scholarly journals Identification of the best housekeeping gene for RT-qPCR analysis of human pancreatic organoids

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0260902
Author(s):  
Alessandro Cherubini ◽  
Francesco Rusconi ◽  
Lorenza Lazzari

In the last few years, there has been a considerable increase in the use of organoids, which is a new three-dimensional culture technology applied in scientific research. The main reasons for their extensive use are their plasticity and multiple applications, including in regenerative medicine and the screening of new drugs. The aim of this study was to better understand these structures by focusing on the choice of the best housekeeping gene (HKG) to perform accurate molecular analysis on such a heterogeneous system. This feature should not be underestimated because the inappropriate use of a HKG can lead to misleading data and incorrect results, especially when the subject of the study is innovative and not totally explored like organoids. We focused our attention on the newly described human pancreatic organoids (hPOs) and compared 12 well-known HKGs (ACTB, B2M, EF1α, GAPDH, GUSB, HPRT, PPIA, RNA18S, RPL13A TBP, UBC and YWHAZ). Four different statistical algorithms (NormFinder, geNorm, BestKeeper and ΔCt) were applied to estimate the expression stability of each HKG, and RefFinder was used to identify the most suitable genes for RT-qPCR data normalization. Our results showed that the intragroup and intergroup comparisons could influence the best choice of the HKG, making clear that the identification of a stable reference gene for accurate and reproducible RT-qPCR data normalization remains a critical issue. In summary, this is the first report on HKGs in human organoids, and this work provides a strong basis to pave the way for further gene analysis in hPOs.

Author(s):  
Matthew J. Genge

Drawings, illustrations, and field sketches play an important role in Earth Science since they are used to record field observations, develop interpretations, and communicate results in reports and scientific publications. Drawing geology in the field furthermore facilitates observation and maximizes the value of fieldwork. Every geologist, whether a student, academic, professional, or amateur enthusiast, will benefit from the ability to draw geological features accurately. This book describes how and what to draw in geology. Essential drawing techniques, together with practical advice in creating high quality diagrams, are described the opening chapters. How to draw different types of geology, including faults, folds, metamorphic rocks, sedimentary rocks, igneous rocks, and fossils, are the subjects of separate chapters, and include descriptions of what are the important features to draw and describe. Different types of sketch, such as drawings of three-dimensional outcrops, landscapes, thin-sections, and hand-specimens of rocks, crystals, and minerals, are discussed. The methods used to create technical diagrams such as geological maps and cross-sections are also covered. Finally, modern techniques in the acquisition and recording of field data, including photogrammetry and aerial surveys, and digital methods of illustration, are the subject of the final chapter of the book. Throughout, worked examples of field sketches and illustrations are provided as well as descriptions of the common mistakes to be avoided.


2021 ◽  
Vol 22 (5) ◽  
pp. 2491
Author(s):  
Yujin Park ◽  
Kang Moo Huh ◽  
Sun-Woong Kang

The process of evaluating the efficacy and toxicity of drugs is important in the production of new drugs to treat diseases. Testing in humans is the most accurate method, but there are technical and ethical limitations. To overcome these limitations, various models have been developed in which responses to various external stimuli can be observed to help guide future trials. In particular, three-dimensional (3D) cell culture has a great advantage in simulating the physical and biological functions of tissues in the human body. This article reviews the biomaterials currently used to improve cellular functions in 3D culture and the contributions of 3D culture to cancer research, stem cell culture and drug and toxicity screening.


1980 ◽  
Vol 7 (1) ◽  
pp. 93-104 ◽  
Author(s):  
A.W. Peterson ◽  
T. Blench

This paper, for river engineers and their environmental counterparts, presents and explains the origin and potential of four-dimensional charts that smooth most of the world's numerical data obtained from the equilibrium dimensions of sand rivers, gravel rivers, and laboratory flumes. These charts aim to provide a practical service comparable with that provided by factual plots on the comprehensive classic three-dimensional Stanton friction-factor diagram for circular pipes and clean Newtonian fluid. In the river problems, especially, the existence of different phases (whose transitions are not susceptible to formulation), the inadequacies of textbook theories even for simple phases, and the unavoidable imperfections of both field and laboratory measurements combine to prevent responsible design. The remedy is a graphing of total information backed by references from which its reliability and practicability can be assessed.The references have been chosen to contain principal information in the forms of: (i) usable photos, graphs, and tables; (ii) explanations free from specialized mathematics and speculative arguments; and (iii) papers with discussions, authors' replies, and further useful references (since a major reference list would be too long for this paper). Because condensation has had to be extreme the authors will be glad to attempt answers to discussions and questions on the subject matter, its practical applications, and its implications in teaching and research.


Author(s):  
Yu Zhou ◽  
Chen Xuedong ◽  
Fan Zhichao ◽  
Jie Dong

Creep failure is one of the most important failure modes in the design of hydroprocessing reactors at elevated temperatures, and the accurate prediction of the creep behavior in structural discontinuities is a critical issue for component design. A physically-based continnum damage mechanics (CDM) model was adopted to describe all three creep stages of 2.25Cr-1Mo-0.25V ferritic steel widely used in manufacturing modern hydroprocessing reactors. The material constants in the damage constitutive equations were identified using an efficient optimization scheme based on genetic algorithm (GA). The user-defined subroutine implementing the CDM model was developed using user programmable features (UPFs) in ANSYS. Three-dimensional finite element analysis of the hydroprocessing reactor was conducted to determine the critical regions, and the studies on the stress redistribution and the prediction of damage evolution in these regions during creep were carried out. The results show that FE modelling based on CDM theory can provide a good tool for creep design of complex engineering components.


Tumor Biology ◽  
2017 ◽  
Vol 39 (5) ◽  
pp. 101042831769833 ◽  
Author(s):  
Wang Jinjun ◽  
Wang Zhaowei ◽  
Li Qiang ◽  
Xue Zhijun ◽  
Zhang Juanzi ◽  
...  

To investigate the effects of soluble fms-like tyrosine kinase-1 on the vascular mimicry formation, proliferation, migration, and invasion of colorectal cancer SW480 cells. The recombinant plasmid pBLAST49-sFLT-1 or pBLAST49 control plasmid was transfected into SW480 cells to obtain hsFLT-1-SW480 or Ctrl-SW480 cells. The three-dimensional model culture, sulforhodamine B assay, scratch assay, and Transwell assay were performed to detect the vascular mimicry formation, proliferation, migration, and invasion of colorectal cancer SW480 cells, respectively. Western blotting was used to detect the expression of vascular endothelial–cadherin protein. Compared with Ctrl-SW480 cells, vascular mimicry formation ((0.85 ± 0.04) vs (7.40 ± 0.69), p < 0.05) and vascular endothelial–cadherin expression ((1.25 ± 0.08) vs (1.89 ± 0.03), p < 0.05) were significantly decreased, and the growth rate was also significantly decreased in hsFLT-1-SW480 cells ((32.54 ± 5.12) vs (88.13 ± 11.52), p < 0.05). Moreover, the migration ((0.46 ± 0.08) vs (0.94 ± 0.03), p < 0.05) and invasion capacity ((59.14 ± 3.64) vs (134.85 ± 10.16), p < 0.05) of SW480 cells were significantly inhibited upon soluble fms-like tyrosine kinase-1 transfection. soluble fms-like tyrosine kinase-1 inhibits cell proliferation, migration, and invasion of colorectal cancer SW480 cells through suppression of vascular mimicry formation, which provides a good basis for the development of new drugs for the treatment of colorectal cancer by targeting both angiogenesis and vascular mimicry formation.


2020 ◽  
pp. 1-9

Acute myeloid leukaemia (AML) is a heterogeneous, most common type of acute leukaemia that involves mutation in haematopoietic and progenitors stem cells (HPSCs) leading to uncontrolled division, self-renewal and differentiation. Though it was untreatable about a half century ago, AML is now considered to be treatable in up to 40% of adults and those who are at or under 60 years of age. For the post-induction treatment, the mutation testing and cytogenetics are still an important prognostic tool. The AML treatment remains unchanged for almost three decades, although the field is advanced with the discovery of new drugs and deep understanding of the disease biology. Still, many people are relapsing and are dying eventually from the disease. This review discusses the broader aspects of AML, reflecting some of the most important and productive areas of research on the subject and was conducted using thoroughly searching databases, including Health Research and Development Information network Plus (HERDIN Plus), google scholar and PubMed to critically analyses the recent advances, available treatments and future prospectives of AML.


2017 ◽  
Vol 73 (5) ◽  
pp. 387-402 ◽  
Author(s):  
Gregory S. Chirikjian ◽  
Sajdeh Sajjadi ◽  
Bernard Shiffman ◽  
Steven M. Zucker

In molecular-replacement (MR) searches, spaces of motions are explored for determining the appropriate placement of rigid-body models of macromolecules in crystallographic asymmetric units. The properties of the space of non-redundant motions in an MR search, called a `motion space', are the subject of this series of papers. This paper, the fourth in the series, builds on the others by showing that when the space group of a macromolecular crystal can be decomposed into a product of two space subgroups that share only the lattice translation group, the decomposition of the group provides different decompositions of the corresponding motion spaces. Then an MR search can be implemented by trading off between regions of the translation and rotation subspaces. The results of this paper constrain the allowable shapes and sizes of these subspaces. Special choices result when the space group is decomposed into a product of a normal Bieberbach subgroup and a symmorphic subgroup (which is a common occurrence in the space groups encountered in protein crystallography). Examples of Sohncke space groups are used to illustrate the general theory in the three-dimensional case (which is the relevant case for MR), but the general theory in this paper applies to any dimension.


1979 ◽  
Vol 49 (2) ◽  
pp. 343-346 ◽  
Author(s):  
Marcella V. Ridenour

30 boys and 30 girls, 6 yr. old, participated in a study assessing the influence of the visual patterns of moving objects and their respective backgrounds on the prediction of objects' directionality. An apparatus was designed to permit modified spherical objects with interchangeable covers and backgrounds to move in three-dimensional space in three directions at selected speeds. The subject's task was to predict one of three possible directions of an object: the object either moved toward the subject's midline or toward a point 18 in. to the left or right of the midline. The movements of all objects started at the same place which was 19.5 ft. in front of the subject. Prediction time was recorded on 15 trials. Analysis of variance indicated that visual patterns of the moving object did not influence the prediction of the object's directionality. Visual patterns of the background behind the moving object did not influence the prediction of the object's directionality except during the conditions of a light nonpatterned moving object. It was concluded that visual patterns of the background and that of the moving object have a very limited influence on the prediction of direction.


Author(s):  
Вячеслав Иванович Моисеев

В статье даётся краткий очерк антиномической природы биоэтического дискурса и возможностей его геометрической визуализации. Рассматриваются два варианта визуализации. Первый связан с представлением той или иной ситуации как системы полярностей, которая в свою очередь моделируется в рамках векторной модели. В простейшем случае тезис и антитезис рассматриваются как два перпендикулярных вектора, а синтез – как их векторная сумма. В этом случае можно ввести и более количественную оценку «меры многомерности» полярной системы – как величины проекции её векторного представления на суммарный вектор. С использованием этих конструкций разбирается один пример из биоэтики, связанный со столкновением принципов милосердия и правдивости (проблема «лжи во спасение»). Деяние (действие или бездействие) интерпретируется как своеобразный оператор на событиях, который переводит одни события в другие. Предполагается, что субъект в своих деяниях рассматривает различные возможности и выбирает те из них, которые максимизируют ту или иную ценностную меру субъекта, в данном случае – меру векторной проекции полярного вектора ситуации на суммарный вектор – вектор синтеза базисных полярностей. Второй вариант визуализации связан с понятием антиномий в биоэтике – таких противоречий, которые не являются формально-логическими ошибками. В отличие от последних, в антиномиях как тезис, так и антитезис имеют свой момент оправдания в рамках тех или иных условий. Используется также понятие «антинома» – логического субъекта антиномии, который предицируется тезисом и антитезисом антиномии. Редукции антиномии соответствуют двум крайним аспектам антинома, которые называются его «редуктами» – по аналогии с редукцией волновой функции в квантовой механике. Приводятся различные примеры антиномов: биоэты, глоболоки, холомеры. В биоэтах один редукт выражает в большей мере биологические (биоредукт), второй – этические (эторедукт) определения антинома. В глоболоках выделяются глобальный (глоборедукт) и локальный (локоредукт) виды редуктов: первый выражает более глобальные (универсальные) этические определения, второй – более локальные, связанные с ценностями и нормами того или иного сообщества. Наконец, холомеры – вид антиномов, где антиномически соединяются определения целого (холоредукт) и части (мероредукт). Даётся их интерпретация как многомерных ментальных объектов в некотором обобщённом пространстве, так что крайние их аспекты (редукции антиномии) можно представить как проекции более многомерного состояния. В заключении делается предположение о связи биоэтических проблем с идеей ментальной многомерности, что составляет основу возможной визуализации как интерпретации ментальной многомерности на векторном её представлении. The article provides a brief outline of the antinomic nature of bioethical discourse and the possibilities of its geometric visualization. Two visualization options are considered. The first is associated with the representation of a particular situation as a system of polarities, which in turn is modeled in the framework of a vector model. In the simplest case, the thesis and the antithesis are considered as two orthogonal vectors P1 and P2, and the synthesis is considered as their vector sum S = P1+P2. In this case, we can also introduce a more quantitative estimate of the “measure of multidimensionality” M(P) of the polar system – as the magnitude of the projection of its vector representation P on the sum vector S, i.e. M(P) = (P,es), where es = S/|S| is the unit vector of the vector S, and (P,es) is the scalar product of the vectors P and es. Using these constructs, the author analyzes one example from bioethics related to the clash of the principles of mercy and truthfulness (the problem of “lying for salvation”). An act (action or omission) is interpreted as a kind of an operator on events that transforms some events into others. It is assumed that the subject considers various possibilities in their actions and chooses those that maximize a particular value measure of the subject, in our case, the measure M(P) of the vector projection of the polar vector P of the situation on the sum vector S – the vector of synthesis of basic polarities. The second version of visualization is related to the concept of antinomies – such contradictions that are not formal logical errors – in bioethics. In contrast to errors, in antinomies, both the thesis and the antithesis have their moment of justification within the framework of certain conditions. The concept “antinome” is also used; it is the logical subject of antinomy, which is predicated by the thesis and the antithesis of antinomy. Antinomy reductions correspond to two extreme aspects of the antinome, which are called its “reducts” – by analogy with the reduction of the wave function in quantum mechanics. Various examples of antinomes are given: bioets, globolocs, and holomers. In bioets, one reduct expresses the biological (bioreduct) definition of the antinome, another the ethical (ethoreduct) one. In globolocs, global (globoreduct) and local (locoreduct) types of reducts are distinguished: the former expresses more global (universal) ethical definitions, the latter more local ones, related to the values and norms of a particular local community. Finally, holomers are a kind of antinomes in which the definitions of the whole (holoreduct) and the part (meroreduct) are antinomically connected. They are interpreted as multidimensional mental objects in some generalized space, so that their extreme aspects (antinomy reductions) can be represented as generalized projections of a more multidimensional state within certain constricted conditions (reduction intervals). In this case, it is possible to geometrically visualize such states as, for example, three-dimensional objects in space, through which antinomes can be modeled, and their reducts as two-dimensional projections of a three-dimensional body on certain projection planes (intervals of reducts). In this case, one of the central tasks of bioethics is to determine the boundaries of the demarcation of some intervals from others. For example, in solving the problem of abortion and the status of the human embryo, such a demarcation is expressed in the search for a time point that would separate the phase of a more biological definition (bioreduct) of the embryo from its more ethical state (ethoreduct). In conclusion, the author suggests that bioethical problems are connected with the idea of mental multidimensionality, which forms the basis of a possible visualization as an interpretation of mental multidimensionality in its vector representation.


2021 ◽  
Author(s):  
McKenzie Bohn

Window displays in the fashion industry are unique sites of meaning that combine advertising and artwork in a three-dimensional space. The current body of research surrounding window displays approaches the subject from a marketer’s position and attempts to evaluate performance. This project shifts the focus to the artistic qualities of window displays as they are used by fashion retailers. The primary theoretical lens is gestalt theory, which has applications in both psychology and design. The specific windows examined are the Christmas windows at retailer Saks Fifth Avenue Toronto in December of 2018. An autoethnographic research design is employed, resulting in an exploratory empirical analysis that serves as an entry into an under-represented area of study: the fashion window as an art object. The key findings of the project are the application of gestalt theory to the design of the windows and the researcher’s observations to suggest an explanation of the public’s response to the displays.


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