scholarly journals Virtual Cell: computational tools for modeling in cell biology

2011 ◽  
Vol 4 (2) ◽  
pp. 129-140 ◽  
Author(s):  
Diana C. Resasco ◽  
Fei Gao ◽  
Frank Morgan ◽  
Igor L. Novak ◽  
James C. Schaff ◽  
...  
Keyword(s):  
Cell Biology ◽  
Computational Tools ◽  
Virtual Cell

scholarly journals Computational Tools for Stem Cell Biology

2016 ◽  
Vol 34 (12) ◽  
pp. 993-1009 ◽  
Author(s):  
Qin Bian ◽  
Patrick Cahan
Keyword(s):  
Stem Cell ◽  
Cell Biology ◽  
Stem Cell Biology ◽  
Computational Tools

Quantitative cell biology with the Virtual Cell☆

2003 ◽  
Vol 13 (11) ◽  
pp. 570-576 ◽  
Author(s):  
Boris M. Slepchenko ◽  
James C. Schaff ◽  
Ian Macara ◽  
Leslie M. Loew
Keyword(s):  
Cell Biology ◽  
Virtual Cell

scholarly journals The Dawn of Virtual Cell Biology

Cell ◽  
2012 ◽  
Vol 150 (2) ◽  
pp. 248-250 ◽  
Author(s):  
Peter L. Freddolino ◽  
Saeed Tavazoie
Keyword(s):  
Cell Biology ◽  
Virtual Cell

scholarly journals From imaging a single cell to implementing precision medicine: an exciting new era

2021 ◽  
Author(s):  
Loukia G. Karacosta
Keyword(s):  
Precision Medicine ◽  
Single Cell ◽  
High Throughput ◽  
Cell Biology ◽  
Cell Imaging ◽  
Machine Learning Algorithms ◽  
Biomedical Sciences ◽  
Computational Tools ◽  
New Era ◽  
Single Cell Imaging

In the age of high-throughput, single-cell biology, single-cell imaging has evolved not only in terms of technological advancements but also in its translational applications. The synchronous advancements of imaging and computational biology have produced opportunities of merging the two, providing the scientific community with tools towards observing, understanding, and predicting cellular and tissue phenotypes and behaviors. Furthermore, multiplexed single-cell imaging and machine learning algorithms now enable patient stratification and predictive diagnostics of clinical specimens. Here, we provide an overall summary of the advances in single-cell imaging, with a focus on high-throughput microscopy phenomics and multiplexed proteomic spatial imaging platforms. We also review various computational tools that have been developed in recent years for image processing and downstream applications used in biomedical sciences. Finally, we discuss how harnessing systems biology approaches and data integration across disciplines can further strengthen the exciting applications and future implementation of single-cell imaging on precision medicine.

Ultrastructure of Some Planktonic Formainifera

1974 ◽  
Vol 32 ◽  
pp. 190-191
Author(s):  
William H. Zucker
Keyword(s):  
Cell Biology ◽  
Water Mass ◽  
Planktonic Foraminifera ◽  
Uranyl Acetate ◽  
Ethanol Dehydration ◽  
Globigerinoides Ruber ◽  
Light Microscope Level ◽  
Globigerina Bulloides ◽  
Glutaraldehyde Solution ◽  
Diamond Knife

Planktonic foraminifera are widely-distributed and abundant zooplankters. They are significant as water mass indicators and provide evidence of paleotemperatures and events which occurred during Pleistocene glaciation. In spite of their ecological and paleological significance, little is known of their cell biology. There are few cytological studies of these organisms at the light microscope level and some recent reports of their ultrastructure.Specimens of Globigerinoides ruber, Globigerina bulloides, Globigerinoides conglobatus and Globigerinita glutinata were collected in Bermuda waters and fixed in a cold cacodylate-buffered 6% glutaraldehyde solution for two hours. They were then rinsed, post-fixed in Palade's fluid, rinsed again and stained with uranyl acetate. This was followed by graded ethanol dehydration, during which they were identified and picked clean of debris. The specimens were finally embedded in Epon 812 by placing each organism in a separate BEEM capsule. After sectioning with a diamond knife, stained sections were viewed in a Philips 200 electron microscope.

Introduction

1978 ◽  
Vol 36 (3) ◽  
pp. 543-544
Author(s):  
W. Bernard
Keyword(s):  
Molecular Weight ◽  
Electron Microscope ◽  
Nucleic Acid ◽  
Gene Mapping ◽  
Molecular Genetics ◽  
Cell Biology ◽  
Gene Activity ◽  
Close Connection ◽  
Basic Information ◽  
Simple Systems

In comparison to many other fields of ultrastructural research in Cell Biology, the successful exploration of genes and gene activity with the electron microscope in higher organisms is a late conquest. Nucleic acid molecules of Prokaryotes could be successfully visualized already since the early sixties, thanks to the Kleinschmidt spreading technique - and much basic information was obtained concerning the shape, length, molecular weight of viral, mitochondrial and chloroplast nucleic acid. Later, additonal methods revealed denaturation profiles, distinction between single and double strandedness and the use of heteroduplexes-led to gene mapping of relatively simple systems carried out in close connection with other methods of molecular genetics.

Application of FRAP and digitized fluorescence microscopy to problems in cell membrane dynamics

1988 ◽  
Vol 46 ◽  
pp. 118-119
Author(s):  
K. Jacobson ◽  
A. Ishihara ◽  
B. Holifield ◽  
F. Zhang
Keyword(s):  
Fluorescence Microscopy ◽  
Cell Biology ◽  
Extended Period ◽  
Dynamic Structure ◽  
Living Cells ◽  
Membrane Dynamics ◽  
Molecular Cell Biology ◽  
Image Averaging ◽  
Single Living Cells ◽  
Single Living

Our laboratory is concerned with understanding the dynamic structure of the plasma membrane with particular reference to the movement of membrane constituents during cell locomotion. In addition to the standard tools of molecular cell biology, we employ both fluorescence recovery after photo- bleaching (FRAP) and digitized fluorescence microscopy (DFM) to investigate individual cells. FRAP allows the measurement of translational mobility of membrane and cytoplasmic molecules in small regions of single, living cells. DFM is really a new form of light microscopy in that the distribution of individual classes of ions, molecules, and macromolecules can be followed in single, living cells. By employing fluorescent antibodies to defined antigens or fluorescent analogs of cellular constituents as well as ultrasensitive, electronic image detectors and video image averaging to improve signal to noise, fluorescent images of living cells can be acquired over an extended period without significant fading and loss of cell viability.

Correlative microscopy in distrubuted (client/server) computing environments: tools for catalyzing the rapid dissemination of information about the cell biology of the human prostate

1995 ◽  
Vol 53 ◽  
pp. 682-683
Author(s):  
A. Hakam ◽  
J.T. Gau ◽  
M.L. Grove ◽  
B.A. Evans ◽  
M. Shuman ◽  
...  
Keyword(s):  
United States ◽  
Cell Biology ◽  
Tissue Bank ◽  
The United States ◽  
Prostate Adenocarcinoma ◽  
Correlative Microscopy ◽  
Client Server ◽  
Critical Elements ◽  
Transplant Organ

Prostate adenocarcinoma is the most common malignant tumor of men in the United States and is the third leading cause of death in men. Despite attempts at early detection, there will be 244,000 new cases and 44,000 deaths from the disease in the United States in 1995. Therapeutic progress against this disease is hindered by an incomplete understanding of prostate epithelial cell biology, the availability of human tissues for in vitro experimentation, slow dissemination of information between prostate cancer research teams and the increasing pressure to “ stretch” research dollars at the same time staff reductions are occurring.To meet these challenges, we have used the correlative microscopy (CM) and client/server (C/S) computing to increase productivity while decreasing costs. Critical elements of our program are as follows:1) Establishing the Western Pennsylvania Genitourinary (GU) Tissue Bank which includes >100 prostates from patients with prostate adenocarcinoma as well as >20 normal prostates from transplant organ donors.

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