763 research outputs found
Sweet butter.
No full textGift of Dr. Mary Jane Esplen.By the author of "Yes! We have no bananas" [note]Piano vocal [instrumentation]Right near the drugstore on our street there is a restaurant [first line]Sweet butter sweet butter sweet butter on my toast [first line of chorus]C major [key]Moderato [tempo]Popular song [form/genre]Man, butter dish; photo: Dell Lampe and his orchestra [illustration]Starmer [engraver]Publisher's advertisement on back cover [note
Farm butter making
No full textby O.G. Simpson.This archived document is maintained by the State Library of Oregon as part of the Oregon Documents Depository Program. It is for informational purposes and may not be suitable for legal purposes.Mode of access: Internet from the Oregon Government Publications Collection.Text in English
Shea butter: connecting rural Burkinabè women to international markets through fair trade
No full textProcessed by rural West African women and desired by wealthy Northern consumers of natural beauty products, shea butter seems a prime candidate for fair trade, yet to date there has been little study of the industry. This article analyses the opportunities and constraints of the development of fair-trade exports of shea butter from Burkina Faso, taking into account the context in which shea is produced and sold locally and internationally, the concept of fair trade, and the impact of gender relations on shea production. Although a definitive positive or negative determination cannot be made, given the complex and divergent factors affecting the potential international market and the production process, the author finds that the development of the fair-trade shea butter industry in Burkina Faso has great potential. However, such development must occur with restraint and consideration of possible challenges and limitations, in order to remain sustainable and viable for rural female producers.This article is hosted by our co-publisher Taylor & Francis.</p
Bibliography on Butter Oil
No full textExcerpts from the Preface: Milk fat has always been highly valued as a food, and much attention has been given to its conservation. The usual methods of conserving it have been by the production and storage of butter or of the fat from which the other milk constituents have been removed. The problems of its conservation for any great period of time are principally those related to bacterial growth and enzyme action and to spontaneous chemical reactions with the oxygen of the atmosphere. Butter oil and milk oil are the terms applied in the United States to the milk fat which remains after the curd and water have been removed from butter. Terms used in other countries are: Australia, dehydrated butter; Egypt, samna or samn; England, clarified butter; France, beurre fondu; Germany, Butteröl, Butterschmalz, Flössbutter, geschmolzene Butter, gesottene Butter, Kuhschmalz, Rindschmalz, Schmalz, Schmelzbutter; India, ghee or ghi; Iran, roghan; Switzerland, eingesottene Butter. This bibliography includes material on the preparation, properties, keeping quality, and uses of pure milk fat; the manufacture, preservation, and storage of butter oil; and the conservation of shipping space in shipping it to the Tropics and other places. In the preparation of the annotations, the same terms have been used in referring to butter oil as were used by the author in the work cited
Computational analysis of quantitative “omics” data
No full textOver the past decades, the rise of "omics" approaches has allowed for systematic, in-depth investigation of each aspect of molecular biology. It has contributed to our changed view on the on the linearity and the regulation of the informational flow of the central dogma. Different regulatory mechanisms have been identified, describing interaction and variety not only on the genetic level but also on the transcript and protein level. The development and integration of multi-omics have allowed for the uncovering of intricate molecular mechanisms underlying different phenotypic manifestations of traits at a high accuracy, in a systematic manner. With this, multi-omics is essentially the basis of network or systems biology.
In this thesis, I have utilized "omics" technologies, specifically proteomics, and the subsequent computational data analysis and integration to investigate the systematic DNA damage response in Tetrahymena thermophila and identify DNA damage proteins across the Tree of Life. Additionally, I co-developed a user-friendly computational pipeline for evolutionary positive selection analysis, which relies on comparative genomics and either large-scale genome sequencing or proteotranscriptomics data.
In Chapter 2, we mapped the system's response to DNA damage over time in Tetrahymena thermophila (Nischwitz, Schoonenberg et al., in preparation). To date, limited studies have combined the strength of proteomics and transcriptomics to investigate DNA damage kinetics in response to various DNA-damage treatments. Our study investigated DNA damage response (DDR) dynamics over eight hours after or during exposure to six different mutagens. We observed upregulation of previously identified DNA damage repair pathways and found novel crosstalk between DDR pathways. All treatments induced a dynamic response at both the transcript and protein levels. Using unsupervised self-organizing maps, we examined the clustering of expression profile trends to better understand the DDR. Many of the quantified proteins and transcripts exhibited damage-specific responses. We are currently employing a novel knockdown system to target a subset of PARP-related proteins to characterize their specific roles in Tetrahymena further.
In Chapter 3, we studied the interactome of specific DNA damage lesions across the Tree of Life, exploring the conservation of pathways responsible for repair and recognition of DNA damage lesions (Nischwitz, Schoonenberg et al., iScience, 2023). Due to the need for precise genome maintenance, DNA repair has been highly conserved across all domains of life. To study the shared and unique elements of the DNA damage response, we performed a phylointeractomic study to identify enriched DNA damage binders in 11 different species at the 8-oxoG and abasic lesions and at a uracil base incorporated into DNA. Our approach identified several known DNA damage factors as binders to the afore-mentioned lesions. Additionally, through orthology, network, and domain analysis, we linked 44 previously unassociated proteins to DNA repair.
Finally, in Chapter 4, we developed a computational pipeline to make positive selection analysis user-friendly (Ceron-Noriega et al., Genome Biology and Evolution, 2023). AlexandrusPS generates orthology relationships, sequence alignments, and phylogenetic trees with its automated process. It then performs site-specific (SSM), branch (BM), and branch-site (BSM) positive selection analyses and produces four main output files, including orthology relationships, positive selection results, and all intermediate files (sequence alignments, phylogenetic trees).xiv, 137 Seiten ; Illustrationen, Diagramm
Investigations of genome instability utilizing quantitative proteomics
No full textThe field of mass spectrometry-based proteomics has had a profound impact on discoveries in almost every field of science. Specifically, bottom-up proteomics enables the exploration of scientific questions at a high-throughput and proteome-wide level. In this thesis, mass spectrometry-based proteomics was employed to understand aspects of genome instability related to: 1) telomere biology in Caenorhabditis elegans , 2) phylogenetic diversity of recognition and repair of in vitro DNA damage lesions, and 3) DNA damage kinetics in Tetrahymena thermophila.
Article I (Dietz et al. 2021) describes the extensive characterization of the first novel double-stranded telomere binders in C. elegans , TEBP-1 and TEBP-2. These proteins were discovered using in vitro telomere pulldown assays coupled with label-free and dimethyl quantitative mass spectrometry. TEBP-1 and TEBP-2 bind directly and specifically to double-stranded telomeric DNA. Both proteins are critical to the negative and positive regulation of telomere homeostasis. The double knockout strain of tebp-1;tebp-2 exhibits severe germline arm atrophy and synthetic sterility, suggesting their critical role in fertility. TEBP-1 and TEBP-2dimerize and directly interact with the known single-stranded binder POT-1, thereby connecting them to the known telomere complex in C. elegans.
Article II (Nischwitz and Schoonenberg et al., 2023) explores the conservation of recognition and repair of DNA damage lesions. Due to the imperative need for accurate maintenance of the genome, DNA repair has been highly conserved across all domains of life. To study both the shared and unique elements of the DNA damage response, we conducted a phylointeractomic study to identify enriched binders in 11 different species at the 8-oxoG and abasic lesions, as well as a uracil base incorporated into DNA. While numerous binders were canonical DNA damage factors, we also observed enrichment of proteins not previously associated with DNA repair. Through orthology, network, and domain analysis, we linked 44 proteins that were previously unassociated to DNA repair.
Article III (unpublished, Nischwitz and Schoonenberg et al., xxxx) delves into the kinetics of the DNA damage response (DDR) in the ciliate Tetrahymena thermophila (Tetrahymena) . To date, there have been limited studies that combine the power of proteomics and transcriptomics to investigate DNA damage kinetics across various treatments. Our screen monitored the dynamic DNA damage response over eight hours after exposure to six different mutagens. We observed upregulation of previously associated DNA damage repair pathways, as well as unexpected DDR crosstalk. All treatments elicited a dynamic response at both the transcript and protein level. Through unsupervised machine learning clustering, we examined expression profile trends to gain a more comprehensive understanding of the DDR, as many of these proteins exhibited damage-specific responses. Currently, we are employing a knockdown system to target a subset of these PARP-related proteins to further characterize their specific roles in Tetrahymena.Artikel I (Dietz et al. 2021) beschreibt die umfassende Charakterisierung der ersten bekannten doppelsträngigen Telomerbinder in C. elegans, TEBP-1 und TEBP-2. Diese Proteine wurden mit Hilfe von in vitro Telomer-Pulldown-Assays in Verbindung mit markierungsfreier und quantitativer Dimethyl-Massenspektrometrie entdeckt. TEBP-1 und TEBP-2 binden direkt und spezifisch an doppelsträngige telomere DNA. Beide Proteine sind entscheidend für die negative und positive Regulierung der Telomer-Homöostase. Der Doppel-Knockout-Stamm vontebp-1;tebp-2 weist eine schwere Keimbahnarmatrophie und synthetische Sterilität auf, was darauf hindeutet, dass beide Proteine eine entscheidende Rolle für die Fruchtbarkeit spielen.TEBP-1 und TEBP-2 dimerisieren und interagieren direkt mit dem bekannten EinzelstrangbinderPOT-1, wodurch sie mit dem bekannten Telomerkomplex in C. elegans verbunden sind.
Artikel II (Nischwitz und Schoonenberg et al., 2023) befasst sich mit der Erhaltung der Erkennung und Reparatur von DNA-Schäden. Aufgrund der zwingenden Notwendigkeit, das Genom akkurat zu erhalten, ist die DNA-Reparatur in allen Bereichen des Lebens in hohem Maße konserviert. Um sowohl die gemeinsamen als auch die einzigartigen Elemente derDNA-Schadensreaktion zu untersuchen, haben wir eine phylointeraktomische Studie durchgeführt, um in 11 verschiedenen Arten angereicherte Proteine, die an den 8-oxoG- und abasischen Läsionen sowie an einer in die DNA eingebauten Uracilbase binden, zu identifizieren. Bei zahlreichen Bindungsstellen handelte es sich um kanonische DNA-Schadensfaktoren, aber wir beobachteten auch eine Anreicherung von Proteinen, die bisher nicht mit der DNA-Reparatur in Verbindung gebracht wurden. Durch Orthologie-, Netzwerk und Domänenanalysen konnten wir 44 Proteine identifizieren, die zuvor nicht mit der DNA-Reparatur assoziiert wurden.
Artikel III (unveröffentlicht, Nischwitz und Schoonenberg et al., xxxx) befasst sich mit der Kinetik der DNA-Schadensreaktion (DDR) in dem Ciliaten Tetrahymena thermophila( Tetrahymena ). Bislang gibt es nur wenige Studien, die die Leistungsfähigkeit von Proteomik und Transkriptomik kombinieren, um die Kinetik von DNA-Schäden bei verschiedenen Behandlungen zu untersuchen. In unserem Screening wurde die dynamische DNA-Schadensreaktion über acht Stunden nach der Exposition gegenüber sechs verschiedenen Mutagenen überwacht. Wir beobachteten die Hochregulierung von zuvor assoziierten DNA-Schadensreparaturwegen sowie unerwartete DDR-Crosstalk. Alle Behandlungen lösten eine dynamische Reaktion sowohl auf der Transkriptions- als auch auf der Proteinebene aus. Mit Hilfe von unüberwachten maschinellen Lernens untersuchten wir die Trends der Expressionsprofile, um ein umfassenderes Verständnis der DDR zu gewinnen, da viele dieser Proteine schadensspezifische Reaktionen zeigten. Gegenwärtig setzen wir ein Knockdown-System ein, um eine Untergruppe dieser PARP-verwandten Proteine anzugreifen und ihre spezifische Rolle in Tetrahymena weiter zu charakterisieren.142 Seiten ; Illustrationen, Diagramm
Proteome-wide positive selection analysis on improved nematode gene annotation by machine learning assisted proteotranscriptomics
No full textZahlreiche Studien an der Nematode und Modellspezies Caenorhabditis elegans haben zu bedeutenden Entdeckungen in den Bereichen Biologie und Biomedizin geführt. Diese sind im Kontext der Evolution schwer zu extrapolieren, da das Nematoden-Phylum eine beträchtlich große phylogenetische Vielfalt aufweist. Als Beispiel für dieses Problem haben wir versucht, die Evolutionsgeschichte der tebp-1- und tebp-2 Gene zu rekapitulieren, von denen wir gezeigt haben, dass sie eine bedeutende Rolle in der Telomerbiologie in C. elegans spielen (Artikel I). Wir konnten zeigen, dass Caenorhabditis briggsae Homologe dieser Proteine ebenfalls Telomere binden. Indem wir die evolutionäre Analyse durch Untersuchung der Phylogenie und Syntenie auf acht weitere Caenorhabditis-Nematoden ausweiteten, zeigten wir, dass diese Proteine möglicherweise eine konservierte Rolle in der gesamten Caenorhabditis-Gattung spielen. Mit dem Ziel, Anzeichen einer positiven Selektion zu erkennen, stellten wir bei vielen der Zielnematoden fehlende oder unzureichende Genannotationen fest. Die Genauigkeit der positiven Selektionsanalyse wird durch die Qualität der in der WormBase Nematoden-Informationsressource verfügbaren Genannotation beeinträchtigt, die in hohem Maße von automatisierten Annotationsworkflows unter Verwendung verfügbarer sequenzierter Genome abhängt.
Zur Schließung dieser Lücke setzten wir eine Proteotranskriptomik-Technik zusammen mit einer durch maschinelles Lernen unterstützten Qualitätskontrolle ein, um die Genannotationen für 12 Nematodenarten zu verbessern, was eine Systemanalyse und neue Einblicke in evolutionäre Prozesse ermöglicht (Artikel II). Durch den Vergleich unserer Annotation mit der sehr guten Annotation von C. elegans demonstrierten wir die Leistungsfähigkeit unserer Methode und identifizierten 2 zuvor nicht identifizierte Gene in dieser Spezies (autorisiert von WormBase Kuratoren), was nach mehr als 20 Jahren sorgfältiger manueller Annotation bemerkenswert ist . Mit unserer Technik konnten wir qualitativ hochwertige Annotationen für 9 genomsequenzierte Arten erstellen und neue proteinkodierende Genannotationen für 3 weitere Arten ohne sequenzierte Genome (C. droshophilae, R. regina und R. axei) in der gleichen Qualität wie die von C. elegans bereitstellen.
Um die Annotationen zu benchmarken und die evolutionäre Analyse zu erleichtern, haben wir eine Pipeline erstellt, die Orthologievorhersagen und positive Selektionsanalysen ermöglicht. Die Implementierung der Pipeline ermöglichte die Bestimmung von 23.090 orthologen Gruppen, die die proteotranskriptomische Annotation der protein-kodierenden Gene der 12 Nematodenarten umfassen. Unter Verwendung der Pipeline für umfassende positive Selektionsanalysen haben wir Orthologiegruppen unter positiver Selektion entdeckt. Ermutigt durch diese Ergebnisse haben wir den Nutzen der Pipeline für die wissenschaftliche Gemeinschaft erkannt und werden sie der Allgemeinheit unter dem Namen AlexandrusPS als Docker-Image zur Verfügung stellen. AlexandrusPS ermöglicht es Benutzern, CodeML-Protokolle automatisiert parallel auf einem Desktop-Computer auszuführen, was Analysen mit hohem Durchsatz ermöglicht, ohne dass Hochleistungs-Computersysteme erforderlich sind. Die Pipeline wird der Community über einen Application Note-Artikel in einer der größeren Bioinformatik-Fachzeitschriften vorgestellt werden (Artikel III).Getrennte Zählung ; Illustrationen, Diagramm
Mass spectrometry-based quantitative proteomics to investigate RNA-protein interactions
No full textMass spectrometry-based proteomics is a versatile tool, offering a global and unbiased
approach to analyse proteins and their interacting partners. Within the realm of molecular
biology, RNA-protein interactions stand as fundamental and intricate components that oversee
vital processes in the cell. These interactions, often mediated by specific RNA-binding proteins
(RBPs), orchestrate a wide array of cellular functions. From the regulation of gene expression to
the maintenance of genomic stability, the post-transcriptional processing of RNA molecules, and
even the spatial organisation of the cell nucleus, RNA-protein interactions play a central role in
shaping the intricate web of cellular activities. In this thesis, the interaction between RNA and
proteins is investigated using state-of-the-art MS.
Article Ⅰ delved into the characterization of Telomeric repeat-containing RNA (TERRA)
molecules in M. musculus, examining their genomic origins and comparing their interactomes to
their H. sapiens counterparts. RNA-FISH analysis revealed disparities in behaviour, with M.
musculus TERRA foci primarily located outside of telomeres, in contrast to H. sapiens TERRA
foci, which recurrently resided at telomeres. As a result, a distinct genomic origin for M.
musculus TERRA molecules outside telomeres was hypothesised. Through a comprehensive
genomic analysis, four major chromosomal regions, including known Telo 18q, PAR-Xq/Yq, and
ChrX Tsix locus regions, and a novel Chr2 region, were identified as potential sources of
TERRA molecules. Conservation of TERRA-associated functions was evaluated with an affinity
purification-mass spectrometry (AP-MS) approach. A comparison of the enriched proteins with
publicly available H. sapiens TERRA-interacting protein datasets revealed that, despite having a
distinct genomic origin, functions are conserved between M. musculus and H. sapiens.
Article Ⅱ centred on the functional assignment of RBPs in S. cerevisiae. An AP-MS
screen was designed to elucidate the interaction partners of 40 selected RBPs, which were
chosen based on their involvement in various stages of mRNA processing. Functional analysis
of the collected data highlighted the overrepresentation of canonical RNA-binding domains
(RBDs) and RNA binding-related GO molecular function terms among the RBPs' interaction
partners. KEGG pathway analysis demonstrated the enrichment of RNA pathways, consistent
with the RBP selection criteria, as well as involvement in metabolic and synthesis pathways.
Finally, network-based function assignment of RBPs was facilitated by concurrent binding
patterns within the network.ix, 108 Seiten ; Illustrationen, Diagramm
Effect of high hydrostatic pressure processing (HHPP) on salmonella enterica in peanut butter
No full textAmerican consumers eat more than 700 million pounds of peanut butter each year, accounting for approximately half the edible use of peanuts in the United States. Salmonella is a unique microorganism that can survive in peanut butter as demonstrated by two large outbreaks in 2007 and 2008, creating the need for methods to augment and improve the current peanut butter manufacturing processes to make them even safer. High Hydrostatic Pressure Processing (HHPP) is a popular processing method used to process foods such as guacamole, meats, oysters, jellies and juices to ensure microbiological safety while retaining quality and organoleptic properties. The application of HHPP as an alternative processing method to inactivate Salmonella in peanut butter was the focus of this research. The objective of this research was to optimize the pressure and time conditions of HHPP for maximum inactivation of Salmonella inoculated in creamy peanut butter. It was found that at varying combinations of pressures between 400 and 600 MPa and hold times between 4 and 18 min, the reductions in Salmonella concentration in peanut butter, from an initial level of 106- 107 CFU/g, were only between 1.6 and 1.9 log CFU/g. This led to further exploration of the effect of (i) pressure cycling during HHPP, (ii) varying water activity of peanut butter, and (iii) added nisin in combination with HHPP. The maximum log reduction achieved in all cases was 2 log CFU/g. Salmonella was inactivated to below detection limit only when the water activity of peanut butter was increased to an extreme value of 0.96, rendering it unrecognizable as peanut butter. It can be concluded that HHPP is not a suitable processing method for significantly improving the microbiological safety of Salmonella contaminated peanut butter. However, the intriguing results from this research will sow the seeds for future research on the molecular mechanism associated with Salmonella survival in low water activity foods like peanut butter during HHPP.M.S.Includes bibliographical referencesby Tanya D'souz
The Story Behind Texas’ Favorite Butter
No full textTexas has a great number of Texas brands:
Southwest Airlines.Texas Instruments.Lone Star Beer.Dell Computer.Imperial Sugar.The King Ranch.
Now, The King Ranch is a brand that came, quite literally, from a brand. King Ranch even has its own brand of Ford Pickup.
The King Ranch also helped launch another old Texas brand, Falfurrias Butter.
It is a little circuitous, but this is how it all came about. Richard King’s partner, Mifflin Kenedy, sold 7,000 cows to Ed Lasater, who then created the dairy that launched Falfurrias butter. Thirty-five years later, the King Ranch bought Lasater’s land, along with many head of cattle, to create the Encino division of the King Ranch.
But that’s not the story I’m here to tell. I’m here to talk about a great old brand of Texas butter.
Falfurrias butter was first made in Falfurrias, of course, in 1909. People have wondered whether the butter is named for the town or the town for the butter, but they were actually both named after Lasater’s ranch, which was named for a grove of trees called La Mota de Falfurrias. Lasater said that that unique word, Falfurrias, came from the Lipan Apache language and, loosely translated, means “Land of Heart’s Delight.”
The butter was certainly the town’s best known export in those early days, and likely remains so today. Even the school mascot, the Jerseys, was named after the butter’s real creators – the Jersey cows. At one point Falfurrias was home to the largest Jersey cattle herd in the world.
And so that gave special meaning to the once popular bumper sticker there: “Watch Your Step – You’re in Jersey Country.” I’m not sure the author of that intended the double meaning, but it certainly provided a good deal of local levity until it was recalled.
Falfurrias butter remains a popular niche brand of butter. In Texas, it’s sold at all the major grocery stores, and some smaller ones, too. It has been quite popular in northern Mexico for generations.
A friend tells me that as a child in Saltillo he remembers his mother bringing back the mantequilla dulce de Falfurrias as a special treat for the kids anytime she traveled to Texas.
A Texas Marine in WWII recalled that as he was wading ashore in the battle for Okinawa, a Falfurrias Butter crate bumped up against his leg in the surf. He found it comforting, an assurance from home that all would be well. And so it was.
Falfurrias Butter outgrew Falfurrias. It became so popular that it was eventually bought by the Dairy Farmers of America, but rest assured it is still made in Texas.
It is made by Keller’s Creamery in Winnsboro, Texas, and has grown at a Texas-sized pace of 40 percent over the last few years. That’s a lot of biscuits and baked potatoes, y’all.
When you drive through Falfurrias today, on state Highway 285, you can still see the vintage Falfurrias Butter sign on the side of the old Creamery Building. The town newspaper, Falfurrias Facts, occupies the building today.
In the interest of full disclosure ethical transparency, I have to reveal that I am also an export of Falfurrias, and even though I know on which side my bread is buttered, so to speak, I assure you that it does not affect the veracity of this commentary
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