scholarly journals Exploiting Generative Self-Supervised Learning For The Assessment of Biological Images With Lack of Annotations: A COVID-19 Case-Study

2021 ◽  
Author(s):  
Alessio Mascolini ◽  
Dario Cardamone ◽  
Francesco Ponzio ◽  
Santa Di Cataldo ◽  
Elisa Ficarra
Keyword(s):  
Cell Lines ◽  
Large Scale ◽  
Representation Learning ◽  
Cell Types ◽  
Learning Task ◽  
Generative Adversarial Networks ◽  
Support Vector ◽  
Biological Images ◽  
Compound Screening

Abstract Computer-aided analysis of biological images typically requires extensive training on large-scale annotated datasets, which is not viable in many situations. In this paper, we present GAN-DL, a Discriminator Learner based on the StyleGAN2 architecture, which we employ for self-supervised image representation learning in the case of fluorescent biological images. We show that Wasserstein Generative Adversarial Networks combined with linear Support Vector Machines enable high-throughput compound screening based on raw images. We demonstrate this by classifying active and inactive compounds tested for the inhibition of SARS-CoV-2 infection in VERO and HRCE cell lines. In contrast to previous methods, our deep learning-based approach does not require any annotation besides the one that is normally collected during the sample preparation process. We test our technique on the RxRx19a Sars-CoV-2 image collection. The dataset consists of fluorescent images that were generated to assess the ability of regulatory-approved or late-stage clinical trials compounds to modulate the in vitro infection from SARS-CoV-2 in both VERO and HRCE cell lines. We show that our technique can be exploited not only for classification tasks but also to effectively derive a dose-response curve for the tested treatments, in a self-supervised manner. Lastly, we demonstrate its generalization capabilities by successfully addressing a zero-shot learning task, consisting of the categorization of four different cell types of the RxRx1 fluorescent images collection.

scholarly journals Expression of the Metalloproteinase ADAM8 Is Upregulated in Liver Inflammation Models and Enhances Cytokine Release In Vitro

2021 ◽  
Vol 2021 ◽  
pp. 1-17
Author(s):  
Tanzeela Awan ◽  
Aaron Babendreyer ◽  
Justyna Wozniak ◽  
Abid Mahmood Alvi ◽  
Viktor Sterzer ◽  
...  
Keyword(s):  
Cell Lines ◽  
Inflammatory Mediators ◽  
Liver Tissue ◽  
Stellate Cell ◽  
Hepatoma Cell ◽  
Cell Types ◽  
Chronic Liver ◽  
Liver Inflammation ◽  
Tnf Α

Acute and chronic liver inflammation is driven by cytokine and chemokine release from various cell types in the liver. Here, we report that the induction of inflammatory mediators is associated with a yet undescribed upregulation of the metalloproteinase ADAM8 in different murine hepatitis models. We further show the importance of ADAM8 expression for the production of inflammatory mediators in cultured liver cells. As a model of acute inflammation, we investigated liver tissue from lipopolysaccharide- (LPS-) treated mice in which ADAM8 expression was markedly upregulated compared to control mice. In vitro, stimulation with LPS enhanced ADAM8 expression in murine and human endothelial and hepatoma cell lines as well as in primary murine hepatocytes. The enhanced ADAM8 expression was associated with an upregulation of TNF-α and IL-6 expression and release. Inhibition studies indicate that the cytokine response of hepatoma cells to LPS depends on the activity of ADAM8 and that signalling by TNF-α can contribute to these ADAM8-dependent effects. The role of ADAM8 was further confirmed with primary hepatocytes from ADAM8 knockout mice in which TNF-α and IL-6 induction and release were considerably attenuated. As a model of chronic liver injury, we studied liver tissue from mice undergoing high-fat diet-induced steatohepatitis and again observed upregulation of ADAM8 mRNA expression compared to healthy controls. In vitro, ADAM8 expression was upregulated in hepatoma, endothelial, and stellate cell lines by various mediators of steatohepatitis including fatty acid (linoleic-oleic acid), IL-1β, TNF-α, IFN-γ, and TGF-β. Upregulation of ADAM8 was associated with the induction and release of proinflammatory cytokines (TNF-α and IL-6) and chemokines (CX3CL1). Finally, knockdown of ADAM8 expression in all tested cell types attenuated the release of these mediators. Thus, ADAM8 is upregulated in acute and chronic liver inflammation and is able to promote inflammation by enhancing expression and release of inflammatory mediators.

scholarly journals Modulating cell state to enhance suspension expansion of human pluripotent stem cells

2018 ◽  
Vol 115 (25) ◽  
pp. 6369-6374 ◽  
Author(s):  
Yonatan Y. Lipsitz ◽  
Curtis Woodford ◽  
Ting Yin ◽  
Jacob H. Hanna ◽  
Peter W. Zandstra
Keyword(s):  
Stem Cells ◽  
Pluripotent Stem Cells ◽  
Large Scale ◽  
Cell Types ◽  
Human Pluripotent Stem Cells ◽  
The Body ◽  
Altered Expression ◽  
Pancreatic Progenitors ◽  
Erk Inhibition

The development of cell-based therapies to replace missing or damaged tissues within the body or generate cells with a unique biological activity requires a reliable and accessible source of cells. Human pluripotent stem cells (hPSC) have emerged as a strong candidate cell source capable of extended propagation in vitro and differentiation to clinically relevant cell types. However, the application of hPSC in cell-based therapies requires overcoming yield limitations in large-scale hPSC manufacturing. We explored methods to convert hPSC to alternative states of pluripotency with advantageous bioprocessing properties, identifying a suspension-based small-molecule and cytokine combination that supports increased single-cell survival efficiency, faster growth rates, higher densities, and greater expansion than control hPSC cultures. ERK inhibition was found to be essential for conversion to this altered state, but once converted, ERK inhibition led to a loss of pluripotent phenotype in suspension. The resulting suspension medium formulation enabled hPSC suspension yields 5.7 ± 0.2-fold greater than conventional hPSC in 6 d, for at least five passages. Treated cells remained pluripotent, karyotypically normal, and capable of differentiating into all germ layers. Treated cells could also be integrated into directed differentiated strategies as demonstrated by the generation of pancreatic progenitors (NKX6.1+/PDX1+ cells). Enhanced suspension-yield hPSC displayed higher oxidative metabolism and altered expression of adhesion-related genes. The enhanced bioprocess properties of this alternative pluripotent state provide a strategy to overcome cell manufacturing limitations of hPSC.

scholarly journals Expression of TAL-1 proteins in human tissues

Blood ◽  
1995 ◽  
Vol 85 (3) ◽  
pp. 675-684 ◽  
Author(s):  
K Pulford ◽  
N Lecointe ◽  
K Leroy-Viard ◽  
M Jones ◽  
D Mathieu-Mahul ◽  
...  
Keyword(s):  
Molecular Weight ◽  
T Cell ◽  
Cell Lines ◽  
Fetal Liver ◽  
Cell Types ◽  
Human Tissues ◽  
Aberrant Expression ◽  
Erythroid Precursor ◽  
Normal Human

Rearrangement of the tal-1 gene (also known as SCL or TCL-5) occurs in at least 25% of T-cell acute lymphoblastic leukemias (T-ALLs) and results in the aberrant expression of tal-1 mRNA in the neoplastic cells. Also, tal-1 mRNA is constitutively expressed in erythroid precursors and megakaryocytes. This report describes a direct immunocytochemical study of the distribution and localization of TAL-1 protein in normal human tissues and cell lines using four monoclonal antibodies raised against recombinant TAL-1 proteins. One of these reagents recognizes a protein of 41 kD molecular weight in in vitro- translated TAL-1 proteins, two others recognize proteins of 39 and 41 kD molecular weight, and the fourth antibody also recognizes a TAL-1 protein of 22 kD in addition to the 39- and 41-kD proteins. These anti- TAL-1 antibodies label the nuclei of erythroid precursor cells and megakaryocytes in fetal liver and adult bone marrow. The punctate pattern of nuclear labeling suggests that TAL-1 may comprise part of a novel nuclear structure, similar to that recently found for the PML protein. The nuclei of T cell lines known to express mRNA encoding the full-length TAL-1 protein (eg, CCRF-CEM, RPMI 8402, and Jurkat) are also labeled. A study of normal human tissues (including thymus) showed labeling of smooth muscle, some tissue macrophages, and endothelial cells. TAL-1 protein is undetectable in other cell types. These reagents may play an important role in the diagnosis of T-ALL and could also be used in the context of lymphoma diagnosis on routinely fixed material.

scholarly journals In Vitro Cytotoxicity Induced by the Bufadienolides 1α,2α-Epoxyscillirosidine and Lanceotoxin B on Rat Myocardial and Mouse Neuroblastoma Cell Lines

Toxins ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 14 ◽  
Author(s):  
Danielle Henn ◽  
Annette Venter ◽  
Christo Botha
Keyword(s):  
Cell Lines ◽  
Neuroblastoma Cell ◽  
Cell Types ◽  
Cell Ultrastructure ◽  
In Vitro Cytotoxicity ◽  
Cytoplasmic Material ◽  
Mouse Neuroblastoma ◽  
Transmission Electron ◽  
Half Maximal Effective Concentration

Consumption of bufadienolide-containing plants are responsible for many livestock mortalities annually. Bufadienolides are divided into two groups; non-cumulative bufadienolides and cumulative bufadienolides. Cumulative bufadienolides are referred to as neurotoxic, as the chronic intoxication with this type of bufadienolide results in a paretic/paralytic syndrome known as ‘krimpsiekte’. The in vitro cytotoxicity of a non-cumulative bufadienolide, 1α,2α-epoxyscillirosidine, and a cumulative bufadienolide, lanceotoxin B, were compared using the MTT ((3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide reduction) assay after exposing rat myocardial (H9c2) and mouse neuroblastoma (Neuro-2a) cell lines. The effect of these two bufadienolides on cell ultrastructure was also investigated using transmission electron microscopy (TEM). H9c2 cells exhibited greater cytotoxicity when exposed to 1α,2α-epoxyscillirosidine, compared to lanceotoxin B. In contrast, Neuro-2a cells were more susceptible to lanceotoxin B. The EC50 (half maximal effective concentration) of lanceotoxin B exposure of Neuro-2a cells for 24–72 h ranged from 4.4–5.5 µM compared to EC50s of 35.7–37.6 µM for 1α,2α-epoxyscillirosidine exposure of Neuro-2a cells over the same period. 1α,2α-Epoxyscillirosidine induced extensive vacuolization in both cell types, with swollen RER (rough endoplasmic reticulum) and perinuclear spaces. Lanceotoxin B caused swelling of the mitochondria and sequestration of cytoplasmic material within autophagic vesicles. These results corroborate the notion that cumulative bufadienolides are neurotoxic.

scholarly journals Perturbation of microRNA signalling by doxorubicin in spermatogonial, Leydig and Sertoli cell lines in vitro

2018 ◽  
Vol 7 (5) ◽  
pp. 760-770 ◽  
Author(s):  
Oluwajoba O. Akinjo ◽  
Timothy W. Gant ◽  
Emma L. Marczylo
Keyword(s):  
Sertoli Cell ◽  
Cell Lines ◽  
Cell Types ◽  
Cell Junctions ◽  
Testicular Toxicity ◽  
Testicular Cell

Doxorubicin-induced testicular toxicity involves perturbation of microRNAs within all three of the main testicular cell types, particularly those involved in germ–Sertoli and Sertoli–Sertoli cell junctions.

The BH3 Mimetic, ABT-737, Is Effective Against Bcl-2 Overexpressing Lymphoid Tumors.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 826-826 ◽  
Author(s):  
Kylie D. Mason ◽  
Cassandra J. Vandenberg ◽  
Mark F. van Delft ◽  
Andrew H. Wei ◽  
Suzanne Cory ◽  
...  
Keyword(s):  
Cell Lines ◽  
Genetic Manipulation ◽  
Single Agent ◽  
B Cell Lymphoma ◽  
Cell Types ◽  
Clinical Samples ◽  
Bh3 Mimetic ◽  
Mouse Lymphoma

Abstract Lymphoid tumors often respond poorly to conventional cytotoxics, a common cause being their impaired sensitivity to apoptosis, such as that caused by Bcl-2 overexpression. A strategy to overcoming this is to use mimics of the natural antagonists of pro-survival Bcl-2, the BH3 only proteins. A promising BH3 mimetic is ABT-737, which targets Bcl-2 and closely related pro-survival proteins. We evaluated its potential utility by testing it on cell lines, clinical samples and on a relevant mouse lymphoma model. We assessed the sensitivity of B cell lymphoma cell lines and primary CLL samples to ABT-737, either alone or in combination. To ascertain its efficacy in vivo, we utilized a mouse model based on the Eμ-myc tumor that is readily transplantable and amenable to genetic manipulation. When syngeneic recipient mice were inoculated with tumors, they develop widespread lymphoma, fatal unless treated by agents such as cyclophosphamide. We found that ABT-737, on its own, was cytotoxic only to a subset of cell lines and primary CLL samples. However, it can synergize potently with agents such as dexamethasone, suggesting that this agent might be useful in combination with currently used chemotherapeutics. In the Eμ myc mouse lymphoma model, treatment with ABT-737 alone did not control the disease as multiple independently derived tumors proved refractory to treatment with this agent. However, ABT-737 was partially effective as a single agent for treating bitransgenic tumors derived from crosses of the Eμmyc and Eμ-bcl-2 transgenic mice. ABT-737 therapy prolonged the survival of recipient mice transplanted with tumors from 30 to 60 days. When combined with a low dose of cyclophosphamide (50mg/kg), long term stable remissions were achieved, which were sustained even longer than control mice treated with much higher doses of cyclophosphamide (300mg/kg). We found that ABT-737 was well tolerated as a single agent and when combined with low doses of cytotoxics such as cyclophosphamide. Thus, ABT-737 may prove to be efficacious for those tumors highly dependent on Bcl-2 for their survival. We found that despite its high affinity for Bcl-2, Bcl-xL and Bcl-w, many cell types proved refractory to ABT-737 as a single agent. We show that this resistance reflects its inability to target another pro-survival relative Mcl-1. Down-regulation of Mcl-1 by several strategies conferred sensitivity to ABT-737. Furthermore, enforced Mcl-1 expression in the Eμmyc/bcl-2 bitransgenic mouse lymphoma model conferred marked resistance as mice transplanted with such tumors died as rapidly as the untreated counterparts. However, enhanced Bcl-2 overexpression on these tumors had little impact on the in vivo response, suggesting that ABT-737 can be utilized even when Bcl-2 is markedly overexpressed. ABT-737 appears to be a promising agent for the clinic. It potently sensitizes certain lymphoid tumors to conventional cytotxics in vitro. The synergy observed between dexamethasone and ABT-737 on some lymphoid lines in culture suggests that it is attractive for clinical testing. Encouragingly, ABT-737 appeared efficacious in vivo against Bcl-2 overexpressing tumors when combined with a reduced dose of cyclophosphamide, suggesting that it will be useful for treating even those Bcl-2-overexpressing tumors that are normally highly chemoresistant.

scholarly journals Binding of YY1 to a site overlapping a weak TATA box is essential for transcription from the uteroglobin promoter in endometrial cells.

1996 ◽  
Vol 16 (11) ◽  
pp. 6398-6407 ◽  
Author(s):  
J Klug ◽  
M Beato
Keyword(s):  
Cell Lines ◽  
Transcription Initiation ◽  
Binding Protein ◽  
Cell Types ◽  
Tata Box ◽  
Initiation Factor ◽  
Clara Cells ◽  
Endometrial Cells ◽  
Tata Box Binding Protein

The gene for rabbit uteroglobin codes for a small calcium-, steroid-, and biphenyl metabolite-binding homodimeric protein which is expressed in a variety of epithelial cell types such as Clara cells (lung) and the glandular and luminal cells of the endometrium. One important region mediating its efficient transcription in a human endometrium-derived cell line, Ishikawa, is centered around a noncanonical TATA box. Two factors, TATA core factor (TCF), expressed in cell lines derived from uteroglobin-expressing tissues, and the ubiquitously expressed TATA palindrome factor, bind to the DNA major groove at two adjacent sites within this region. Here, we report the identification of the TATA palindrome factor as the transcription/initiation factor YY1 by microsequencing of the biochemically purified factor from HeLa cells. The binding site for YY1 within the uteroglobin gene is unique in its sequence and its location overlapping a weak TATA box (TACA). Binding of YY1 was required for efficient transcription in TCF-positive Ishikawa cells, which responded only weakly to a change of TACA to TATA, although in vitro binding affinity for the TATA-box-binding protein increased by 1 order of magnitude. In contrast, in CV-1 cells, lacking TCF, binding of YY1 was not required for transcription in the context of a wild-type TACA box, whereas a change from TACA to TATA led to significantly increased reporter gene expression. DNA binding data exclude a role of YY1 in stabilizing the interaction of the TATA-box-binding protein with the uteroglobin promoter. We conclude that cell lines derived from uteroglobin-expressing tissues overcome the weak TATA box with the help of auxiliary factors, one of them being YY1.

scholarly journals Attachment and invasion ofToxoplasma gondiiandNeospora caninumto epithelial and fibroblast cell linesin vitro

Parasitology ◽  
2005 ◽  
Vol 131 (5) ◽  
pp. 583-590 ◽  
Author(s):  
YING LEI ◽  
M. DAVEY ◽  
J. T. ELLIS
Keyword(s):  
Cell Lines ◽  
Neospora Caninum ◽  
Fibroblast Cell ◽  
Cell Types ◽  
Vero Cells ◽  
Host Cells ◽  
Trypsin Treatment ◽  
Epithelial Cell Lines ◽  
Pre Treatment

Attachment and invasion ofToxoplasma gondiiandNeospora caninumto a cat and a dog fibroblast cell line and 2 epithelial cell lines (a cat kidney and Vero) were comparedin vitrousing fluorescence antibody methodology. In addition, trypsin treatment of tachyzoites was used to determine whether protein molecules were essential to the process of invasion. The results show that bothT. gondiiandN. caninuminvaded all 4 cell lines, and that pre-treatment ofT. gondiitachyzoites with trypsin caused an increase in the ability of the parasite to invade these host cells. FurthermoreT. gondii, in comparison toN. caninum, invaded all 4 cell lines at greater levels. The results here support the conclusion that bothT. gondiiandN. caninumhave the ability to invade a variety of cell types including both dog and cat cells, and questions the utility of Vero cells as an appropriate host cell forin vitrostudies on the biology of these taxa.

scholarly journals Characterization of primary cilia features reveal cell-type specific variability in in vitro models of osteogenic and chondrogenic differentiation

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9799
Author(s):  
Priyanka Upadhyai ◽  
Vishal Singh Guleria ◽  
Prajna Udupa
Keyword(s):  
Cell Lines ◽  
Chondrogenic Differentiation ◽  
Primary Cilia ◽  
Molecular Mechanisms ◽  
Current Knowledge ◽  
Cell Types ◽  
Treatment Modalities ◽  
Cell Type ◽  
Cell Type Specific

Primary cilia are non-motile sensory antennae present on most vertebrate cell surfaces. They serve to transduce and integrate diverse external stimuli into functional cellular responses vital for development, differentiation and homeostasis. Ciliary characteristics, such as length, structure and frequency are often tailored to distinct differentiated cell states. Primary cilia are present on a variety of skeletal cell-types and facilitate the assimilation of sensory cues to direct skeletal development and repair. However, there is limited knowledge of ciliary variation in response to the activation of distinct differentiation cascades in different skeletal cell-types. C3H10T1/2, MC3T3-E1 and ATDC5 cells are mesenchymal stem cells, preosteoblast and prechondrocyte cell-lines, respectively. They are commonly employed in numerous in vitro studies, investigating the molecular mechanisms underlying osteoblast and chondrocyte differentiation, skeletal disease and repair. Here we sought to evaluate the primary cilia length and frequencies during osteogenic differentiation in C3H10T1/2 and MC3T3-E1 and chondrogenic differentiation in ATDC5 cells, over a period of 21 days. Our data inform on the presence of stable cilia to orchestrate signaling and dynamic alterations in their features during extended periods of differentiation. Taken together with existing literature these findings reflect the occurrence of not only lineage but cell-type specific variation in ciliary attributes during differentiation. These results extend our current knowledge, shining light on the variabilities in primary cilia features correlated with distinct differentiated cell phenotypes. It may have broader implications in studies using these cell-lines to explore cilia dependent cellular processes and treatment modalities for skeletal disorders centered on cilia modulation.

Sign in / Sign up

Export Citation Format

Share Document