scholarly journals Centromeres of the yeast Komagataella phaffii (Pichia pastoris) have a simple inverted-repeat structure

2016 ◽  
Author(s):  
Aisling Y. Coughlan ◽  
Sara J. Hanson ◽  
Kevin P. Byrne ◽  
Kenneth H. Wolfe
Keyword(s):  
Candida Albicans ◽  
Pichia Pastoris ◽  
Inverted Repeat ◽  
Methylotrophic Yeast ◽  
H3k9 Methylation ◽  
Komagataella Phaffii ◽  
Repeat Structure ◽  
Different Types ◽  
Mating Type Switching ◽  
The Relationship

AbstractCentromere organization has evolved dramatically in one clade of fungi, the Saccharomycotina. These yeasts have lost the ability to make normal eukaryotic heterochromatin with histone H3K9 methylation, which is a major component of pericentromeric regions in other eukaryotes. Following this loss, several different types of centromere emerged, including two types of sequence-defined ("point") centromeres, and the epigenetically-defined "small regional" centromeres of Candida albicans. Here we report that centromeres of the methylotrophic yeast Komagataella phaffii (formerly called Pichia pastoris) are structurally-defined. Each of its four centromeres consists of a 2-kb inverted repeat (IR) flanking a 1-kb central core (mid) region. The four centromeres are unrelated in sequence. CenH3 (Cse4) binds strongly to the cores, with a decreasing gradient along the IRs. This mode of organization resembles Schizosaccharomyces pombe centromeres but is much more compact and lacks the extensive flanking heterochromatic otr repeats. Different isolates of K. phaffii show polymorphism for the orientation of the mid regions, due to recombination in the IRs. CEN4 is located within a 138-kb region that changes orientation during mating-type switching, but switching does not induce recombination of centromeric IRs. The existing genetic toolbox for K. phaffii should facilitate analysis of the relationship between the IRs and the establishment and maintenance of centromeres in this species.

scholarly journals Metabolic Engineering of the Methylotrophic Yeast Pichia Pastoris (Komagataella phaffii) for the Production of Β-alanine From Methanol

2021 ◽  
Author(s):  
Liangtian Miao ◽  
Yin Li ◽  
Taicheng Zhu
Keyword(s):  
Pichia Pastoris ◽  
Methylotrophic Yeast ◽  
Cell Factory ◽  
Chemical Production ◽  
Komagataella Phaffii ◽  
Methylotrophic Yeast Pichia Pastoris ◽  
Renewable Feedstocks ◽  
Naturally Occurring ◽  
Renewable Feedstock ◽  
Different Sources

Abstract β-Alanine (3-aminopropionic acid), is the only naturally occurring β-amino acid and an important precursor for the synthesis of a variety of nitrogen-containing chemicals. Fermentative production of β-alanine from renewable feedstocks such as glucose has attracted significant interest in recent years. Methanol has become an emerging and promising renewable feedstock for biomanufacturing as an alternative to glucose. In this work, we demonstrated the feasibility of β-alanine production from methanol using Pichia pastoris (Komagataella phaffii) as a methylotrophic cell factory. Aspartate decarboxylases (ADCs) from different sources were screened and expressed in P. pastoris, followed by the optimization of aspartate decarboxylation by increasing the ADC copy number and C4 precursor supply via the overexpression of aspartate dehydrogenase. The production potential of the best strain was further evaluated in a 1-liter fermenter, and a β-alanine titer of 5.6 g/L was obtained. To our best knowledge, this is the highest chemical production titer ever reached in P. pastoris using methanol as the substrate.

Carbon source requirements for mating and mating‐type switching in the methylotrophic yeasts Ogataea (Hansenula) polymorpha and Komagataella phaffii (Pichia pastoris)

Yeast ◽  
2020 ◽  
Vol 37 (2) ◽  
pp. 237-245 ◽  
Author(s):  
Dahao Feng ◽  
Anton Stoyanov ◽  
Juliana C. Olliff ◽  
Kenneth H. Wolfe ◽  
Kantcho Lahtchev ◽  
...  
Keyword(s):  
Pichia Pastoris ◽  
Carbon Source ◽  
Mating Type ◽  
Hansenula Polymorpha ◽  
Methylotrophic Yeasts ◽  
Komagataella Phaffii ◽  
Mating Type Switching

scholarly journals Centromeres of the YeastKomagataella phaffii(Pichia pastoris)Have a Simple Inverted-Repeat Structure

2016 ◽  
Vol 8 (8) ◽  
pp. 2482-2492 ◽  
Author(s):  
Aisling Y. Coughlan ◽  
Sara J. Hanson ◽  
Kevin P. Byrne ◽  
Kenneth H. Wolfe
Keyword(s):  
Pichia Pastoris ◽  
Inverted Repeat ◽  
Repeat Structure

scholarly journals A Stable, Autonomously Replicating Plasmid Vector Containing Pichia pastoris Centromeric DNA

2018 ◽  
Vol 84 (15) ◽  
Author(s):  
Yasuyuki Nakamura ◽  
Teruyuki Nishi ◽  
Risa Noguchi ◽  
Yoichiro Ito ◽  
Toru Watanabe ◽  
...  
Keyword(s):  
Pichia Pastoris ◽  
Recombinant Proteins ◽  
Dna Sequences ◽  
Inverted Repeat ◽  
Genetic Manipulation ◽  
Plasmid Vector ◽  
Methylotrophic Yeast ◽  
Centromeric Dna ◽  
Content Type ◽  
Repeat Sequences

ABSTRACT The methylotrophic yeast Pichia pastoris is widely used to produce recombinant proteins, taking advantage of this species' high-density cell growth and strong ability to secrete proteins. Circular plasmids containing the P. pastoris-specific autonomously replicating sequence (PARS1) permit transformation of P. pastoris with higher efficiency than obtained following chromosomal integration by linearized DNA. Unfortunately, however, existing autonomously replicating plasmids are known to be inherently unstable. In this study, we used transcriptome sequencing (RNA-seq) data and genome sequence information to independently identify, on each of the four chromosomes, centromeric DNA sequences consisting of long inverted repeat sequences. By examining the chromosome 2 centromeric DNA sequence (Cen2) in detail, we demonstrate that an ∼111-bp region located at one end of the putative centromeric sequence had autonomous replication activity. In addition, the full-length Cen2 sequence, which contains two long inverted repeat sequences and a nonrepetitive central core region, is needed for the accurate replication and distribution of plasmids in P. pastoris. Thus, we constructed a new, stable, autonomously replicating plasmid vector that harbors the entire Cen2 sequence; this episome facilitates genetic manipulation in P. pastoris, providing high transformation efficiency and plasmid stability. IMPORTANCE Secretory production of recombinant proteins is the most important application of the methylotrophic yeast Pichia pastoris, a species that permits mass production of heterologous proteins. To date, the genetic engineering of P. pastoris has relied largely on integrative vectors due to the lack of user-friendly tools. Autonomously replicating Pichia plasmids are expected to facilitate genetic manipulation; however, the existing systems, which use autonomously replicating sequences (ARSs) such as the P. pastoris-specific ARS (PARS1), are known to be inherently unstable for plasmid replication and distribution. Recently, the centromeric DNA sequences of P. pastoris were identified in back-to-back studies published by several groups; therefore, a new episomal plasmid vector with centromere DNA as a tool for genetic manipulation of P. pastoris is ready to be developed.

THEORY OF LAW AND PHILOSOPHY OF LAW AS THEORETICAL DISCOURSES: SPECIFICS AND RELATIONSHIP

2020 ◽  
pp. 9-17
Author(s):  
Вадим Леонидович Афанасьевский
Keyword(s):  
Scientific Knowledge ◽  
Scientific Theory ◽  
Theoretical Concept ◽  
Philosophy Of Law ◽  
The West ◽  
Scientific Creativity ◽  
Key Characteristics ◽  
Different Types ◽  
Theory Of Law ◽  
The Relationship

В статье анализируется проблема взаимоотношений философии права и научной теории права. Рассматриваемая проблема стала особенно актуальной в российском образовательном пространстве в связи с введением после длительного перерыва в государственный образовательный стандарт магистратуры по юриспруденции учебной дисциплины «Философия права». Автор статьи в качестве базисного принимает тезис, согласно которому философия права, являясь сферой философской мысли, и теория права как область научного социогуманитарного знания представляют собой разные типы теоретического дискурса. Исходя из этого, в статье выстраивается теоретическая концепция, согласно которой задачей философии права как философского типа мышления является конструирование или экспликация онтологических, эпистемологических, аксиологических, феноменологических оснований для формирования и функционирования научных теоретико-правовых и историко-правовых построений. Для реализации поставленной в статье задачи подробно рассматриваются ключевые характеристики как теории философского типа, так и идеалов, норм и характеристик научного знания. Выявленное различие экстраполируется на взаимоотношение теории права как продукта научного творчества и философии права как конструкции, задающей базовые мировоззренческие смыслы. В качестве примера выработанных философией права и государства оснований научных теорий прогресса, государства, морали и права, автор приводит взгляды мыслителей западноевропейской философской классики: Т. Гоббса, Ж.-Ж. Руссо, И. Канта, Г.В.Ф. Гегеля. Именно их философские концепции предопределили образы теоретико- и историко-правовых учений XVIII, XIX, XX и даже начала XXI в. Таким образом, отношение философии права и теории права выстраивается по «вертикали»: от онтологического основания к возведению теоретико-правовых и историко-правовых научных построений. The article analyzes the problem of the relationship between the philosophy of law and the scientific theory of law. The problem under consideration has become especially urgent in the Russian educational space in connection with the introduction of the Philosophy of Law discipline master's degree in law after a long break. The author of the article takes as the basis the thesis that the philosophy of law, being the sphere of philosophical thought, and the theory of law as a field of scientific socio-humanitarian knowledge are different types of theoretical discourse. Based on this, the article builds a theoretical concept according to which the task of the philosophy of law as a philosophical type of thinking is the construction or explication of ontological, epistemological, axiological, phenomenological grounds for the formation and functioning of concrete scientific theoretical and legal and historical and legal constructions. To implement the task posed in the article, the key characteristics of both a theory of a philosophical type and ideals, norms and characteristics of scientific knowledge are examined in detail. The revealed difference is extrapolated to the relationship between the theory of law as a product of scientific creativity and the philosophy of law as a construction that sets basic philosophical meanings. As an example of the foundations of the scientific theories of progress, state, morality and law developed by the philosophy of law and the state, the author gives the views and thinkers of the West European philosophical classics T. Hobbes, J.-J. Russo, I. Kant, G.V.F. Hegel. It was their philosophical concepts that predetermined the images of theoretical and historical-legal doctrines of the XVIII, XIX, XX and even the beginning of the XXI centuries. Thus, the attitude of the philosophy of law and the theory of law is built along the «vertical»: from the ontological foundation to the construction of theoretical and historical and historical legal scientific constructions.

Characteristics of Different Types of Childhood Violence and the Risk of Revictimization

2019 ◽  
Vol 25 (14) ◽  
pp. 1696-1716 ◽  
Author(s):  
Ida Frugaard Stroem ◽  
Helene Flood Aakvaag ◽  
Tore Wentzel-Larsen
Keyword(s):  
Childhood Abuse ◽  
Telephone Survey ◽  
Regression Analyses ◽  
Multiple Forms ◽  
Different Types ◽  
Children And Young Adults ◽  
Childhood Violence ◽  
Forms Of Violence ◽  
The Relationship

This study investigates the relationship between the characteristics of different types of childhood violence and adult victimization using two waves of data from a community telephone survey (T1) and a follow-up survey, including 505 cases and 506 controls, aged 17-35 years (T2). The logistic regression analyses showed that exposure to childhood abuse, regardless of type, was associated with adult victimization. Exposure to multiple types of abuse, victimization both in childhood and in young adulthood, and recency of abuse increased these odds. Our findings emphasize the importance of assessing multiple forms of violence when studying revictimization. Practitioners working with children and young adults should be attentive to the number of victimization types experienced and recent victimization to prevent further abuse.

scholarly journals Endolysosomal Cation Channels and MITF in Melanocytes and Melanoma

Biomolecules ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1021
Author(s):  
Carla Abrahamian ◽  
Christian Grimm
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Transcription Factor ◽  
Convincing Evidence ◽  
Signaling Cascades ◽  
Cation Channels ◽  
Pore Channel ◽  
Different Types ◽  
Canonical Wnt ◽  
The Relationship

Microphthalmia-associated transcription factor (MITF) is the principal transcription factor regulating pivotal processes in melanoma cell development, growth, survival, proliferation, differentiation and invasion. In recent years, convincing evidence has been provided attesting key roles of endolysosomal cation channels, specifically TPCs and TRPMLs, in cancer, including breast cancer, glioblastoma, bladder cancer, hepatocellular carcinoma and melanoma. In this review, we provide a gene expression profile of these channels in different types of cancers and decipher their roles, in particular the roles of two-pore channel 2 (TPC2) and TRPML1 in melanocytes and melanoma. We specifically discuss the signaling cascades regulating MITF and the relationship between endolysosomal cation channels, MAPK, canonical Wnt/GSK3 pathways and MITF.

scholarly journals Overdiagnosis and overtreatment of nipple and breast candidiasis: A review of the relationship between diagnoses of mammary candidiasis and Candida albicans in breastfeeding women

2021 ◽  
Vol 17 ◽  
pp. 174550652110314
Author(s):  
Pamela Douglas
Keyword(s):  
Candida Albicans ◽  
Human Milk ◽  
Signs And Symptoms ◽  
Breast Pain ◽  
Breastfeeding Support ◽  
Candida Spp ◽  
Healthy Human ◽  
Nipple Areolar Complex ◽  
Areolar Complex ◽  
The Relationship

Background: Breastfeeding mothers commonly experience nipple pain accompanied by radiating, stabbing or constant breast pain between feeds, sometimes associated with pink shiny nipple epithelium and white flakes of skin. Current guidelines diagnose these signs and symptoms as mammary candidiasis and stipulate antifungal medications. Aim: This study reviews existing research into the relationship between Candida albicans and nipple and breast pain in breastfeeding women who have been diagnosed with mammary candidiasis; whether fluconazole is an effective treatment; and the presence of C. albicans in the human milk microbiome. Method: The author conducted three searches to investigate (a) breastfeeding-related pain and C. albicans; (b) the efficacy of fluconazole in breastfeeding-related pain; and (c) composition of the human milk mycobiome. These findings are critiqued and integrated in a narrative review. Results: There is little evidence to support the hypothesis that Candida spp, including C. albicans, in maternal milk or on the nipple-areolar complex causes the signs and symptoms popularly diagnosed as mammary candidiasis. There is no evidence that antifungal treatments are any more effective than the passage of time in women with these symptoms. Candida spp including C. albicans are commonly identified in healthy human milk and nipple-areolar complex mycobiomes. Discussion: Clinical breastfeeding support remains a research frontier. The human milk microbiome, which includes a mycobiome, interacts with the microbiomes of the infant mouth and nipple-areolar complex, including their mycobiomes, to form protective ecosystems. Topical or oral antifungals may disrupt immunoprotective microbial homeostasis. Unnecessary use contributes to the serious global problem of antifungal resistance. Conclusion: Antifungal treatment is rarely indicated and prolonged courses cannot be justified in breastfeeding women experiencing breast and nipple pain. Multiple strategies for stabilizing microbiome feedback loops when nipple and breast pain emerge are required, in order to avoid overtreatment of breastfeeding mothers and their infants with antifungal medications.

scholarly journals More than a method: trusting relationships, productive tensions, and two-way learning as mechanisms of authentic co-production

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Sarah E. Knowles ◽  
Dawn Allen ◽  
Ailsa Donnelly ◽  
Jackie Flynn ◽  
Kay Gallacher ◽  
...  
Keyword(s):  
Patient Involvement ◽  
Ways Of Knowing ◽  
Knowledge Mobilisation ◽  
Academic Knowledge ◽  
Willingness To Change ◽  
Different Types ◽  
Hybrid Knowledge ◽  
Key Issues ◽  
Field Notes ◽  
The Relationship

Abstract Background Knowledge mobilisation requires the effective elicitation and blending of different types of knowledge or ways of knowing, to produce hybrid knowledge outputs that are valuable to both knowledge producers (researchers) and knowledge users (health care stakeholders). Patients and service users are a neglected user group, and there is a need for transparent reporting and critical review of methods used to co-produce knowledge with patients. This study aimed to explore the potential of participatory codesign methods as a mechanism of supporting knowledge sharing, and to evaluate this from the perspective of both researchers and patients. Methods A knowledge mobilisation research project using participatory codesign workshops to explore patient involvement in using health data to improve services. To evaluate involvement in the project, multiple qualitative data sources were collected throughout, including a survey informed by the Generic Learning Outcomes framework, an evaluation focus group, and field notes. Analysis was a collective dialogic reflection on project processes and impacts, including comparing and contrasting the key issues from the researcher and contributor perspectives. Results Authentic involvement was seen as the result of “space to talk” and “space to change”. "Space to talk" refers to creating space for shared dialogue, including space for tension and disagreement, and recognising contributor and researcher expertise as equally valuable to the discussion. ‘Space to change’ refers to space to adapt in response to contributor feedback. These were partly facilitated by the use of codesign methods which emphasise visual and iterative working, but contributors emphasised that relational openness was more crucial, and that this needed to apply to the study overall (specifically, how contributors were reimbursed as a demonstration of how their input was valued) to build trust, not just to processes within the workshops. Conclusions Specific methods used within involvement are only one component of effective involvement practice. The relationship between researcher and contributors, and particularly researcher willingness to change their approach in response to feedback, were considered most important by contributors. Productive tension was emphasised as a key mechanism in leading to genuinely hybrid outputs that combined contributor insight and experience with academic knowledge and understanding.

scholarly journals Autophagy Modulators in Cancer Therapy

2021 ◽  
Vol 22 (11) ◽  
pp. 5804
Author(s):  
Kamila Buzun ◽  
Agnieszka Gornowicz ◽  
Roman Lesyk ◽  
Krzysztof Bielawski ◽  
Anna Bielawska
Keyword(s):  
Cancer Research ◽  
Cancer Therapy ◽  
Adverse Effects ◽  
Nutrient Deficiency ◽  
Molecular Regulation ◽  
Regulatory Pathways ◽  
Selective Autophagy ◽  
Atg Proteins ◽  
Different Types ◽  
The Relationship

Autophagy is a process of self-degradation that plays an important role in removing damaged proteins, organelles or cellular fragments from the cell. Under stressful conditions such as hypoxia, nutrient deficiency or chemotherapy, this process can also become the strategy for cell survival. Autophagy can be nonselective or selective in removing specific organelles, ribosomes, and protein aggregates, although the complete mechanisms that regulate aspects of selective autophagy are not fully understood. This review summarizes the most recent research into understanding the different types and mechanisms of autophagy. The relationship between apoptosis and autophagy on the level of molecular regulation of the expression of selected proteins such as p53, Bcl-2/Beclin 1, p62, Atg proteins, and caspases was discussed. Intensive studies have revealed a whole range of novel compounds with an anticancer activity that inhibit or activate regulatory pathways involved in autophagy. We focused on the presentation of compounds strongly affecting the autophagy process, with particular emphasis on those that are undergoing clinical and preclinical cancer research. Moreover, the target points, adverse effects and therapeutic schemes of autophagy inhibitors and activators are presented.

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