentrations, the contrasting nutrient regimes found in the Atlantic and Pacific Oceans might influence distributions of the two clades differently. Unraveling the differences among species of Trichodesmium begins to explain their coexistence and enables us to understand factors controlling global N2 fixation.
    Description: National Science Foundation (NSF) Biocomplexity Program Grant (OCE-0323332); the Center for Microbial Oceanography Research and Education (C-MORE), an NSF Science and Technology Center (EF-0424599); the Woods Hole Oceanographic Institution (WHOI) Ocean Life Institute (OLI) grant to J. Waterbury, and the WHOI Academic Programs Office.
    Keywords: Trichodesmium ; Bacteria ; Kilo Moana (Ship) Cruise KM0701 ; Kilo Moana (Ship) Cruise KM0703 ; Seward Johnson (Ship) Cruise SJ0609
    Repository Name: Woods Hole Open Access Server
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  • 31
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    Blackening of Pompeian Cinnabar paintings: X-ray micro-spectroscopy analysis (2007)
    American Chemical Society
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    Publication Date: 2017-04-04
    Description: Red Pompeian paintings, very famous for their deep intensity, are currently suffering from darkening. The origins of this darkening degradation are not clearly identified yet and remain a major issue for curators. In the specific case of cinnabar (HgS)-based red pigment, a photoinduced conversion into black metacinnabar is usually suspected. This work is focused on the blackening of red cinnabar paintings coated on a sparry calcite mortar. Different samples exhibiting different levels of degradation were selected upon visual observations and analyzed by synchrotron-based microanalytical techniques. Atomic and molecular compositions of the different debased regions revealed two possible degradation mechanisms. On one hand, micro X-ray fluorescence elemental maps show peculiar distributions of chlorine and sulfur. On the other hand, X-ray absorption spectroscopy performed at both Cl and S K-edges confirms the presence of characteristic degradation products: (i) Hg- Cl compounds (e.g., corderoite, calomel, and terlinguaite), which may result from the reaction with exogenous NaCl, in gray areas; (ii) gypsum, produced by the calcite sulfation, in black coatings. Metacinnabar is never detected. Finally, a cross section was analyzed to map the in-depth alteration gradient. Reduced and oxidized sulfur distributions reveal that the sulfated black coating consists of a 5-ím-thick layer covering intact cinnabar.
    Description: Published
    Description: 7484-7492
    Description: reserved
    Keywords: Microspectroscopy Analysis ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 32
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    Rate zonal density gradient ultracentrifugation analysis of repair of radiation damage to the folded chromosome of Escherichia coli (2007)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-05-25
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution April 1978
    Description: The structure of the membrane-free nucleoid of Escherichia coli and of unfolded chromosomal DNA was investigated by sedimentation on neutral sucrose gradients after irradiation with 60Co gamma-rays and ultraviolet light (2S4nm). Irradiation both in vivo and in vitro was used as a molecular probe of the constraints on DNA~packaging in the bacterial chromosome. The extremely gentle lysis and unfolding procedures which were developed yielded undamaged, replicating genomes, thus permitting direct measurement of the formation and repair of DNA double-strand breaks at biologically-significant doses of ionizing radiation. In vitro UV-irradiation of nucleoids resulted in an increase in the observed rate of sedimentation due to the formation of an unknown photo-product. In contrast, UV-irradiation of wild-type cells in vivo showed evidence of the formation of incision breaks which resulted in the relaxation of supercoiling in the nucleoid. Strand breakage was also observed following in vivo UV-irradiation of a uvrB-5 strain, but at a lower rate and also accompanied by considerable unfolding of the chromosome. Such lesions may have been the result of direct photochemical reactions in the nucleoid, or enzyme activity associated with a uvr-independent mode of repair. The number of domains of supercoiling was estimated at 170 per genome equivalent of DNA based on measurements of relaxation caused by single-strand break formation in in vivo- and in vitro-gamma-irradiated folded chromosomes. Similar estimates based on the target size of RNA molecules responsible for maintaining the compact packaging of the nucleoid predicted negligible unfolding due to the formation of RNA single-strand breaks at doses up-to 10 Krad, and were born out by experimental measurements. Unfolding of the nucleoid in vitro by limit-digestion with RNase or by heating at 70° resulted in DNA complexes with sedimentation coefficients of 1030±59S and 625±15S respectively. The difference in these rates was apparently due to more complete deproteinization and thus less mass in the heated material. These structures are believed to represent intact, replicating genomes in the form of complex-theta structures containing 2-3 genome equivalents of DNA. The rate of formation of double-strand breaks was determined from molecular weight measurements of thermally unfolded chromosomal DNA gamma-irradiated in vitro. Break formation was linear with dose up to 10 Krad, resulting in 0.27 double-strand breaks per kilorad per genome equivalent of DNA and requiring 1080 eV/double-strand break. The influence of possible non-linear DNA conformations of these calculations is discussed. Repair of ionizing radiation damage to folded chromosomes was observed within 2-3 hours of post-irradiation incubation in growth medium. A model based on recombinational repair is proposed to explain the formation of 2200-2300S material during early stages of incubation and subsequent changes in the gradient profiles. Such behavior is not observed for post-irradiation incubation of wild-type cells in buffer or for a recA-13 strain incubated in growth medium. Association of unrepaired DNA with plasma membrane is proposed to explain the formation of a peak of rapidly sedimenting material (〉〉3100S) during the later stages of repair. Direct evidence of repair of double-strand breaks during post-irradiation incubation in growth medium was obtained from gradient profiles of DNA from RNAse-digested chromosomes. The sedimentation coefficient of broken molecules was restored to the value of unirradiated DNA after 2-3 hours of incubation, and the fraction of the DNA repaired in this fashion was equal to the fraction of cells which survived at the same dose. An average of 2.7 double-strand breaks per genome per lethal event was observed, suggesting that 1-2 double-strand breaks per genome are repairable in this strain of E. coli.
    Keywords: Escherichia coli ; Bacteria ; Bacterial genetics ; DNA repair ; Chromosomes ; Centrifugation
    Repository Name: Woods Hole Open Access Server
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