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Genome-wide identification and characterization of genes determining cellular polyamine homeostasis in senescing barley leaves
Get PDFWydział BiologiiStarzenie rozwojowe jest procesem nieodwracalnym, po którym następuje bezwarunkowo śmierć komórki. Indukowane ciemnością starzenie liści (ang. dark-induced leaf senescence, DILS) jest do pewnego stadium procesem odwracalnym. W roślinach indukowane starzenie jest wysoce kontrolowanym i aktywnym procesem wymagającym globalnego przeprogramowania metabolicznego, mającego na celu zorganizowaną dezintegrację i ponowną remobilizację cennych zasobów. Sprawność regulacji indukowanego procesu starzenia jest oznaką żywotności starzejących się komórek, które na każdym etapie muszą zachować zdolność do utrzymania homeostazy, przejawiającej się m.in. kontrolowaniem homeostazy cyklu poliamin (PA). Homeostaza PA w komórce jest utrzymywana przez mechanizmy sprzężenia zwrotnego z poziomu biosyntezy, katabolizmu, importu i eksportu. Poliaminy są niskocząsteczkowymi organicznymi kationami należącymi do grupy biogennych amin, kluczowymi w wielu fizjologicznych i rozwojowych procesach u bakterii, zwierząt i roślin. Metabolizm PA może odgrywać istotną rolę w procesie starzenia się liścia. Zespół prof. Ewy Sobieszczuk-Nowickiej za cel postawił sobie poznanie wielokierunkowych powiązań metabolizmu poliamin z siecią metaboliczną organizującą proces starzenia liści jęczmienia oraz ocenę, czy zmiana kierunku starzeniowo-zależnego metabolizmu PA wpłynie na ten proces. Kierunek metabolizmu PA i transport może kontrolować efektywność zależnej od starzenia remobilizacji azotu. Do realizacji celu wybrano podejście oparte na genomice funkcjonalnej. Brak w literaturze informacji na temat sekwencji genów metabolizmu PA w jęczmieniu był dużym ograniczeniem tego podejścia. Stąd też potrzebna była identyfikacja genów metabolizmu PA w jęczmieniu, która stała się celem mojej rozprawy doktorskiej. Do badań włączyłam również analizę transporterów PA. Transportery PA są rozpoznane u roślin w niewielkim stopniu. Importery PA zostały opisane u rzodkiewnika, ryżu i pomarańczy. Eksportery PA zostały zasugerowane jako potencjalne eksportery PA u rzodkiewnika i ryżu. W wyniku badań w skali całego genomu jęczmienia wyodrębniłam rodziny genów warunkujące homeostazę PA w komórce, które obejmowały 23 geny metabolizmu PA i 13 genów transporterów. Przeprowadziłam również szczegółową charakterystykę zidentyfikowanych genów oraz ich białkowych produktów. Modelowanie homologiczne badanych transporterów pozwoliło z dużą dokładnością przewidzieć struktury trójwymiarowe białek, a analizy dokowania molekularnego potwierdziły możliwość interakcji pomiędzy białkami transportującymi a PA. Obecność w genomie zidentyfikowanych in silico genów potwierdziłam eksperymentalnie i zbadałam ich organospecyficzną ekspresję. Następnie w modelu starzenia liści jęczmienia indukowanego ciemnością zbadałam profile ekspresji genów homeostazy PA. Na podstawie tej analizy wytypowałam geny kandydujące do badań funkcjonalnych. Niniejsza rozprawa doktorska przedstawia wyniki pierwszej identyfikacji, izolacji i kompleksową charakterystykę genów jęczmienia warunkujących komórkową homeostazę PA oraz ocenę ich organospecyficznej i starzeniowo-zależnej ekspresji w metabolizmie liścia ekspresji. Wyniki moich badań stanowią punkt odniesienia badań funkcjonalnych wielu zespołów naukowców wyjaśniających mechanizmy molekularnej kontroli i regulacji przez PA procesów rozwojowych zbóż i ich reakcji na (a)biotyczne czynniki środowiska. Szczególnie badań funkcjonalnych nad mechanizmem działania PA w starzeniu liści.
Developmental senescence is an irreversible process that is inevitably followed by cell death. Dark-induced leaf senescence (DILS) is a reversible process to a certain stage. In plants, induced senescence is a highly controlled and active process requiring global metabolic reprogramming aimed at the organized disintegration and remobilization of valuable resources. The efficiency of the regulation of the induced senescence process is a sign of the viability of senescent cells, which at each stage must maintain the ability to maintain homeostasis, manifested, among others, by controlling polyamine (PA) cycle homeostasis. PA homeostasis in the cell is maintained by feedback mechanisms from the levels of biosynthesis, catabolism, import and export. Polyamines are low molecular weight organic cations belonging to the group of biogenic amines, crucial in many physiological and developmental processes in bacteria, animals and plants. PA metabolism may play an important role in the leaf senescence process. Professor Ewa Sobieszczuk-Nowicka's team set themselves the goal to understand the multidirectional connections of polyamine metabolism with the metabolic network organizing the senescence process of barley leaves and to assess whether a change in the direction of senescence-dependent PA metabolism will affect this process. The direction of PA metabolism and transport may control the efficiency of senescence-dependent nitrogen remobilization. An approach based on functional genomics was chosen to achieve the goal. The lack of information in the literature on the sequence of PA metabolism genes in barley was a major limitation of this approach. Hence, there was a need to identify PA metabolism genes in barley, which became the goal of my doctoral thesis. I also included the analysis of PA transporters in my research. PA transporters are little known in plants. PA importers have been described in Arabidopsis, rice and orange. PA exporters have been suggested as potential PA exporters in Arabidopsis and rice. As a result of research on the entire barley genome, I identified gene families determining PA homeostasis in the cell, which included 23 PA metabolism genes and 13 transporter genes. I also carried out a detailed characterization of the identified genes and their protein products. Homology modeling of the studied transporters allowed to predict the three-dimensional structures of proteins with high accuracy, and molecular docking analyzes confirmed the possibility of interactions between transport proteins and PA. I experimentally confirmed the presence of the genes identified in silico in the genome and examined their organospecific expression. Then, in a dark-induced barley leaf senescence model, expression profiles of PA homeostasis genes. Based on this analysis, I selected candidate genes for functional research. This doctoral dissertation presents the results of the first identification, isolation and comprehensive characterization of barley genes determining cellular PA homeostasis, as well as the assessment of their organospecific and senescence-dependent expression in leaf metabolism. The results of my research constitute a reference point for functional studies of many teams of scientists explaining the mechanisms of molecular control and regulation by PA of crop development processes and their response to (a)biotic environmental factors. Especially functional studies on the mechanism of action of PA in leaf senescence.Badania finansowano z projektu OPUS Narodowego Centrum Nauki nr UMO-2018/29/B/NZ9/00734, tytuł projektu: „Poliaminy – nowy przełącznik metaboliczny starzenia liścia jęczmienia. Opracowanie molekularnej podstawy sieciowej regulacji procesu jako cel strategii uprawy zbóż”. Autorka otrzymywała stypendium motywacyjne w ramach programu Paszport do przyszłości – Interdyscyplinarne studia doktoranckie na Wydziale Biologii UAM (POWR.03.02.00-00-I006/17) współfinansowanego ze środków Europejskiego Funduszu Społecznego w ramach Programu Operacyjnego Wiedza Edukacja Rozwój (POWER)
Establishment and phenotypic characterization of genetically diverse core collections of Lupinus albus
Get PDFBackground: Lupinus albus is a food grain legume recognized for its high levels of seed protein (30–40%) and oil (6–13%), and its adaptability to different climatic and soil conditions. The availability of well-characterized, genetically and phenotypically diverse germplasm will facilitate the development of next-generation L. albus cultivars, encourage biodiversity conservation, and promote the sustainable utilization of this species. Results: We evaluated more than 2000 L. albus accessions based on 35 agro-morphological traits and passport data to establish Intelligent Collections. The Reference-CORE (R-CORE), covering global diversity, exemplified the genotypic variation among accessions differing in biological status (cultivars, breeding/research materials, landraces, and wild relatives). The Training-CORE (T-CORE), a subset of 300 R-CORE accessions, represents the diversity of the entire collection. Principal component analysis showed that the L. albus R-CORE encompasses four phenotypic groups (A1, A2, A3, and B), and that groups A3 and B can be characterized by the main phenotypic traits of pod shattering and seed ornamentation, respectively. The coefficient of total genetic variation differed across morphological traits, phenotypic groups, geographic regions, and according to biological status. Conclusions: The core collections established in this study will facilitate agricultural research by providing the broad phenotypic data needed for crop improvement programs and by shedding light on the undiscovered biodiversity of L. albus genetic resources. Understanding the variation found in such resources will allow us to develop sustainable tools and technologies that address global challenges such as the provision of healthy and sustainable diets for all and the mitigation of climate change
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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