Em Ab Research Articles

Joint density-functional theory for electronic structure of solvated systems

We introduce a new form of density functional theory for the {\em ab initio} description of electronic systems in contact with a molecular liquid environment. This theory rigorously joins an electron density-functional for the electrons of a solute with a classical density-functional theory for the liquid into a single variational principle for the free energy of the combined system. A simple approximate functional predicts, without any fitting of parameters to solvation data, solvation energies as well as state-of-the-art quantum-chemical cavity approaches, which require such fitting.

Structure and Polarization in the HighTcFerroelectricBi(Zn,Ti)O3−PbTiO3Solid Solutions

Theoretical ab initio and experimental methods are used to investigate the [Bi(Zn1/2Ti1/2)O3]x[PbTiO3]1-x solid solution. We find that hybridization between Zn 4s and 4p and O 2p orbitals allows the formation of short, covalent Zn-O bonds, enabling favorable coupling between A-site and B-site displacements. This leads to unusually large polarization, strong tetragonality, and an elevated ferroelectric to paraelectric phase transition temperature.

Realistic nuclear Hamiltonian: Ab exitu approach

Fully-microscopic No-core Shell Model (NCSM) calculations of all stable $s$ and $p$ shell nuclei are used to determine realistic $NN$ interaction JISP16 describing not only the two-nucleon data but the binding energies and spectra of nuclei with $A\leq 16$ as well. The JISP16 interaction, providing rapid convergence of the NCSM calculations, is obtained in an {\em ab exitu} approach by phase-equivalent transformations of the JISP6 $NN$ interaction.

Cellular processing in the SW1222 cell line of mAb A33 directly and indirectly radiohalogenated

Investigations into the cellular processing of radiolabeled monoclonal antibodies (mAbs) for their further use in radioimmunodiagnosis and cancer therapy are needed in order to understand the fate of internalized and catabolized mAbs. The anti-colorectal cancer mAb, A33, was labelled with 76Br and 125I using the direct Chloramine-T method, or by labelling N-succinimidyl para-(tri-methylstannyl) benzoate and its further conjugation to the mAb. The cellular processing of the four conjugates was investigated in SW1222 cells in vitro. Uptake of mAb was rapid, peaking after 14-16 h. Intracellular degradation was slow and the early loss of radioactivity was due to dissociation of cell-surface bound mAb. The indirect labelling resulted in stronger binding of the mAb as well as prolonged intracellular retention of the radiolabel. Direct and indirect halogen radiolabelling results in different cell-processing patterns of radiolabels, and radioactive catabolic products follow different routes of cellular excretion. The results of this cellular study indicate that indirect labelling is preferable to the direct Chloramine-T method.

Breit interaction and parity nonconservation in many-electron atoms

We present accurate {\em ab initio} non-perturbative calculations of the Breit correction to the parity non-conserving (PNC) amplitudes of the $6s-7s$ and $6s-5d_{3/2}$ transitions in Cs, $7s-8s$ and $7s-6d_{3/2}$ transitions in Fr, $6s-5d_{3/2}$ transition in Ba$^+$, $7s-6d_{3/2}$ transition in Ra$^+$, and $6p_{1/2} - 6p_{3/2}$ transition in Tl. The results for the $6s-7s$ transition in Cs and $7s-8s$ transition in Fr are in good agreement with other calculations while calculations for other atoms/transitions are presented for the first time. We demonstrate that higher-orders many-body corrections to the Breit interaction are especially important for the $s-d$ PNC amplitudes. We confirm good agreement of the PNC measurements for cesium and thallium with the standard model .

On the theory underlying the Car-Parrinello method and the role of the fictitious mass parameter

The theory underlying the Car-Parrinello extended-Lagrangian approach to ab initio molecular dynamics (CPMD) is reviewed and reexamined using "heavy" ice as a test system. It is emphasized that the adiabatic decoupling in CPMD is not a decoupling of electronic orbitals from the ions but only a decoupling of a subset of the orbital vibrational modes from the rest of the necessarily coupled system of orbitals and ions. Recent work [J. Chem. Phys. 116, 14 (2002)] has pointed out that, due to the orbital-ion coupling that remains once adiabatic decoupling has been achieved, a large value of the fictitious mass mu can lead to systematic errors in the computed forces in CPMD. These errors are further investigated in the present work with a focus on those parts of these errors that are not corrected simply by rescaling the masses of the ions. It is suggested that any comparison of the efficiencies of Born-Oppenheimer molecular dynamics (BOMD) and CPMD should be performed at a similar level of accuracy. If accuracy is judged according to the average magnitude of the systematic errors in the computed forces, the efficiency of BOMD compares more favorably to that of CPMD than previous comparisons have suggested.

Monoclonal antibody conjugated to gadolinium as a contrast agent for magnetic resonance imaging of human rectal carcinoma

Local disease is the most frequent recurrence pattern of rectal carcinoma, and its prognosis is not good. One reason for the poor prognosis is the difficulty of making the diagnosis at an early stage. To detect local recurrence as early as possible, we produced the monoclonal antibody, A7-gadolinium (Mab A7-Gd), conjugate as a contrast agent for magnetic resonance imaging to distinguish between carcinoma and normal tissue. We examined the in vitro immunoreactivity of Mab A7 coupled to Gd by chelate, and stability of Mab A7-EDTA-Gd in human serum. Its in vivo distribution in nude mice with human colorectal carcinoma was also examined. Mab A7-Gd retained binding activities that were nearly identical to intact Mab A7. Mab A7-Gd was stable in human serum. More radiolabeled Mab A7-Gd accumulated in the tumor than normal mouse IgG-Gd. Both Mab A7-Gd and normal mouse IgG-Gd disappeared from blood linearly over time. Accumulation levels in normal tissues decreased linearly over time but were lower than those in tumors. Mab A7 conjugated to gadolinium selectively accumulated in the tumor. Our results suggest that it is potentially suitable as a contrast agent for MR imaging to detect local rectal carcinoma recurrence.

Universal ionization threshold for strongly driven Rydberg states

We observe a universal ionization threshold for microwave driven one-electron Rydberg states of H, Li, Na, and Rb, in an {\em ab initio} numerical treatment without adjustable parameters. This sheds new light on old experimental data, and widens the scene for Anderson localization in light matter interaction.

Monoclonal antibody A7 coupled to magnetic particles as a contrast enhancing agent for magnetic resonance imaging of human colorectal carcinoma.

Local recurrence, the most frequent pattern of recurrence of rectal carcinoma, is almost always fatal. The difficulty of diagnosing local recurrence contributes importantly to the poor prognosis. We coupled monoclonal antibody (Mab) A7, which reacts specifically with human colorectal carcinoma, to ferromagnetic lignosite (FML) particles to distinguish rectal carcinoma from other tissues by magnetic resonance (MR) imaging. We examined retention of immunoreactivity by the A7-FML complexes in vitro, and also their distribution in vivo according to radiolabeling and MR imaging when injected into nude mice bearing human colorectal carcinoma xenografts. A7-FML retained binding activity nearly identical to that of Mab A7. Significantly more (125)I-labeled A7-FML accumulated in engrafted tumors than did (125)I-labeled normal mouse IgG-FML complexes (P < 0.05). A7-FML disappeared rapidly from the blood. Normal tissues accumulated less (125)I-labeled A7-FML than tumors; this accumulation decreased linearly with time. In MR imaging, signal intensity was reduced in the tumor by the injection of A7-FML. A7-FML is potentially useful as a MR contrast enhancing agent for human colorectal carcinoma xenografts implanted subcutaneously.

Monoclonal antibody A7-superparamagnetic iron oxide as contrast agent of MR imaging of rectal carcinoma.

Superparamagnetic iron oxide (SPIO)-based colloid has been used clinically as a tissue-specific magnetic resonance contrast agent. We coupled monoclonal antibody A7 (Mab A7), which reacts specifically with human colorectal carcinoma, to Ferumoxides (SPIO) and examined the accumulation of this conjugate in xenografted tumours in nude mice. We examined in vitro immunoreactivity of Mab A7 coupled to Ferumoxides and its in vivo distribution in nude mice with human colorectal carcinoma. Magnetic resonance imaging of tumour-bearing nude mice was performed 72 h after injection of A7-Ferumoxides. A7-Ferumoxides retained binding activities that were nearly identical to intact Mab A7. More of the radiolabelled A7-Ferumoxides accumulated in the tumour than normal mouse IgG-Ferumoxides from 12 h onwards after injection (P<0.05). Both A7-Ferumoxides and normal mouse IgG-Ferumoxides disappeared from blood linearly over time. The accumulation levels in normal tissue decreased linearly over time but were lower than levels in tumours from 6 h. In magnetic resonance T2-weighted imaging of the tumour-bearing nude mice, signal intensity was reduced at the margin of the tumour by injection of A7-Ferumoxides. Mab A7 coupled to Ferumoxides is potentially suitable as a magnetic resonance contrast agent for detecting local recurrence of rectal carcinoma.

Magnetic and orbital blocking in Ni nanocontacts

We address the fundamental question of whether magneto-resistance (MR) of atomic-sized contacts of Nickel is very large because of the formation of a domain wall (DW) at the neck. Using {\em ab initio} transport calculations we find that, as in the case of non-magnetic electrodes, transport in Ni nanocontacts depends very much on the orbital nature of the electrons. Our results are in agreement with several experiments in the average value of the conductance. On the other hand, contrary to existing claims, DW scattering does {\em not} account for large MR in Ni nanocontacts.

Expression of epithelial-cell adhesion molecule (Ep-CAM) in small cell lung cancer as defined by monoclonal antibodies 17-1A and BerEP4

Small cell lung cancer (SCLC) comprises 15–20% of all lung cancer. Despite high initial response to chemotherapy chemoresistance at relapse leads to a less than 5% five-year survival rate. Adjuvant treatment with monoclonal antibodies (Mabs) against SCLC antigens may offer a therapeutic option. Mab 17-1A directed against the epithelial-cell adhesion molecule (Ep-CAM) has been extensively tested for therapy in patients with colorectal carcinoma. Expression of Ep-CAM in SCLC has been earlier described. However, reactivity of Mab 17-1A and another Ep-CAM-binding Mab BerEP4 has not yet been described for SCLC. Using immunohistology first with BerEP4 and confirmatory with 17-1A a homogenous and strong expression of Ep-CAM was seen in all SCLC specimens tested (n = 10). For comparison, heterogenous expression was seen in the non-SCLC tumors tested (n = 15). These findings strongly suggest that Mab 17-1A can be useful for adjuvant immunotherapy in patients with SCLC. For detection of Ep-CAM in tumor tissue in patients that might be considered for immunotherapy with Mab 17-1A, Mab BerEP4 appears to be preferred.

Ab Initio Calculations of Hc2 for Nb, NbSe2, and MgB2

We report on quantitative calculations of the upper critical field $H_{c2}$ for clean type-II superconductors Nb, NbSe$_{2}$, and MgB$_{2}$ using Fermi surfaces from {\em ab initio} electronic structure calculations. The results for Nb and NbSe$_2$ excellently reproduce both temperature and directional dependences of measured $H_{c2}$ curves without any adjustable parameters, including marked upward curvature of NbSe$_{2}$ near $T_{c}$. As for MgB$_2$, a good fit is obtained for a $\pi / \sigma$ gap ratio of $\sim 0.3$, which is close to the value from a first-principles strong-coupling theory [H. J. Choi \textit{et al}. Nature, \textbf{418} 758 (2002)]. Our results indicate essential importance of Fermi surface anisotropy for describing $H_{c2}$.

Targeting human Ep-CAM in transgenic mice by anti-idiotype and antigen based vaccines.

Anti-idiotypic antibodies (anti-Id) as surrogate TAAs have been shown to induce immunity against tumours in animals and humans. SM262 is a human monoclonal anti-Id raised against MAb 17-1A recognising Ep-CAM. Plasmids encoding the variable regions of SM262 with either murine or human Fc regions, both with and without fusion to GM-CSF were constructed. DNA was delivered by gene gun to C57BL/6 (wt) mice and mice expressing the transgene for human Ep-CAM (tg). The immunogenicity of anti-Id DNA constructs, anti-Id protein and Ep-CAM DNA vaccines was compared. SM262 plasmids induced antibodies (Abs) inhibiting MAb 17-1A binding to SM262 as well as recognising Ep-CAM in wt and tg mice. Fusion to GM-CSF evoked significantly higher Ab titres, whereas a xenogeneic Fc region had no significant effect. The highest Ab titres were elicited by protein immunisation. The original Ag was superior as compared to the anti-Id vaccines in wt but not tg mice in terms of Ab induction. A weak Ep-CAM-specific cytotoxic response was induced in wt but not tg mice. The data suggest that B cell tolerance to Ep-CAM can be circumvented by anti-Id DNA, anti-Id protein as well as Ep-CAM DNA immunisation. Fusion of GM-CSF to anti-Id increased the magnitude of the immune response with no requirement of a foreign Fc domain. Furthermore, no superiority of Ep-CAM as compared to anti-Id DNA vaccine was noted in tg mice and protein immunisation induced a more potent humoral response than DNA. The results might have implications for the design of future vaccine trials using Ep-CAM as a target structure.

Bioengineering of Surface GD3 Ganglioside for Immunotargeting Human Melanoma Cells

N-Propionyl, N-butyryl (N-Bu), and N-benzoyl mannosamine, as precursors of sialic acid biosynthesis, were incubated with human melanoma SK-MEL-28 cells and resulted in the replacement of N-acetyl groups on the cell surface sialic acid residues, including those associated with GD3. Meanwhile, vaccines containing GD3 and modified GD3 tetrasaccharide-keyhole limpet hemocyanin conjugates were synthesized, and BALB/c mice were immunized with them together with monophosphoryl lipid A adjuvant. The GD3Bu-keyhole limpet hemocyanin conjugate raised the highest IgG titers without any cross-reactivity to unmodified GD3. Expression of GD3Bu epitopes on the surface of SK-MEL-28 cells was confirmed in vitro and in vivo by the binding of a polyclonal antiserum and monoclonal antibody (mAb) 2A, both of which specifically recognize GD3Bu, and by mass spectroscopic analysis of glycolipids extracted from cells. Following expression of GD3Bu on the surface of SK-MEL-28 cells, the cells could be lysed by mAb 2A and GD3Bu antiserum in the presence of complement. Although less effective in the control of existing large size tumors ( approximately 10 mm inner diameter) on BALB/c nu/nu mice, mAb 2A in combination with ManNBu effectively protected mice from SK-MEL-28 tumor grafting. This approach may provide a method to augment the immunogenicity of sialylated human antigens and to avoid generating an autoimmune response to them at same time.

Monoclonal antibodies in the treatment of colorectal cancer

Monoclonal antibodies have been developed to target specific proteins involved in the development and progression of cancer. These reagents have the advantage of exquiste specificity, and as currently engineered, low toxicity. The impact monoclonal antibody therapy has recently been demonstrated in colorectal cancer, in which two pathways critical to carcinogenesis have been targeted. The targets are the epidermal growth factor receptor signaling pathway and angiogenesis. Antibodies directed to proteins in both pathways have shown significant activity especially in combination with chemotherapy, and studies in the adjuvant setting are in progress. We review the use of monoclonal antibodies in the treatment of colorectal cancer with particular attention to edrecolomab (Mab 17-1A), bevacizumab (Avastin), cetuximab (IMC-C225), ABX-EGF and EMD 72000. Additional compounds are in earlier stages of development, and the future of this approach in solid tumours is promising.

Generation and preliminary characterization of an antibody library with preferential reactivity to human colorectal cancer cells as compared to normal human blood cells

We are developing recombinant polyclonal antibody libraries (PCALs) reactive to human colorectal cancer cells as an anti-cancer therapeutic approach. To test the hypothesis that PCALs with preferential recognition of tumor cells as compared to normal cells could be generated, a Fab phage display library reactive to human colorectal cancer cell lines was absorbed with normal human blood cells. ELISA analysis of the absorbed Fab phage display library showed that 70% of tested clones reacted to colorectal cancer cells. Reactivity of the library to blood cells was reduced 4–10-fold, with many clones unreactive to one or more of the blood cell types. DNA fingerprint analysis of colorectal cancer-binding clones showed that the absorbed library remained polyclonal. The H and L chain V region gene pairs of the absorbed library were transferred in mass from the Fab phage display vector to a mammalian vector and expressed as IgG following transfection into Sp2/0 myeloma cells. ELISA analysis showed that 79% of transfectants expressed IgG and of those 74% were positive for binding to the SW480 human colorectal cancer cell line. A template of 95 SW480-reactive wells was assembled, designated Lib-Col2.1, and IgG purified from a consolidated mass culture. The purified Lib-Col2.1 IgG was compared to the clinically used anti-colorectal cancer mAb 17-1A, by ELISA and flow cytometry, for binding density on SW480 colorectal cancer cells and on normal human blood cells. The results showed that Lib-Col2.1 bound to SW480 cells at higher density than mAb 17-1A and that its binding to normal human blood cells was reduced 2.4–24-fold relative to an unabsorbed anti-SW480 serum. Furthermore, Lib-Col2.1 was more effective than mAb 17-1A at inhibiting the growth of SW480 cells in culture. These results suggest that a polyclonal antibody library with preferential reactivity to cancer cells as compared to normal cells could be generated.

Application of 99mTc labeled chimeric Fab fragments of monoclonal antibody A7 for immunoscintigraphy of pancreatic carcinoma.

One of the reasons for the poor prognosis of pancreatic carcinoma is the difficulty of obtaining an early diagnosis of pancreatic carcinoma. One possibility is the application of radioimmunoscintigraphy using radiolabeled monoclonal antibodies (Mabs). We labeled chimeric (human/mouse) Fab fragments of Mab A7 (chA7Fab) with (99m)Tc and examined the distribution of (99m)Tc-labeled chA7Fab in nude mice bearing human pancreatic carcinoma. The tumor accumulation of (99m)Tc-labeled chA7Fab was larger than that of (99m)Tc-labeled A7 from 2 to 6 hr after injection. (99m)Tc-labeled chA7Fab disappeared from blood more rapidly than (99m)Tc-labeled A7. For all resected normal tissues except kidney, the accumulation of (99m)Tc-labeled chA7Fab was low and similar to that of (99m)Tc-labeled A7. Because the half-life of (99m)Tc is short (6 hr), chA7Fab, which accumulates rapidly in tumors, may be a better carrier of (99m)Tc than intact Mab A7.

Synthesis, solution structure analysis and antibody binding of cyclic epitope peptides from glycoprotein D of Herpes simplex virus type I

Two cyclic peptides with a thioether bond have been synthesised corresponding to the 9–22 ( 9LKMADPNRFRGKDL 22) sequence of glycoprotein D (gD-1) of Herpes simplex virus. The role of the secondary structure in protein-specific monoclonal antibody recognition was investigated. The sequence selected for this study comprises a strongly antigenic site adopting a β-turn at residues 14Pro– 15Asn. Thioether bond was formed between the free thiol group of cysteine or homocysteine inserted in position 11 and the chloroacetylated side chain of lysine in position 18. We report here the preparation of cyclic peptides containing Cys or Hcy in position 11, differing only in one methylene group. The linear precursor peptides were synthesised by Boc/Bzl strategy on MBHA resin, and the cyclisation was carried out in alkaline solution. The secondary structure of the peptides was studied by CD, FT-IR and NMR spectroscopy. The CD and FT-IR data have revealed fundamental changes in the solution conformation of the two compounds. The CH 2 group difference significantly resulted in the altered turn structure at the 12Ala and 13Asp as identified by NMR spectroscopy. The antibody binding properties of the cyclopeptides studied by gD-specific monoclonal antibody (A16) in direct and competition enzyme-linked immunosorbent assay (ELISA) were also not the same. We found that peptide LK[HcyADPNRFK]GKDL exhibited higher affinity to Mab A16 than peptide LK[CADPNRFK]GKDL, however, their reactivity was significantly lower compared to the linear ones. Our results clearly show the importance of secondary structure in an antibody binding and demonstrate that even a slight modification of the primary structure dramatically could influence the immune recognition of the synthetic antigens.

Physical properties of aGeS2glass using approximateab initiomolecular dynamics

With the use of {\em ab initio} based molecular dynamics simulations we study the structural, dynamical and electronic properties of glassy g-GeS$_2$ at room temperature. From the radial distribution function we find nearest neighbor distances almost identical to the experimental values and the static structure factor is close to its experimental counterpart. From the Ge-S-Ge bond angle distribution we obtain the correct distribution of corner and edge-sharing GeS$_4$ tetrahedra. Concerning the dynamical characteristics we find in the mean square displacement of the atoms discontinuous variations corresponding either to the removal of coordination defects around a single particle or to structural rearrangements involving a larger number of atoms. Finally we calculate the vibrational density of states, which exhibits two well separated bands as well as some features characteristic of the amorphous state, and the electronic density of states showing an optical gap of 3.27 eV.