Hydromechanical characterization of gas transport amidst uncertainty for underground nuclear explosion detection

Given the challenge of definitively discriminating between chemical and nuclear explosions using seismic methods alone,surface detection of signature noble gas radioisotopes is considered a positive identification of underground nuclear explosions(UNEs).However,the migration of signature radionuclide gases between the nuclear cavity and surface is not well understood because complex processes are involved,including the generation of complex fracture networks,reactivation of natural fractures and faults,and thermo-hydro-mechanical-chemical(THMC)coupling of radionuclide gas transport in the subsurface.In this study,we provide an experimental investigation of hydro-mechanical(HM)coupling among gas flow,stress states,rock deformation,and rock damage using a unique multi-physics triaxial direct shear rock testing system.The testing system also features redundant gas pressure and flow rate measurements,well suited for parameter uncertainty quantification.Using porous tuff and tight granite samples that are relevant to historic UNE tests,we measured the Biot effective stress coefficient,rock matrix gas permeability,and fracture gas permeability at a range of pore pressure and stress conditions.The Biot effective stress coefficient varies from 0.69 to 1 for the tuff,whose porosity averages 35.3%±0.7%,while this coefficient varies from 0.51 to 0.78 for the tight granite(porosity<1%,perhaps an underestimate).Matrix gas permeability is strongly correlated to effective stress for the granite,but not for the porous tuff.Our experiments reveal the following key engineering implications on transport of radionuclide gases post a UNE event:(1)The porous tuff shows apparent fracture dilation or compression upon stress changes,which does not necessarily change the gas permeability;(2)The granite fracture permeability shows strong stress sensitivity and is positively related to shear displacement;and(3)Hydromechanical coupling among stress states,rock damage,and gas flow appears to be stronger in tight granite than in porous tuff.

Nuclear lamina-like filaments and nuclear matrix in Allium cepa as revealed by scanning electron microscopy

In this study, freeze - fractured specimens of Allium cepa root tip meristems were examined under the scanning electron microscope (SEM). This technique permitted the visualization of the outer membrane of the nuclear envelope with nuclear pore complexes and polyribosomes. Some of the cell nuclei prepared with this procedure had fissures of various widths on their nuclear envelopes through which the nuclear lamina-like filaments (LLF) underneath the nucleoplasmic side of the envelopes were clearly visible. The diameters of these filaments varied between 25 and 125 nm. Many of the LLFs showed granular thickenings at places, and were attached to the inner surface of nuclear envelope in some regions. Similar LLFs were also seen at the peripheries of the freeze -fractured faces of nuclei. Meanwhile,the spatial relation between the nuclear matrix filaments (NMF) and other nuclear structures (nucleoli, chromatin and peripheral lamina - like filaments) was revealed in these fractured preparations. In addition, the methods and techniques in studying the nuclear lamina morphology and the roles played by NMFs in activities of various nuclear structures were discussed in brief.

Human papillomavirus 16 E6 is associated with the nuclear matrix of esophageal carcinoma cells

AIM: To explore the etiologic role of HPV infection in esophageal carcinoma, and the association of HPV-16 E6with the nuclear metrix of carcinoma cells.METHODS: Two esophageal carcinoma cell lines, EC/CUHK1 and EC/CUHK2, were tested for HPV-16 E6subgenetic fragment by polymerase chain reaction amplification of virus DNA associated nuclear matrix. RT-PCR and immunocytochemistry were also used to visualizethe expression of E6 subgene in the cells.RESULTS: The HPV-16 E6 subgenetic fragment wes found to be present in nuclear metrix-associeted DNA, E6oncoprotein localized in the nucleus where it is tightly associated with nuclear matrix after sequential extraction in EC/CUHK2 cells. It was not detected, however, in EC/CUHK1 cells.CONCLUSION: The interaction between HPV-16 E6 and nuclear matrix may contribute to the virus induced carcinogenesis in esophageal carcinoma.

Comparisons of voided urine cytology, nuclear matrix protein-22 and bladder tumor associated antigen tests for bladder cancer of geriatric male patients in Taiwan, China

Aim： To compare the results of bladder tumor associated antigen （BTA TRAK）, nuclear matrix protein 22 （NMP 22） and voided urine cytology （VUC） in detecting bladder cancer. Methods： A total of 135 elderly male and 50 healthy volunteers enrolled in this study were classified into three groups： （i） 93 patients with bladder cancer; （ii） 42 patients with urinary benign conditions; and （iii） 50 healthy volunteers. BTA TRAK and NMP 22 kits were used to detect bladder cancer. Voided urine cytology was used to compare the sensitivity and specificity of the screening tests. Results： The sensitivity and specificity of cytology, BTA TRAK and NMP 22 were 24% and 97%, 51% and 73%, 78% and 73%, respectively. The level of NMP 22 increased with tumor grading. The BTA TRAK kit has the lowest sensitivity among the screening tests. The NMP 22 with the best sensitivity can be an adjunct to cytology for evaluating bladder cancer. Conclusion： The NMP 22 test has a better correlation with the grading of the bladder cancer than BTA TRAK. As cytology units are typically not available in hospitals or in outpatient clinics, NMP 22 might be a promising tool for screening bladder cancer.

Altered profiles of nuclear matrix proteins during the differentiation of human gastric mucous adenocarcinoma MGc80-3 cells

AIM： To find and identify specific nuclear matrix proteins associated with proliferation and differentiation of carcinoma cells, which will be potential markers for cancer diagnosis and targets in cancer therapy. METHODS： Nuclear matrix proteins were selectively extracted from MGcS0-3 cells treated with or without hexamethylamine bisacetamide （HMBA）, and subjected to 2-D gel electrophoresis. The resulted protein patterns were analyzed by Melanie software. Spots of nuclear matrix proteins differentially expressed were excised and subjected to in situ digestion with trypsin. Peptide masses were obtained by matrix-assisted laser-desorption/ ionization time of flight mass spectrometry （MALDI-TOFMS） analysis and submitted for database searching using Mascot tool. RESULTS： The MGc80-3 cells were induced into differentiation by HMBA. There were 22 protein spots which changed remarkably in the nuclear matrix, from differentiation of MGcS0-3 cells compared to control. Eleven of which were identified. Seven proteinsactin, prohibitin, porin 31HL, heterogeneous nuclear dbonucleoprotein A2/B1, vimentin, ATP synthase, and heat shock protein 60 were downregulated, whereas three proteins - heat shock protein gp96, heat shock protein 90-beta, and valosin-containing protein were upregulated, and the oxygen-regulated protein was only found in the differentiated MGc80-3 cells. CONCLUSION： The induced differentiation of carcinoma cells is accompanied by the changes of nuclear matrix proteins. Further characterization of those proteins will show the mechanism of cellular proliferation and differentiation, as well as cancer differentiation.

Alreration of nuclear matrix-intermediate filament system and differential expression of nuclear matrix proteins during human hepatocarcinoma cell differentiation

AIM： To investigate the association between the configurational and compositional changes of nuclear matrix and the differentiation of carcinoma cells. METHODS： Cells cultured with or without 5 × 10^-3 mmol/L of hexamethylene bisacetamide （HMBA） on Nickel grids were treated by selective extraction and prepared for whole mount observation under electron microscopy. The samples were examined under transmission electron microscope. Nuclear matrix proteins were selectively extracted and subjected to subcellular proteomics study. The protein expression patterns were analyzed by PDQuest software. Spots of differentially expressed nuclear matrix proteins were excised and subjected to in situ digestion with trypsin. The peptides were analyzed by matrix-assisted laser- desorption/ionization time of flight mass spectrometry （MALDI-TOF-MS）. Data were submitted for database searching using Mascot tool （www.matrixscience.com）. RESULTS： The nuclear matrix （NM） and intermediate filament （IF） in SMMC-7721 hepatocarcinoma cells were found relatively sparse and arranged irregularly. The nuclear lamina was non-uniform, and two kinds of filaments were not tightly connected. After induction for differentiation by HMBA, the NM-IF filaments were concentrated and distributed uniformly. The heterogeneous population of filaments, including highly branched utrathin filaments could also be seen in the regular meshwork. The connection between the two kinds of filaments and the relatively thin, condensed and sharply demarcated lamina composed of intermediate- sized filaments was relatively fastened. Meanwhile, 21 NM proteins changed remarkably during SMMC-7721 cell differentiation. Four proteins, i.e. mutant Pystl, hypothetical protein, nucleophosminl, and LBP were downregulated, whereas four other proteins, eIF6, p44 subunit, 13-tubulin, and SIN3B were upregulated with the last one, SR2/ASF found only in the differentiated SMMC-7721 cells. CONCLUSION： The induced differentiation of SMMC-7721 cells by HMBA is accompanied by the configurational changes of nuclear matrix-intermediate filament （NM-IF） system and the compositional changes of nuclear matrix protein expression. These changes may be important morphological or functional indications of the cancer cell reversion.

Aberrant expression of nuclear matrix proteins during HMBA-induced differentiation of gastric cancer cells

AIM: To investigate the aberrant expression of nuclear matrix proteins in human gastric cancer cells before and after hexamethylene bisacetamide (HMBA) treatment.METHODS: Proteomics analysis of differential nuclear matrix proteins was performed by two dimensional electrophoresis polyacrylamide gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.The expression levels of three nuclear matrix proteins were further confirmed by Western blotting and their locations in nuclear matrix filament were observed by quantum dots-based immunofluorescence.RESULTS: Proteomics analysis showed that 43 protein spots were significantly changed due to HMBA treatment.Fifteen proteins were identified in the HMBAinduced differentiation of gastric tumor cells.Eight proteins spots were down-regulated while seven were up-regulated.Among these proteins,prohibitin,nucleophosmin and hnRNP A2/B1 were significantly decreased in HMBA-treated human gastric cancer cells,and their locations in nuclear matrix were altered by HMBA.Our results proved the alteration of specific nuclear matrix proteins during the differentiation of human gastric cancer cells.And the aberrant expressions of nuclear matrix proteins were of significance in revealing the regulatory mechanism of tumor cell proliferation and differentiation.CONCLUSION: The aberrant expressions and intracellular redistributions of nuclear matrix proteins before and after HMBA treatment indicated that nuclear matrix proteins play a pivotal role in the differentiation of gastric cancer cells.

Methanol extract of Codium fragile inhibits tumor necrosis factor-ɑ-induced matrix metalloproteinase-9 and invasiveness of MDA-MB-231 cells by suppressing nuclear factor-κB activation

Objective:To evaluate whether the methanol extract of Codium fragile(MECF) regulates tumor necrosis factor-α(TNF-α)-induced invasion of human breast cancer MDA-MB-231 cells by suppressing matrix metalloproteinase-9(MMP-9).Methods:Reverse transcriptionpolymerase chain reaction(RT-PCR) and western blot analysis were performed to analyze the expression of MMP-9 and nuclear factor-κB(NF-κB) subunits,p65 and p50,and IκB in MDA-MB-231 cells.3-(4,5-Dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide(MTT) assay was used for cell viability.MMP-9 activity and invasion were measured by gelatin zymography and a matrigel invasion assay,respectively.NF- κB activity was measured by an electrophoretic mobility shift assay and luciferase activity.Results:MECF had no effects on cell viability up to a concentration of 100 μg/mL in human breast cancer MDA-MB-231 cells regardless of the presence of TNF-α.MDA-MB-231 cells that were stimulated with TNF-α showed a marked increase of invasion compared to the untreated control,whereas pretreatment with MECF downregulated the TNF-α-induced invasion of MDA-MB-231 cells.Additionally,zymography,western blot analysis,and reverse transcriptase-polymerase chain reaction(RT-PCR) confirmed that MECF decreased TNF-α-induced MMP-9 expression and activity which is a key regulator for cancer invasion.According to an electrophoretic morbidity shift assay,pretreatment with MECF in MDA-MB-231 cells significantly decreased the TNF-α-induced DNA-binding activity of nuclear factor- κB(NF- κB),which is an important transcription factor for regulating cancer invasion-related genes such as MMP-9.Furthermore,treatment with MECF sustained the expression of p65 and p50 in response to TNF-α in the cytosolic compartment.The luciferase assay demonstrated that MECF attenuated TNF-α-induced NF- κB luciferase activity.Conclusion:MECF exhibited its antiinvasive capability by downregulating TNF-α-induced MMP-9 expression,resulting from the suppression of NF- κB activity in the human breast cancer cell line MDA-MB-231.

Tropomyosin is localized in the nuclear matrix and chromosome scaffold of physarum polycephalum

The nuclei and chromosomes were isolated from plasmodia of Physarum polycephalum. The nuclear matrir and chromosome scaffold were obtained after the DNA and most of the proteins were extracted with DNase I and 2 M NaCl. SDS-PAGE analyses revealed that the nuclear matrir and chromosome scaffold contained a 37 kD polypeptide which is equivalent to tropomyosin in molecular weight. Immunofluorescence observations upon slide preparations labeled with anti-tropomyosin antibody showed that the nuclear matrix and chromosome scaffold emanated bright fluorescence, suggesting the presence of the antigen in them.Immunodotting results confirmed the presence of tropomyosin in the nuclear matrix and chromosome scaffold. Immunoelectron microscopic obserwtions further demonstrated that tropomyosin was dispersively distributed in the interphase nuclei and metaphase chromosomes.

Altered expression of nuclear matrix proteins in etoposide induced apoptosis in HL-60 cells

The events of cell death and the expression of nuclear matrix protein (NMP) have been investigated in a promyelocytic leukemic cell line HL-60 induced with etoposide. By means of TUNEL assay, the nuclei displayed a characteristic morphology change, and the amount of apoptotic cells increased early and reached maximun about 39% after treatment with etoposide for 2 h. Nucleosomal DNA fragmentation was observed after treatment for 4 h. The morphological change of HL-60 cells, thus, occurred earlier than the appearance of DNA ladder. Total nuclear matrix proteins were analyzed by 2-dimensional gel electrophoresis. Differential expression of 59 nuclear matrix proteins was found in 4 h etoposide treated cells. Western blotting was then performed on three nuclear matrix acssociated proteins, PML, HSC70 and NuMA. The expression of the suppressor PML protein and heat shock protein HSC70 were significantly upregulated after etoposide treatment, while NuMA, a nuclear mitotic apparatus protein, was down regulated. These results demonstrate that significant biochemical alterations in nuclear matrix proteins take place during the apoptotic process.

The detection of nuclear matrix in most primitive presentexisting eukaryote, Giardia lamblia

The nuclear matrix of diplomonad Giardia lamblia was detected for the first time with DGD embedmentsectioning- embedment free electron microscopy after a series of specific extractions. The result showed that archaezoa Giardia lamblia already possessed nuclear matrix within its two nuclei. The finest fibrils of the nuclear matrix of Giardia lamblia were measured to be about 11 to 13 nm in thickness. However, the nuclear lamina and nucleolus have never been observed. These results seem to suggest that nuclear matrix is an indispensable intranuclear structural component even in the primitive nucleus.

CHANGES OF NUCLEAR MATRIX PROTEIN AND ITS RELATIONSHIP WITH c-erbB-2 IN HUMAN COLON ADENOCARCINOMA

Objective： Nuclear matrix protein is tissue, cell-type specific, and tumor-relative. It plays an important role in the regulation of intranuclear processes. Some researches also showed that a c-erbB-2 promoter-specific DNA-binding nuclear matrix protein is present only in malignant human breast tissues and induces mitogenesis and cell surface expression of the c-erbB-2 protein in resting NIH/3T3 cells. But it is not clear that how it in colon adenocarcinomas. Methods： Two-dimensional gel electrophoretic method was used for NMP identification and immunohistochemistry was used for c-erbB-2 detection in 12 cases of colon adenocarcinomas and matched adjacent normal colon tissues. Results： 5 different nuclear matrix proteins （named C1-C5） were identified in 12 colon adenocarcinoma specimens, but not in the matched adjacent normal colon tissues; 3 nuclear matrix proteins （named N1-N3） were identified in all 12 matched adjacent normal colon tissues, but not in colon adenocarcinoma specimens. A nuclear matrix protein （named N4） was detected in all of 9 moderated-well differentiated adenocarcinomas and all 12 matched adjacent normal colon tissues, but not in 3 poor-differentiated adenocarcinomas. All of the 10 colon adenocarcinomas which had the nuclear matrix protein C4 were c-erbB-2 expression positive. Conclusion： The data suggest that there are specific nuclear matrix proteins in colon adenocarcinomas and its subtypes, which maybe valuable to serve as markers of colon adenocarcinomas in future. Nuclear matrix protein C4 probably is a c-erbB-2 promotor-specific nuclear matrix protein in colon adenocarcinomas, and may induce the expression of c-erbB-2.

NUCLEAR MATRIX PROTEIN IN LEUKEMIA CELLS

Objective: To compare the composition of nuclear matrix proteins (NMP) between leukemia cells and normal bone marrow cells. Methods: NMP was isolated by high-salt extraction and identified in acute and chronic myelogenous leukemia cells as well as in the blast phase of chronic leukemia. On SDS-PAGE, NMPs with molecular myelogenous ferment from what were seen in normal bone marrow cells were present in both acute and chronic myelogenous leukemia. Conclusion: Marked changes of NMP, not only in contents but also in compositions, exist in leukemic cells compared with normal bone marrow cells. NMP may serve as a target of chemotherapeutic drug against leukemia.

The interaction between the human β-globin locus control region and nuclear matrix

Our previous study showed that hydroxyurea (Hu) could induce HEL cells to express humanβ-globin gene. However the molecular mechanisms by which the expression of β-globin gene is activated and regulated are poorly understood. Here we show that the binding patterns between the core DNA sequences (HS2 core sequence -10681- -10971 bp , HS3 core sequence -14991- -14716 bp and HS4 core sequence -18586- -18306 bp) of DNase I hypersensitive sites in the human β-globin LCR and nuclear matrix proteins isolated from Hu induced and uninduced HEL cells are quite different. Results demonstrated that nuclear matrix proteins might play important roles in regulating the expression of humanβ-like globin genes through their interaction with HSs (HS2,HS3 and HS4 core sequences) in the LCR. Moreover, the results obtained from the in vitro DNA-matrix binding assay showed that the core DNA sequences of DNase I hypersensitive sites (HS2, HS3 and HS4) were unable to bind to the nuclear matrix isolated from uninduced HEL cells; in addition, HS2 core DNA sequence was capable of binding to the nuclear matrix prepared from Hu-induced HEL cells, while both HS3 and HS4 core DNA sequences could not do so. Results indicated that the HS2 core DNA sequence may be a functional MAR (matrix attachment region). We suggest that the HS2 core DNA sequence binding to the nuclear matrix in Hu-induced HEL cells may open the structure of chromatin to make the LCR accessible to the promoter of β-globin gene and to promote its transcription.

The 5'-flanking cis-acting elements of the human ε-globin gene associates with the nuclear matrix and binds to the nuclear matrix proteins

The nucleax mains attachment regions(MARs) and the binding nuclear matrix proteins in the 5’-flalildng cisacting elements of the humanε-globin gene have been examined. Using in vitro DNA-matrix binding assay,it has been shown that the positive stage-specific regulatory element (ε-PREII, -446bp-419bp) upstream of this gene could specifically associate with the nuclear matrix from K562 cells, indicating thatε-PREII mad be an erythroidspecilic facultstive MAR. In gel mobility shift assay and Southwestern blotting assal an eothroid-specific nuclear matrix protein (ε-NMPk) in K562 cells has been revealed to bind to this positive regulatory element (E-PREII). Furthermore, we demonstrated that the silencer (-392hp -177bp) uP8tream of the humanε-globin gene could associate with the nuclear matrices from K562, HEL and Raji cells. In addition, the nucleax matrix proteins prepared from these three cell lines could also bind to this silencer, suggesting that this silencer element linght be a constitutive nuclear mains attachment region (constitutive MAR). Our results demonstrated that the nucleax madrid and nuclear mains proteins lxilght play an important role in the regulation of the human 5-globin gene expression.

On the history of nuclear matrix manifestation

The nonchromatin proteinous residue of the cell nucleus was revealed in our laboratory as early aJs in 1948and then identified by light and electron microscoPy as residual nucleoli. intranuclear network and nuclear envelope before 1960. This structure termed afterwards as "nuclear residue", "nuclear skeleton", "nuclear cage" 3 "nuclearcarcass" etc., was much later (in 1974) isolated, studied,and entitled as "nuclear matrix" by Berezney and Coffey,to whom the discovery of this residual structure is of ten wronly ascribed. The real history of nuclear matrix manifestation is reported in this paper.

Association of DNA with nuclear matrix in in vitro assembled nuclei induced by rDNA from Tetrahymena shanghaiensis in Xenopus egg extracts

The nuclei assembled from exogenous DNA or chromatin in egg extracts resemble their in vivo counterparts in many aspects. However, the distribution pattern of DNA in these nuclei remains unknown. We introduced rDNA from the macronuclei of Tetrabymena into Xenopus cellfree extracts to examine the association of specific DNA sequences with nuclear matrix (NM) in the nuclei assembled in vitro. Our previous works showed the 5’NTS (nontranscription sequences) of the rDNA specifically bind to the NM system in the macronuclei. We show now the rDNA could induce chromatin assembly and nuclear formation in Xenopus cell-free system. When we extracted the NM system and compared the binding affinity of different regions of rDNA with the NM system, we found that the 5’NTS still hold their binding affinity with insoluble structure of the assembled nuclei in the extracts of Xenopus eggs.

Identification of the nuclear matrix and chromosome scaffold in dinoflagellate Crypthecodinium cohnii^1

Dinoflagellate is one of the primitive eukaryotes, whose nucleus may represent one of the transition stages from prokaryotic nucleoid to typical eukaryotic nucleus. Using selective extraction together with embeddment - free section and whole mount electron microscopy, a delicate nuclear matrix filament network was shown, for the first time, in dinoflagellate Crypthecodinium cohnii nucleus. Chromosome residues are connected with nuclear matrix filaments to form a complete network spreading over the nucleus. Moreover, we demonstrated that the dinoflagellate chromosome retains a protein scaffold after the depletion of DNA and soluble proteins. This scaffold preserves the characteristic morphology of the chromosome. Two dimensional elec-trophoreses indicated that the nuclear matrix and chromosome scaffold are mainly composed of acidic proteins. Our results demonstrated that a framework similar to the nuclear matrix and chromosome scaffold in mammalian cells appears in this primitive eukaryote,suggesting that these structures may have been originated from the early stages of eukaryote evolution.

Phosphorylation and biosynthesis of high molecular weight proteins of tumor nuclear matrix

Our previous studies showed a predominance of high molecular weight protein group in tumor nuclear matrices. Contrary to normal cells, proteins of this group are preferentially phosphorylated. Phosphoproteins of hepatoma nuclear matrix are selectively subjected to rapid proteolysis. By alkali treatment and a monoclonal antibody against phosphotyrosyl residue the presence of two high molecular weight bands of phosphotyrosyl-containing proteins was detected in nuclear matrices of tumor but not of normal liver cells. High molecular weight protein group of tumor nuclear matrices revealed also a rapid turnover and preferential incorporation of labeled amino acids selectively inhibited by chloramphenicol.

Structure of Hamiltonian Matrix and the Shape of Eigenfunctions：Nuclear Octupole Deformation Model

The structure of a Hamiltonian matrix for a quantum chaotic system, the nuclear octupole deformation model, has been discussed in detail. The distribution of the eigenfunctions of this system expanded by the eigenstates of a quantum integrable system is studied with the help of generalized Brillouin?Wigner perturbation theory. The results show that a significant randomness in this distribution can be observed when its classical counterpart is under the strong chaotic condition. The averaged shape of the eigenfunctions fits with the Gaussian distribution only when the effects of the symmetry have been removed.