7 results on '"Finstad, Kari"'
Search Results
2. Clades of huge phages from across Earth’s ecosystems
- Author
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Al-Shayeb, Basem, Sachdeva, Rohan, Chen, Lin-Xing, Ward, Fred, Munk, Patrick, Devoto, Audra, Castelle, Cindy J, Olm, Matthew R, Bouma-Gregson, Keith, Amano, Yuki, He, Christine, Méheust, Raphaël, Brooks, Brandon, Thomas, Alex, Lavy, Adi, Matheus-Carnevali, Paula, Sun, Christine, Goltsman, Daniela SA, Borton, Mikayla A, Sharrar, Allison, Jaffe, Alexander L, Nelson, Tara C, Kantor, Rose, Keren, Ray, Lane, Katherine R, Farag, Ibrahim F, Lei, Shufei, Finstad, Kari, Amundson, Ronald, Anantharaman, Karthik, Zhou, Jinglie, Probst, Alexander J, Power, Mary E, Tringe, Susannah G, Li, Wen-Jun, Wrighton, Kelly, Harrison, Sue, Morowitz, Michael, Relman, David A, Doudna, Jennifer A, Lehours, Anne-Catherine, Warren, Lesley, Cate, Jamie HD, Santini, Joanne M, and Banfield, Jillian F
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Microbiology ,Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Human Genome ,2.2 Factors relating to the physical environment ,Generic health relevance ,Amino Acyl-tRNA Synthetases ,Animals ,Bacteria ,Bacteriophages ,Biodiversity ,CRISPR-Cas Systems ,Earth ,Planet ,Ecosystem ,Evolution ,Molecular ,Gene Expression Regulation ,Bacterial ,Gene Expression Regulation ,Viral ,Genome ,Viral ,Host Specificity ,Humans ,Lakes ,Molecular Sequence Annotation ,Oceans and Seas ,Phylogeny ,Prophages ,Protein Biosynthesis ,RNA ,Transfer ,Ribosomal Proteins ,Seawater ,Soil Microbiology ,Transcription ,Genetic ,General Science & Technology - Abstract
Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems.
- Published
- 2020
3. Diverse organic carbon dynamics captured by radiocarbon analysis of distinct compound classes in a grassland soil.
- Author
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Grant, Katherine E., Repasch, Marisa N., Finstad, Kari M., Kerr, Julia D., Marple, Maxwell, Larson, Christopher J., Broek, Taylor A. B., Pett-Ridge, Jennifer, and McFarlane, Karis J.
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GRASSLAND soils ,CARBON sequestration ,SOIL profiles ,PLANT residues ,MARINE sediments - Abstract
Soil organic carbon (SOC) is a large, dynamic reservoir composed of a complex mixture of plant- and microbe-derived compounds with a wide distribution of cycling timescales and mechanisms. The distinct residence times of individual carbon components within this reservoir depend on a combination of factors, including compound reactivity, mineral association, and climate conditions. To better constrain SOC dynamics, bulk radiocarbon measurements are commonly used to trace biosphere inputs into soils and to estimate timescales of SOC cycling. However, understanding the mechanisms driving the persistence of organic compounds in bulk soil requires analyses of SOC pools that can be linked to plant sources and microbial transformation processes. Here, we adapt approaches, previously developed for marine sediments, to isolate organic compound classes from soils for radiocarbon (14 C) analysis. We apply these methods to a soil profile from an annual grassland in Hopland, California (USA), to assess changes in SOC persistence with depth (down to 1 m). We measured the radiocarbon values of water-extractable organic carbon (WEOC), total lipid extracts (TLEs), total hydrolyzable amino acids (AAs), and an acid-insoluble (AI) fraction from bulk and physically separated size fractions (< 2 mm, 2 mm–63 µ m, and < 63 µ m). Our results show that Δ14 C values of bulk soil, size fractions, and extracted compound classes became more depleted with depth, and individual SOC components have distinct age–depth distributions that suggest distinguishable cycling rates. We found that AAs and TLEs cycle faster than the bulk soils and the AI fraction. The AI was the most 14 C-depleted fraction, indicating that it is the most chemically inert in this soil. Our approach enables the isolation and measurement of SOC fractions that separate functionally distinct SOC pools that can cycle relatively quickly (e.g., plant and microbial residues) from more passive or inert SOC pools (associated with minerals or petrogenic) from bulk soils and soil physical fractions. With the effort to move beyond SOC bulk analysis, we find that compound class 14 C analysis can improve our understanding of SOC cycling and disentangle the physical and chemical factors driving OC cycling rates and persistence. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
4. Microbial Community Structure and the Persistence of Cyanobacterial Populations in Salt Crusts of the Hyperarid Atacama Desert from Genome-Resolved Metagenomics
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Finstad, Kari M, Probst, Alexander J, Thomas, Brian C, Andersen, Gary L, Demergasso, Cecilia, Echeverría, Alex, Amundson, Ronald G, and Banfield, Jillian F
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Microbiology ,Biological Sciences ,Ecology ,Genetics ,Human Genome ,Life Below Water ,metagenome ,Atacama Desert ,salt crust ,hyperarid ,hypersaline ,environmental genomics ,salar ,Environmental Science and Management ,Soil Sciences ,Medical microbiology - Abstract
Although once thought to be devoid of biology, recent studies have identified salt deposits as oases for life in the hyperarid Atacama Desert. To examine spatial patterns of microbial species and key nutrient sources, we genomically characterized 26 salt crusts from three sites along a fog gradient. The communities are dominated by a large variety of Halobacteriales and Bacteroidetes, plus a few algal and Cyanobacterial species. CRISPR locus analysis suggests the distribution of a single Cyanobacterial population among all sites. This is in stark contrast to the extremely high sample specificity of most other community members. Only present at the highest moisture site is a genomically characterized Thermoplasmatales archaeon (Marine Group II) and six Nanohaloarchaea, one of which is represented by a complete genome. Parcubacteria (OD1) and Saccharibacteria (TM7), not previously reported from hypersaline environments, were found at low abundances. We found no indication of a N2 fixation pathway in the communities, suggesting acquisition of bioavailable nitrogen from atmospherically derived nitrate. Samples cluster by site based on bacterial and archaeal abundance patterns and photosynthetic capacity decreases with increasing distance from the ocean. We conclude that moisture level, controlled by coastal fog intensity, is the strongest driver of community membership.
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- 2017
5. A new view of the tree of life.
- Author
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Hug, Laura A, Baker, Brett J, Anantharaman, Karthik, Brown, Christopher T, Probst, Alexander J, Castelle, Cindy J, Butterfield, Cristina N, Hernsdorf, Alex W, Amano, Yuki, Ise, Kotaro, Suzuki, Yohey, Dudek, Natasha, Relman, David A, Finstad, Kari M, Amundson, Ronald, Thomas, Brian C, and Banfield, Jillian F
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Bacteria ,Archaea ,Ecosystem ,Biodiversity ,Evolution ,Molecular ,Phylogeny ,Eukaryota ,Human Genome ,Genetics ,2.2 Factors relating to physical environment ,Evolution ,Molecular ,Microbiology ,Medical Microbiology - Abstract
The tree of life is one of the most important organizing principles in biology(1). Gene surveys suggest the existence of an enormous number of branches(2), but even an approximation of the full scale of the tree has remained elusive. Recent depictions of the tree of life have focused either on the nature of deep evolutionary relationships(3-5) or on the known, well-classified diversity of life with an emphasis on eukaryotes(6). These approaches overlook the dramatic change in our understanding of life's diversity resulting from genomic sampling of previously unexamined environments. New methods to generate genome sequences illuminate the identity of organisms and their metabolic capacities, placing them in community and ecosystem contexts(7,8). Here, we use new genomic data from over 1,000 uncultivated and little known organisms, together with published sequences, to infer a dramatically expanded version of the tree of life, with Bacteria, Archaea and Eukarya included. The depiction is both a global overview and a snapshot of the diversity within each major lineage. The results reveal the dominance of bacterial diversification and underline the importance of organisms lacking isolated representatives, with substantial evolution concentrated in a major radiation of such organisms. This tree highlights major lineages currently underrepresented in biogeochemical models and identifies radiations that are probably important for future evolutionary analyses.
- Published
- 2016
6. Soil Processes and Microbial Communities in a Hyperarid System
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Finstad, Kari Michelle
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Environmental science ,Geochemistry ,Geobiology - Abstract
The Atacama Desert is a coastal desert in South America spanning both Peru and Chile. While the desert experiences a range of climate regimes, perhaps the most unique region of the desert lies in the north of Chile where annual precipitation is less than 2 mm. This hyperarid region of the desert often goes decades without precipitation and is believed to have maintained a semi-continuous hyperarid climate for the last few million years. Hyperaridity has had a profound impact on the geochemical and biological processes of the region. One of the most notable and economically important features of the desert are the salars. Salars are the location of past lakes that have lost their surface water due to changes in climate and/or tectonic activity. They provide minable concentrations of iodine, boron, and other salts, and are recognized as one of the only habitats for microbial life in this region. Presently, they are covered in thick and rugged salt crusts, often made of sodium chloride (halite) and calcium sulfate (gypsum). Due to the extreme and persistent aridity, shallow groundwater is pulled upward towards the surface via capillary flow. This upward water movement is the reverse direction of most well drained desert soils, and leaves a diagnostic imprint in the soil chemistry. The first chapter of my dissertation explores how soils in salars differ from those found in other more humid deserts, and proposes changes to the USDA Soil Taxonomy that would allow for a more accurate and informative classification of them.To further understand and catalogue the rates and processes of soil formation in this unique environment, in my second chapter I examine the chemical and isotopic profiles of two soils of differing ages in the Salar Llamara, Chile. I found that soil development is actively occurring, with evaporation of shallow groundwater driving the major geochemical processes. The upward movement of water produces a distinctive salt profile, with the most soluble salts concentrated on the surface and the least soluble salts near the base. Through monitoring and experimental work, I calculated long-term evaporation rates, and found that they decrease with soil age as the salt crust thickness increases. While it has been suggested that these salars are part of an ancient landscape, this work provides evidence that they are dynamic and evolve on relatively short timescales. Finally, despite the lack of rainfall, I found that the crusts are able to sustain microbial growth by buffering environmental changes in temperature and relative humidity. While the hyperarid region of the Atacama Desert only receives rare and infrequent precipitation, it is exposed to marine fog from the Pacific Ocean on a regular basis. The amount of fog changes predictably from west to east as the distance from the coast increases. For many years the Atacama Desert was suggested to be the dry limit to life. However, in the last decade it has been recognized that microbial communities are capable of surviving in salt crusts on the surface of salars. At a relative humidity over 75%, halite is able to absorb enough moisture from the atmosphere to create a saline solution in its mineral pores. In this way, salt crusts can provide organisms with liquid water in the absence of precipitation.My third chapter is a detailed investigation of the microbial community composition and structure in this unique ecosystem. Using next metagenomics techniques, I reconstructed 124 distinct draft quality genomes from three sites along a fog frequency transect. All communities are comprised of a large variety of Halobacteriales, Salinibacter, Chlorophyta, and Cyanobacteria. Additionally, some communities contain lower abundances of Nanohaloarchaea, Actinobacteria, Gammaproteobacteria, Thermoplasmatales, and Naegleria. Candidate Phyla Radiation bacteria (OD1 and TM7) not previously reported from hypersaline environments before, were also found in low abundance in some of the communities.While there is a lot of overlap in community membership across sites, samples cluster by site based on bacterial and archaeal abundance patterns. The concentration of photosynthetic organisms declines with increasing distance from the fog source (Pacific Ocean), and radiocarbon dating showed that carbon cycling is occurring more rapidly in sites with more fog events. I conclude that the strongest driver of community membership is fog delivered moisture, controlled by proximity to the coast.The final chapter of my dissertation explores a unique late Quaternary paleoenvironmental record in loess deposits. Within what is largely a deflationary landscape, I found small loess dunes that have been slowly accreting for the last 20,000 years in depressions of the highly eroded Soledad formation. One of the unique local climate characteristics of this area is the strong and persistent on-shore winds.Radiocarbon ages of organic matter embedded within the deposits show that the dunes began accumulating rapidly at the Last Glacial Maximum, and that the accumulation of sediment slowed considerably after the Pacific Ocean attained its present post-glacial level. Chemical and isotopic analysis of the sediment and fatty acids preserved within the dunes provide evidence for increased marine fog density and intensity of onshore westerly winds beginning 10,000 yr BP. At this time, grain size increases while accumulation rates simultaneously decrease, suggesting greater wind speeds and/or decrease in sediment supply. Organic sediment δ15N values steadily decrease, suggesting a shorter path length between N upwelling (Pacific Ocean) and N deposition in the dunes. This unique and continuous record of paleo-conditions provides a window into local processes occurring over the last 20,000 years.
- Published
- 2016
7. Exploring the development of school readiness in kindergarten in Norway : A case study of the implementation of the Gausdal Model
- Author
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Finstad, Kari Larsson
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skolestart ,School ,Parents ,Case Reports [Publication Type] ,motorisk utvikling ,barn ,barnehagelærere ,helsesøster ,Socialization ,folkehelse ,Nurses, Community Health ,Child Development ,Motor Skills ,foreldre ,Public Health ,VDP::Medical disciplines: 700::Health sciences: 800::Community medicine, Social medicine: 801 ,Gausdalmodellen ,sosialisering - Abstract
English abstract: Background: This research was initiated by a request from Gausdal municipality to have a master’s thesis written about the sensori-motoric project the Gausdal Model. One of the aims of the Gausdal Model is to better prepare children for school through a programme based on proportionate universalism. Aim: The aim was to explore key stakeholders understandings of school readiness and generate in-depth knowledge about their processes of implementation of the Gausdal Model. This could shed light on processes that develop children’s motor proficiency and its possible relation to school readiness. Methods: A case study of the implementation of the Gausdal Model was carried out in order to explore key stakeholders’ understanding of school readiness. The sample was strategic and the nine kindergarten teachers and parent informants were recruited from four municipal kindergartens in Gausdal. The health nurse connected to the programme was also an informant. Data were collected through qualitative interviews, partly informed by prior observations of the activities in the programme. The data analysis was inspired by principles from grounded theory as described by Charmaz (2014). The analysis aimed to identify components that could shed light on the processes that was studied. Bronfenbrenner’s ecological systems theory and Bandura’s social cognitive theory (SCT) and concept self-efficacy (SE), in particular were used as sensitising concepts in order to analyse the data and generate an understanding of how the Gausdal Model could develop children’s motor proficiency, and how this might be related to children’s school readiness. Results: The findings from the implementation of the Gausdal Model show that children’s motor proficiency can be understood as being developed through a process of socialisation where support through strong mesosystems and significant others, in this case kindergarten teachers and parents, could help develop the children’s mastery of their own bodies. At the mesosystem-level, quality and quantity of communication and aiming consistently towards the same goals was important. At the microsystem level, a combination of the four sources of SE and relational qualities between the kindergarten teachers and children seemed to develop children’s motoric SE and mastery of their own bodies. Motor proficiency seems to be related to school readiness through both the transferability of certain components of motoric SE as well as a social dimension, as social inclusion was an important component of school readiness. Hence, motor proficiency was related to a multidimensional understanding of school readiness. Conclusion: The Gausdal Model is in line with public health recommendations of early intervention and proportionate universalism, and has the potential to better prepare children for school as well as contributing to children’s socialization in general. Norsk sammendrag: Bakgrunn: Denne forskningen ble initiert av en forespørsel fra Gausdal kommune om å skrive en masteroppgave om det sanse-motoriske programmet Gausdalsmodellen. Et av målene for Gausdalsmodellen er å gi barn et bedre utgangspunkt for skolestart gjennom tiltak for alle – for å nå de få og styrke alle. Mål: Å utforske barnehagelærere, foreldre og helsesøsters forståelse av hva det vil si å være skoleforberedt og generere kunnskap om gjennomføringen av Gausdalsmodellen. Dette kan belyse prosesser som utvikler barnas motoriske ferdigheter, samt en mulig sammenheng mellom dette og det å være skoleforberedt. Metoder: En kasus-studie av gjennomføringen av Gausdalsmodellen og barnehagelærere, foreldre og helsesøsters forståelse av hva det vil si å være skoleforberedt. Utvalget er strategisk og ni informanter (barnehageansatte og foreldre) ble rekruttert fra fire kommunale barnehager i Gausdal. En helsesøster som arbeider med Gausdalsmodellen er også informant. Data ble samlet inn gjennom kvalitative intervjuer som blant annet ble utarbeidet på bakgrunn av observasjoner av aktiviteter i Gausdalsmodellen. Analysen av datamaterialet er inspirert av prinsipper fra grounded theory beskrevet av Charmaz (2014). Analysen tar sikte på å identifisere komponenter som kan kaste lys over de prosessene som ble studert. Bronfenbrenners utviklingsøkologiske modell og Banduras sosial kognitive teori og konseptet mestringsforventning, ble brukt for å for analysere datamaterialet og forstå hvordan gjennomføringen av Gausdalsmodellen kan utvikle barnas motoriske ferdigheter, samt hvordan disse ferdighetene kan knyttes til det å være skoleforberedt. Resultater: Funnene viser at barns motoriske ferdigheter kan forstås som å bli utviklet i en sosialiseringsprosess der støtte fra sterke mesosystemer og signifikante andre, i dette tilfellet barnehagelærere og foreldre, er av betydning. På mesosystem-nivå gjennom kvantitet og kvalitet på kommunikasjon og en felles målsetning rundt barnets utvikling. På mikronivå synes en kombinasjon av relasjonelle kvaliteter mellom barnehagelærerne og barna, og kilder til utvikling av barnas mestringsforventning, å bidra til barnas motoriske utvikling og kroppslige mestring. Motoriske ferdigheter synes å være knyttet til det å være skoleforberedt, både gjennom overførbarhet av visse komponenter av motorisk mestringsforventning, samt gjennom en sosial dimensjon hvor sosial inkludering var viktig for at barna skal være skoleforberedt. Derfor er motoriske ferdigheter knyttet til en helhetlig forståelse av hva det vil si å være skoleforberedt. Konklusjon: Gausdalsmodellen er i tråd med folkehelseanbefalinger om tidlig intervensjon og proposjonell universalisme og har potensiale til å forberede barna til skolestart i tillegg til å bidra i en generell sosialiseringsprosess.
- Published
- 2015
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