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Article ; Online: Automated 3D scoring of fluorescence in situ hybridization (FISH) using a confocal whole slide imaging scanner.

Frankenstein, Ziv / Uraoka, Naohiro / Aypar, Umut / Aryeequaye, Ruth / Rao, Mamta / Hameed, Meera / Zhang, Yanming / Yagi, Yukako

Applied microscopy

2021 Volume 51, Issue 1, Page(s) 4

Abstract: Fluorescence in situ hybridization (FISH) is a technique to visualize specific DNA/RNA sequences within the cell nuclei and provide the presence, location and structural integrity of genes on chromosomes. A confocal Whole Slide Imaging (WSI) scanner ... ...

Abstract	Fluorescence in situ hybridization (FISH) is a technique to visualize specific DNA/RNA sequences within the cell nuclei and provide the presence, location and structural integrity of genes on chromosomes. A confocal Whole Slide Imaging (WSI) scanner technology has superior depth resolution compared to wide-field fluorescence imaging. Confocal WSI has the ability to perform serial optical sections with specimen imaging, which is critical for 3D tissue reconstruction for volumetric spatial analysis. The standard clinical manual scoring for FISH is labor-intensive, time-consuming and subjective. Application of multi-gene FISH analysis alongside 3D imaging, significantly increase the level of complexity required for an accurate 3D analysis. Therefore, the purpose of this study is to establish automated 3D FISH scoring for z-stack images from confocal WSI scanner. The algorithm and the application we developed, SHIMARIS PAFQ, successfully employs 3D calculations for clear individual cell nuclei segmentation, gene signals detection and distribution of break-apart probes signal patterns, including standard break-apart, and variant patterns due to truncation, and deletion, etc. The analysis was accurate and precise when compared with ground truth clinical manual counting and scoring reported in ten lymphoma and solid tumors cases. The algorithm and the application we developed, SHIMARIS PAFQ, is objective and more efficient than the conventional procedure. It enables the automated counting of more nuclei, precisely detecting additional abnormal signal variations in nuclei patterns and analyzes gigabyte multi-layer stacking imaging data of tissue samples from patients. Currently, we are developing a deep learning algorithm for automated tumor area detection to be integrated with SHIMARIS PAFQ.
Language	English
Publishing date	2021-04-09
Publishing country	Korea (South)
Document type	Journal Article
ISSN	2287-4445
ISSN (online)	2287-4445
DOI	10.1186/s42649-021-00053-y
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: NSD2 maintains lineage plasticity and castration-resistance in neuroendocrine prostate cancer.

bioRxiv : the preprint server for biology

2023

Abstract: The clinical use of potent androgen receptor (AR) inhibitors has promoted the emergence of novel subtypes of metastatic castration-resistant prostate cancer (mCRPC), including neuroendocrine prostate cancer (CRPC-NE), which is highly aggressive and ... ...

Abstract	The clinical use of potent androgen receptor (AR) inhibitors has promoted the emergence of novel subtypes of metastatic castration-resistant prostate cancer (mCRPC), including neuroendocrine prostate cancer (CRPC-NE), which is highly aggressive and lethal
Language	English
Publishing date	2023-07-19
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.07.18.549585
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Article ; Online: A unique spatial arrangement of the snRNPs within the native spliceosome emerges from in silico studies.

Frankenstein, Ziv / Sperling, Joseph / Sperling, Ruth / Eisenstein, Miriam

Structure (London, England : 1993)

2012 Volume 20, Issue 6, Page(s) 1097–1106

Abstract: The spliceosome is a mega-Dalton ribonucleoprotein (RNP) assembly that processes primary RNA transcripts, producing functional mRNA. The electron microscopy structures of the native spliceosome and of several spliceosomal subcomplexes are available; ... ...

Abstract	The spliceosome is a mega-Dalton ribonucleoprotein (RNP) assembly that processes primary RNA transcripts, producing functional mRNA. The electron microscopy structures of the native spliceosome and of several spliceosomal subcomplexes are available; however, the spatial arrangement of the latter within the native spliceosome is not known. We designed a computational procedure to efficiently fit thousands of conformers into the spliceosome envelope. Despite the low resolution limitations, we obtained only one model that complies with the available biochemical data. Our model localizes the five small nuclear RNPs (snRNPs) mostly within the large subunit of the native spliceosome, requiring only minor conformation changes. The remaining free volume presumably accommodates additional spliceosomal components. The constituents of the active core of the spliceosome are juxtaposed, forming a continuous surface deep within the large spliceosomal cavity, which provides a sheltered environment for the splicing reaction.
MeSH term(s)	Computer Simulation ; Fungal Proteins/chemistry ; Humans ; Models, Molecular ; Protein Interaction Domains and Motifs ; Protein Structure, Quaternary ; Ribonucleoproteins, Small Nuclear/chemistry ; Spliceosomes/chemistry ; Surface Properties
Chemical Substances	Fungal Proteins ; Ribonucleoproteins, Small Nuclear
Language	English
Publishing date	2012-05-10
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1213087-4
ISSN	1878-4186 ; 0969-2126
ISSN (online)	1878-4186
ISSN	0969-2126
DOI	10.1016/j.str.2012.03.022
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Article ; Online: Stromal reactivity differentially drives tumour cell evolution and prostate cancer progression.

Frankenstein, Ziv / Basanta, David / Franco, Omar E / Gao, Yan / Javier, Rodrigo A / Strand, Douglas W / Lee, MinJae / Hayward, Simon W / Ayala, Gustavo / Anderson, Alexander R A

Nature ecology & evolution

2020 Volume 4, Issue 6, Page(s) 870–884

Abstract: Prostate cancer (PCa) progression is a complex eco-evolutionary process driven by the feedback between evolving tumour cell phenotypes and microenvironmentally driven selection. To better understand this relationship, we used a multiscale mathematical ... ...

Abstract	Prostate cancer (PCa) progression is a complex eco-evolutionary process driven by the feedback between evolving tumour cell phenotypes and microenvironmentally driven selection. To better understand this relationship, we used a multiscale mathematical model that integrates data from biology and pathology on the microenvironmental regulation of PCa cell behaviour. Our data indicate that the interactions between tumour cells and their environment shape the evolutionary dynamics of PCa cells and explain overall tumour aggressiveness. A key environmental determinant of this aggressiveness is the stromal ecology, which can be either inhibitory, highly reactive (supportive) or non-reactive (neutral). Our results show that stromal ecology correlates directly with tumour growth but inversely modulates tumour evolution. This suggests that aggressive, environmentally independent PCa may be a result of poor stromal ecology, supporting the concept that purely tumour epithelium-centric metrics of aggressiveness may be incomplete and that incorporating markers of stromal ecology would improve prognosis.
MeSH term(s)	Humans ; Male ; Prostatic Neoplasms ; Stromal Cells
Language	English
Publishing date	2020-05-11
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	2397-334X
ISSN (online)	2397-334X
DOI	10.1038/s41559-020-1157-y
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Article ; Online: The immune-body cytokine network defines a social architecture of cell interactions

Alon Uri / Frankenstein Ziv / Cohen Irun R

Biology Direct, Vol 1, Iss 1, p

2006 Volume 32

Abstract: Abstract Background Three networks of intercellular communication can be associated with cytokine secretion; one limited to cells of the immune system (immune cells), one limited to parenchymal cells of organs and tissues (body cells), and one involving ... ...

Abstract	Abstract Background Three networks of intercellular communication can be associated with cytokine secretion; one limited to cells of the immune system (immune cells), one limited to parenchymal cells of organs and tissues (body cells), and one involving interactions between immune and body cells (immune-body interface). These cytokine connections determine the inflammatory response to injury and subsequent healing as well as the biologic consequences of the adaptive immune response to antigens. We informatically probed the cytokine database to uncover the underlying network architecture of the three networks. Results We now report that the three cytokine networks are among the densest of complex networks yet studied, and each features a characteristic profile of specific three-cell motifs. Some legitimate cytokine connections are shunned (anti-motifs). Certain immune cells can be paired by their input-output positions in a cytokine architecture tree of five tiers: macrophages (MΦ) and B cells (BC) comprise the first tier; the second tier is formed by T helper 1 (Th1) and T helper 2 (Th2) cells; the third tier includes dendritic cells (DC), mast cells (MAST), Natural Killer T cells (NK-T) and others; the fourth tier is formed by neutrophils (NEUT) and Natural Killer cells (NK); and the Cytotoxic T cell (CTL) stand alone as a fifth tier. The three-cell cytokine motif architecture of immune system cells places the immune system in a super-family that includes social networks and the World Wide Web. Body cells are less clearly stratified, although cells involved in wound healing and angiogenesis are most highly interconnected with immune cells. Conclusion Cytokine network architecture creates an innate cell-communication platform that organizes the biologic outcome of antigen recognition and inflammation. Informatics sheds new light on immune-body systems organization. Reviewers This article was reviewed by Neil Greenspan, Matthias von Herrath and Anne Cooke.
Keywords	Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2006-10-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: FitEM2EM--tools for low resolution study of macromolecular assembly and dynamics.

Frankenstein, Ziv / Sperling, Joseph / Sperling, Ruth / Eisenstein, Miriam

PloS one

2008 Volume 3, Issue 10, Page(s) e3594

Abstract: Studies of the structure and dynamics of macromolecular assemblies often involve comparison of low resolution models obtained using different techniques such as electron microscopy or atomic force microscopy. We present new computational tools for ... ...

Abstract	Studies of the structure and dynamics of macromolecular assemblies often involve comparison of low resolution models obtained using different techniques such as electron microscopy or atomic force microscopy. We present new computational tools for comparing (matching) and docking of low resolution structures, based on shape complementarity. The matched or docked objects are represented by three dimensional grids where the value of each grid point depends on its position with regard to the interior, surface or exterior of the object. The grids are correlated using fast Fourier transformations producing either matches of related objects or docking models depending on the details of the grid representations. The procedures incorporate thickening and smoothing of the surfaces of the objects which effectively compensates for differences in the resolution of the matched/docked objects, circumventing the need for resolution modification. The presented matching tool FitEM2EMin successfully fitted electron microscopy structures obtained at different resolutions, different conformers of the same structure and partial structures, ranking correct matches at the top in every case. The differences between the grid representations of the matched objects can be used to study conformation differences or to characterize the size and shape of substructures. The presented low-to-low docking tool FitEM2EMout ranked the expected models at the top.
MeSH term(s)	Animals ; Humans ; Kinetics ; Macromolecular Substances/chemistry ; Macromolecular Substances/metabolism ; Models, Molecular ; Protein Interaction Mapping/methods ; Protein Structure, Quaternary ; Sensitivity and Specificity ; Software
Chemical Substances	Macromolecular Substances
Language	English
Publishing date	2008
Publishing country	United States
Document type	Evaluation Studies ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0003594
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: CAPRI targets T29-T42: proving ground for new docking procedures.

Eisenstein, Miriam / Ben-Shimon, Avraham / Frankenstein, Ziv / Kowalsman, Noga

Proteins

2010 Volume 78, Issue 15, Page(s) 3174–3181

Abstract: The critical assessment of protein interactions (CAPRI) experiment provides a unique opportunity for unbiased assessment of docking procedures. The recent CAPRI targets T29-T42 entailed docking of bound, unbound, and modeled structures, presenting a wide ...

Abstract	The critical assessment of protein interactions (CAPRI) experiment provides a unique opportunity for unbiased assessment of docking procedures. The recent CAPRI targets T29-T42 entailed docking of bound, unbound, and modeled structures, presenting a wide range of prediction difficulty. We submitted accurate predictions for targets T40, T41, and T42, a good prediction for T32 and acceptable predictions for T29 and T34. The accuracy of our docking results generally matched the prediction difficulty; hence, docking of modeled proteins produced less accurate results. However, there were interesting exceptions: an accurate prediction was submitted for the dimer of modeled tetratricopeptide repeat (T42) and only an acceptable prediction for the bound/unbound case T29. The ensembles of docking models produced in the scans included an acceptable or better prediction for every target. We show here that our recently developed postscan reevaluation procedure, which tests propensity and solvation measures of the whole interface and the interface core, successfully distinguished these predictions from false docking models. For enzyme-inhibitor targets, we show that the distance of the interface from the enzyme's centroid ranked high native like docking models. Also, for one case we demonstrate that docking of an ensemble of conformers produced by normal modes analysis can improve the accuracy of the prediction.
MeSH term(s)	Computational Biology/methods ; Models, Chemical ; Models, Molecular ; Models, Statistical ; Protein Binding ; Protein Conformation ; Protein Interaction Mapping/methods ; Proteins/chemistry ; Proteins/metabolism ; Software
Chemical Substances	Proteins
Language	English
Publishing date	2010-11-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	806683-8
ISSN	1097-0134 ; 0887-3585
ISSN (online)	1097-0134
ISSN	0887-3585
DOI	10.1002/prot.22793
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Article ; Online: The immune-body cytokine network defines a social architecture of cell interactions.

Frankenstein, Ziv / Alon, Uri / Cohen, Irun R

Biology direct

2006 Volume 1, Page(s) 32

Abstract: Background: Three networks of intercellular communication can be associated with cytokine secretion; one limited to cells of the immune system (immune cells), one limited to parenchymal cells of organs and tissues (body cells), and one involving ... ...

Abstract	Background: Three networks of intercellular communication can be associated with cytokine secretion; one limited to cells of the immune system (immune cells), one limited to parenchymal cells of organs and tissues (body cells), and one involving interactions between immune and body cells (immune-body interface). These cytokine connections determine the inflammatory response to injury and subsequent healing as well as the biologic consequences of the adaptive immune response to antigens. We informatically probed the cytokine database to uncover the underlying network architecture of the three networks. Results: We now report that the three cytokine networks are among the densest of complex networks yet studied, and each features a characteristic profile of specific three-cell motifs. Some legitimate cytokine connections are shunned (anti-motifs). Certain immune cells can be paired by their input-output positions in a cytokine architecture tree of five tiers: macrophages (MPhi) and B cells (BC) comprise the first tier; the second tier is formed by T helper 1 (Th1) and T helper 2 (Th2) cells; the third tier includes dendritic cells (DC), mast cells (MAST), Natural Killer T cells (NK-T) and others; the fourth tier is formed by neutrophils (NEUT) and Natural Killer cells (NK); and the Cytotoxic T cell (CTL) stand alone as a fifth tier. The three-cell cytokine motif architecture of immune system cells places the immune system in a super-family that includes social networks and the World Wide Web. Body cells are less clearly stratified, although cells involved in wound healing and angiogenesis are most highly interconnected with immune cells. Conclusion: Cytokine network architecture creates an innate cell-communication platform that organizes the biologic outcome of antigen recognition and inflammation. Informatics sheds new light on immune-body systems organization. Reviewers: This article was reviewed by Neil Greenspan, Matthias von Herrath and Anne Cooke.
Language	English
Publishing date	2006-10-24
Publishing country	England
Document type	Journal Article
ISSN	1745-6150
ISSN (online)	1745-6150
DOI	10.1186/1745-6150-1-32
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Article ; Online: Variable internal flexibility characterizes the helical capsid formed by agrobacterium VirE2 protein on single-stranded DNA.

Bharat, Tanmay A M / Zbaida, David / Eisenstein, Miriam / Frankenstein, Ziv / Mehlman, Tevie / Weiner, Lev / Sorzano, Carlos Oscar S / Barak, Yoav / Albeck, Shira / Briggs, John A G / Wolf, Sharon G / Elbaum, Michael

Structure (London, England : 1993)

2013 Volume 21, Issue 7, Page(s) 1158–1167

Abstract: Agrobacterium is known for gene transfer to plants. In addition to a linear ssDNA oligonucleotide, Agrobacterium tumefaciens secretes an abundant ssDNA-binding effector, VirE2. In many ways VirE2 adapts the conjugation mechanism to transform the ... ...

Abstract	Agrobacterium is known for gene transfer to plants. In addition to a linear ssDNA oligonucleotide, Agrobacterium tumefaciens secretes an abundant ssDNA-binding effector, VirE2. In many ways VirE2 adapts the conjugation mechanism to transform the eukaryotic host. The crystal structure of VirE2 shows two compact domains joined by a flexible linker. Bound to ssDNA, VirE2 forms an ordered solenoidal shell, or capsid known as the T-complex. Here, we present a three-dimensional reconstruction of the VirE2-ssDNA complex using cryo-electron microscopy and iterative helical real-space reconstruction. High-resolution refinement was not possible due to inherent heterogeneity in the protein structure. By a combination of computational modeling, chemical modifications, mass spectroscopy, and electron paramagnetic resonance, we found that the N-terminal domain is tightly constrained by both tangential and longitudinal links, while the C terminus is weakly constrained. The quaternary structure is thus rigidly assembled while remaining locally flexible. This flexibility may be important in accommodating substrates without sequence specificity.
MeSH term(s)	Agrobacterium tumefaciens/ultrastructure ; Bacterial Proteins/chemistry ; Bacterial Proteins/ultrastructure ; Cryoelectron Microscopy ; DNA, Bacterial/chemistry ; DNA, Single-Stranded/chemistry ; DNA-Binding Proteins/chemistry ; DNA-Binding Proteins/ultrastructure ; Electron Spin Resonance Spectroscopy ; Ion Channels/chemistry ; Ion Channels/ultrastructure ; Kinetics ; Models, Molecular ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Protein Structure, Quaternary
Chemical Substances	Bacterial Proteins ; DNA, Bacterial ; DNA, Single-Stranded ; DNA-Binding Proteins ; Ion Channels ; virE2 protein, Agrobacterium
Language	English
Publishing date	2013-07-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1213087-4
ISSN	1878-4186 ; 0969-2126
ISSN (online)	1878-4186
ISSN	0969-2126
DOI	10.1016/j.str.2013.04.027
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