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2004 International Conference on Image Processing, ICIP 2004

作者： Kasson, Peter M. Huppa, Johannes B. Davis, Mark M. Brunger, Axel T. Biophysics Program Stanford CA 94305 Medical Scientist Training Program Stanford CA 94305 Department of Molecular and Cellular Physiology Stanford CA 94305 Department of Microbiology and Immunology Stanford CA 94305 Stanford Synchrotron Radiation Laboratory Stanford University Stanford CA 94305 Howard Hughes Medical Institute Stanford CA 94305

The relocalization of plasma membrane proteins is critical for establishing cellular polarity and regulating cell signaling. Three-dimensional fluorescence video microscopy allows the dynamic visualization of proteins in living cells. We have developed a robust and automated method to employ fluorescence data acquired in this manner for quantitative analysis of membrane protein movements across the cell surface. Our method utilizes level-set-based surface reconstruction followed by a maximum likelihood surface registration algorithm for rigid-body alignment of noisy images. A surface-walking technique yields distance maps for the cell surface, which are then used to measure changes in protein surface distribution over time. Applying this method to signaling in T lymphocytes, we have used it to monitor receptor movements and have validated these results against previously reported single-particle tracking data. ©2004 IEEE.

关键词： Proteins

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A New Thread in an Intricate Web

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Science 2001年第5548期294卷 1845-1847页

作者： Mark von Zastrow Keith Mostov The authors are in the Program in Cell Biology Departments of Psychiatry Cellular and Molecular Pharmacology Anatomy and Biochemistry and Biophysics University of California San Francisco CA 94143 USA.

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Altered expression patterns of syndecan-1 and ,2 predicl biochemical recurrence in prostate cancer

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Asian Journal of Andrology 2011年第3期13卷 476-480,514页

作者： Rodrigo Ledezma Federico Cifuentes Ivan Gallegos Juan Fulla Enrique Ossandon Enrique A Castellon Hector R Contreras Laboratory of Molecular and Cellular Andrology Physiology and Biophysics Program. Institute of Biomedical Sciences Faculty of Medicine University of Chile Santiago 70005 Chile pathology Service Clinic Hospital University of Chile Santiago 70005 Chile Urology Service Clinic Hospital University of Chile Santiago 70005 Chile

The clinical features of prostate cancer do not provide an accurate determination of patients undergoing biochemical relapse and are therefore not suitable as indicators of prognosis for recurrence. New molecular markers are needed for proper pre-treatment risk stratification of patients. Our aim was to assess the value of altered expression of syndecan-1 and -2 as a marker for predicting biochemical relapse in patients with clinically localized prostate cancer treated by radical prostatectomy. The expression of syndecan-1 and -2 was examined by immunohistochemical staining in a series of 60 paraffin-embedded tissue samples from patients with localized prostate cancer. Ten specimens from patients with benign prostatic hyperplasia were used as non-malignant controls. Semiquantitative analysis was performed to evaluate the staining patterns. To investigate the prognostic value, Kaplan-Meier survival curves were performed and compared by a log-rank test. In benign samples, syndecan-1 was expressed in basal and secretory epithelial cells with basolateral membrane Iocalisation, whereas syndecan-2 was expressed preferentially in basal cells. In prostate cancer samples, the expression patterns of both syndecans shifted to granular-cytoplasmic Iocalisation. Survival analysis showed a significant difference （P〈0.05） between normal and altered expression of syndecan-1 and -2 in free prostate-specific antigen recurrence survival curves. These data suggest that the expression of syndecan-1 and -2 can be used as a prognostic marker for patients with clinically localized orostate cancer, improving the larostate-specific antigen recurrence risk stratification.

关键词： biochemical recurrence prostate cancer syndecans

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Expression Analysis of miRNAs and Highly-expressed Small RNAs in Two Rice Subspecies and their Reciprocal Hybrids

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Journal of Integrative Plant Biology 2010年第11期52卷 971-980页

作者： Fangfang Chen Guangming He Hang He Wei Chen Xiaopeng Zhu Manzhong Liang Liangbi Chen Xing Wang Deng Graduate Program in Chinese Academy of Medical Sciences and Peking Union Medical College Beijing 100730China National Institute of Biological Sciences Zhongguancun Life Science ParkBeijing 102206China Department of Molecular Cellular and Developmental BiologyYale UniversityNew HavenConnecticut 06520USA Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology College of Life SciencesPeking UniversityBeijing 100871China Institute of Biophysics the Chinese Academy of SciencesBeijing 100101China Department of Botany College of Life SciencesHunan Normal UniversityChangsha 410081China

Heterosis,or hybrid vigor,is the phenomenon whereby progeny of two inbred lines exhibit superior agronomic performance compared with either *** analyzed the expression of miRNAs and highly expressed small RNAs （defined according to Solexa sequencing results） in two rice （Oryza sativa） subspecies （japonica *** and indica cv.93-11） and their reciprocal hybrids using *** found that of all the 1141 small RNAs tested,140 （12%,140 of 1141） and 157 （13%,157 of 1141） were identified being significantly differentially expressed in two reciprocal hybrids,*** possible modes of action,including additive,high-and low-parent,above high-and below low-parent modes were *** F1 hybrids showed non-additive expression patterns,with downregulation ***,15 miRNAs displayed stark opposite expression trends relative to midparent in reciprocal *** prediction of targets of differentially expressed miRNAs showed that they participated in multifaceted developmental pathways,and were not distinguishable from the targets of non-differentially expressed ***,our findings reveal that small RNAs play roles in heterosis and add a new layer in the understanding and exploitation of molecular mechanisms of heterosis.

关键词： HETEROSIS MESSENGER RNA HYBRIDIZATION FERTILITY PLANT growth

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Solution Stucture of the d(T-C-G-A) Duplex at Acidic pH

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Journal of molecular Biology 1994年第4期242卷 508-526页

作者： Yong Wang Dinshaw J. Patel Department of Biochemistry and Molecular Biophysics College of Physicians and Surgeions Columbia University New York NY 10032 U.S.A. Cellular Biochemistry and Biophysics Program Memorial Sloan-Kettering Cancer Center New York NY 10021 U.S.A.

The solution structure of the d(T-C-G-A) sequence at acidic pH has been determined by a combination of NMR and molecular dynamics calculations including NOE intensity based refinements. This sequence forms a right-handed parallel-stranded duplex with C + · C (three hydrogen bonds along Watson-Crick edge), G · G (two symmetry related N 2 -H · · N 3 hydrogen bonds) and A · A (two symmetry related N 6 -H · · N 7 hydrogen bonds) homo base-pair formation at acidic pH. The duplex is stabilized by intra-strand base stacking at the C2-G3 step and cross-strand base stacking at the G3-A4 step. The thymine residues on partner strands are directed towards each other and are positioned over the C + · C base-pair. All four residues adopt anti glycosidic torsion angles and C2′- endo type sugar conformations in the parallel-stranded d(T-C-G-A) duplex which exhibits large changes in twist angles between adjacent steps along the duplex. This study rules out previously proposed models for the structure of the d(T-C-G-A) duplex at acidic pH and supports earlier structural contributions, which established that d(C-G) and d(C-G-A) containing sequences at acidic pH pair through parallel-stranded alignment. We have also monitored hydration patterns in the symmetry related grooves of the parallel-stranded d(T-C-G-A) duplex.

关键词： parallel-stranded DNA duplex homo base mismatches solution structure NMR spectroscopy molecular dynamics refinement

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Matrix confinement modulates 3D spheroid sorting and burst-like collective migration

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Acta Biomaterialia 2024年 179卷 192-206页

作者： Cai, Grace Li, Xinzhi Lin, Shan-Shan Chen, Samuel J. Rodgers, Nicole C. Koning, Katherine M. Bi, Dapeng Liu, Allen P. Applied Physics Program University of Michigan Ann ArborMI United States Department of Physics Carnegie Mellon University PittsburghPA United States Institute of Molecular Medicine College of Medicine National Taiwan University Taipei Taiwan Department of Mechanical Engineering University of Michigan Ann ArborMI United States Cellular and Molecular Biology Program University of Michigan Ann ArborMI United States Department of Physics Northeastern University BostonMA United States Department of Biomedical Engineering University of Michigan Ann ArborMI United States Department of Biophysics University of Michigan Ann ArborMI United States

While it is known that cells with differential adhesion tend to segregate and preferentially sort, the physical forces governing sorting and invasion in heterogeneous tumors remain poorly understood. To investigate this, we tune matrix confinement, mimicking changes in the stiffness and confinement of the tumor microenvironment, to explore how physical confinement influences individual and collective cell migration in 3D spheroids. High levels of confinement lead to cell sorting while reducing matrix confinement triggers the collective fluidization of cell motion. Cell sorting, which depends on cell-cell adhesion, is crucial to this phenomenon. Burst-like migration does not occur for spheroids that have not undergone sorting, regardless of the degree of matrix confinement. Using computational Self-Propelled Voronoi modeling, we show that spheroid sorting and invasion into the matrix depend on the balance between cell-generated forces and matrix resistance. The findings support a model where matrix confinement modulates 3D spheroid sorting and unjamming in an adhesion-dependent manner, providing insights into the mechanisms of cell sorting and migration in the primary tumor and toward distant metastatic sites. Statement of significance: The mechanical properties of the tumor microenvironment significantly influence cancer cell migration within the primary tumor, yet how these properties affect intercellular interactions in heterogeneous tumors is not well understood. By utilizing calcium and calcium chelators, we dynamically alter collagen-alginate hydrogel stiffness and investigate tumor cell behavior within co-culture spheroids in response to varying degrees of matrix confinement. High confinement is found to trigger cell sorting while reducing confinement for sorted spheroids facilitates collective cell invasion. Notably, without prior sorting, spheroids do not exhibit burst-like migration, regardless of confinement levels. This work establishes that matrix confin

关键词： Tumors

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A protein dissection study demonstrates that two specific hydrophobic clusters play a key role in stabilizing the core structure of the molten globule state of human α‐lactalbumin

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Proteins: Structure, Function, and Bioinformatics 2000年第2期42卷 237-242页

作者： Stephen J. Demarest Jia‐Cherng Horng Daniel P. Raleigh Department of Chemistry State University of New York at Stony Brook Stony Brook New York Graduate Program in Biophysics and Graduate Program in Molecular and Cellular Biology State University of New York at Stony Brook Stony Brook New York

The molten globule state of α‐lactalbumin (αLA) has served as a paradigm for understanding the role of these partially folded states in protein folding. We previously showed that a peptide construct consisting of the A and B helices (residues 1–38) cross‐linked to the D‐ and C‐terminal 310 helices (residues 101–120) of αLA is capable of folding to a stable molten globule‐like state. Here, we report the study of three peptide constructs that are designed to investigate the contribution two short hydrophobic sequences located near the C‐terminus of αLA make to the structure and stability of the αLA molten globule state. These regions of the protein have been shown to form stable non‐native structures in isolation. The three peptide constructs contain residues 1–38 cross‐linked to three separate C‐terminal peptides via the native 28–111 disulfide bond. The C‐terminal peptides consist of residues 101–114, 106–120, and 106–114. The results of CD, fluorescence, ANS binding, and urea denaturation experiments indicate that constructs that lack either of the hydrophobic sequences (residues 101–105 and 115–120) are significantly less structured. These results highlight the importance of long‐range, mutually stabilizing interactions within the molten globule state of the protein. Proteins 2001;42:237–242. © 2000 Wiley‐Liss, Inc.

关键词： protein folding α‐lactalbumin molten globule denatured state hydrophobic interactions

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Compressive Stress Enhances Invasive Phenotype of Cancer Cells via Piezo1 Activation

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医用生物力学 2019年第A01期34卷 125-126页

作者： Mingzhi Luo Kenneth KYHo Zhaowen Tong Linhong Deng Allen PLiu Institute of Biomedical Engineering and Health Sciences Changzhou UniversityChangzhouJiangsuChina Department of Mechanical Engineering University of MichiganAnn ArborMichiganUSA Department of Biophysics University of MichiganAnn ArborMichiganUSA Department of Biomedical Engineering University of MichiganAnnArborMichiganUSA Cellular and Molecular Biology Program University of MichiganAnn ArborMichiganUSA

In this study,we hypothesized that Piezo 1 channels mediate the compression-enhanced invasive phenotype of cancer cells via a caveolae-dependent *** test this hypothesis,we examined in vitro cultured human breast cancer cells for their ability to invade and degrade extracellular matrix in the presence or absence of compressive stress,together with corresponding changes in Piezo1 as well as cytoskeletal remodeling and calcium *** we show that compressive stress enhanced invasion,matrix degradation,and invadopodia formation of breast cancer *** further identified Piezo1 as the putative mechanosensitive cellular component that transmits compression to induce calcium influx,which in turn triggers several downstream ***,for the first time we observed inv-adopodia with matrix degradation ability on the apical side of the cells, similar to those commonly observed at the cell s ventral ***,we demonstrate that Piezo1 and caveolae were both involved in mediating the compressive stress-induced cancer cell invasive phenotype as Piezo 1 and caveolae were often colocalized,and reduction of Cav-1 expression or disruption of caveolae with methyl-β-cyclodextrin led to not only reduced Piezo1 expression but also attenuation of the invasive phenotypes promoted by compressive *** together,we first observed that in breast cancer cells,simulating uncontrolled growth-induced compressive stress enhanced cancer cell invasion,matrix degradation,and invadopodia and stress fiber *** study also confirmed that Piezo1 channels are highly expressed in breast cancer cells compared to normal breast cells,and is consistent with the data that compressive stress regulates cell migration of breast cancer cells but not normal breast ***,we identified that Piezol mediated these processes and the invasive phenotypes also depended on the integrity of *** findings provide the first demonstration that compres

关键词： compressive stress caveolae Piezo1 invadopodia mechanotransduction

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Renaturation of denatured λ repressor requires heat shock proteins

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Cell 1990年第6期61卷 1013-1020页

作者： Gaitanaris, George A. Papavassiliou, Athanasios G. Rubock, Paul Silverstein, Saul J. Gottesman, Max E. Institute of Cancer Research College of Physicians Surgeons Columbia University New York NY 10032 United States Integrated Program in Cellular Molecular Biophysical Studies College of Physicians NY 10032 United States Department of Microbiology College of Physicians Surgeons Columbia University New York NY 10032 United States Department of Biochemistry Molecular Biophysics College of Physicians Surgeons Columbia University New York NY 10032 United States

The temperature-sensitive bacteriophage λc1857 repressor protein rapidly renatures after thermal inactivation. E. coli mutants in the heat shock protein genes dnaK, dnaJ, and grpE do not efficiently reactivate heat-denatured repressor. Our results suggest that protein refolding is promoted by heat shock proteins and that such a process is the basis of the homeostatic role played by these proteins in the heat shock response. © 1990.

关键词： Bacteriophage lambda/genetics Bacteriophage lambda/metabolism* DNA Probes DNA Probes DNA-Binding Proteins* Escherichia coli/genetics Escherichia coli/metabolism* Galactokinase/metabolism Genotype Heat-Shock Proteins/metabolism* Kinetics Mutation Protein Binding Protein Conformation Protein Denaturation Protein Denaturation Repressor Proteins/metabolism* Transcription Factors/metabolism* Viral Proteins Viral Regulatory and Accessory Proteins

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KDM3A and KDM3B regulate alternative splicing in mouse pluripotent stem cells

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iScience 2025年

作者： Caleb M. Dillingham Harshini Cormaty Ellen C. Morgan Andrew I. Tak Dakarai E. Esgdaille Paul L. Boutz Rupa Sridharan Wisconsin Institute for Discovery University of Wisconsin-Madison Madison WI 53715 USA Department of Cell and Regenerative Biology University of Wisconsin-Madison Madison WI 53792 USA Pathology and Laboratory Medicine University of Wisconsin-Madison Madison WI 53705 USA Laboratory of Genetics University of Wisconsin-Madison Madison WI 53706 USA Molecular and Cellular Pharmacology Training Program University of Wisconsin-Madison Madison WI 53705 USA Department of Biochemistry and Biophysics Center for RNA Biology Wilmot Cancer Center University of Rochester School of Medicine and Dentistry Department of Biomedical Genetics University of Rochester School of Medicine and Dentistry

Histone modifying enzymes are crucial in preserving cell identity by establishing a conducive chromatin environment for lineage specific transcription factor activity. Mouse pluripotent embryonic stem cells (mESCs) show lower levels of gene repression associated histone modifications, facilitating rapid response to differentiation cues. The KDM3 family of histone demethylases removes repressive histone H3 lysine 9 dimethylation (H3K9me2). We uncover a surprising role for the KDM3 proteins in post-transcriptional regulation of mESCs. Proteomic analysis shows KDM3A and KDM3B interacting with RNA processing factors such as EFTUD2 and PRMT5. Acute degradation of the endogenous KDM3A and KDM3B proteins resulted in altered splicing independent of H3K9me2 status or catalytic activity. These splicing changes partially resemble the splicing pattern of the more blastocyst-like ground state of pluripotency and occur in important chromatin and transcription factors such as Dnmt3b and Tcf12 . Our findings reveal non-canonical roles of histone demethylating enzymes in splicing to regulate cell identity.

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