Fast Implementation of Approximated Maximum Likelihood Parameter Estimation for Frequency Agile Radar under Jamming Environment.

A computationally efficient target parameter estimation algorithm for frequency agile radar (FAR) under jamming environment is developed. First, the barrage noise jamming and the deceptive jamming are suppressed by using adaptive beamforming and frequency agility. Second, the analytical solution of the parameter estimation is obtained by a low-order approximation to the multi-dimensional maximum likelihood (ML) function. Due to that, fine grid-search (FGS) is avoided and the computational complexity is greatly reduced.

InSAR Baseline Estimation for Gaofen-3 Real-Time DEM Generation.

For Interferometry Synthetic Aperture Radar (InSAR), the normal baseline is one of the main factors that affects the accuracy of the ground elevation. For Gaofen-3 (GF-3) InSAR processing, the poor accuracy of the real-time orbit determination results in a large baseline error, leads to a modulation error in azimuth and a slope error in the range for timely Digital Elevation Model (DEM) generation. In order to address this problem, a novel baseline estimation approach based on Shuttle Radar Topography Mission (SRTM) DEM is proposed in this paper. Firstly, the orbit fitting is executed to remove the non-linear error factor, which is different from traditional methods. Secondly, the height errors are obtained in a slant-range plane between SRTM DEM and the GF-3 generated DEM, which can be used to estimate the baseline error with a linear variation. Then, the real-time orbit can be calibrated by the baseline error. Finally, the DEM generation is performed by using the modified baseline and orbit. This approach has the merit of spatial and precise orbital free ability. Based on the results of GF-3 interferometric SAR data for Hebei, the effectiveness of the proposed algorithm is verified and the accuracy of GF-3 real-time DEM products can be improved extensively.

Sharp transition in the immunoimmobilization of E. coli O157:H7.

This work focuses on immobilization of living enterohemorrhagic Escherichia coli O157:H7 on a gold surface as a function of the concentration of antibody tethered to the surface in the physiological environment of the organisms. Experiments are conducted using antibodies raised against bacterial surface lipopolysaccharides (LPS) tethered to gold-coated silicon wafers at surface concentrations spanning a range from submonolayers of antibodies to full coverage, an estimated 1 antibody per ∼100 nm(2). A careful optimization of surface chemistry is conducted to obtain the most efficient tethering of the antibodies to the surface. The mechanism of immobilizing the bacteria is antibody-antigen interactions between the tethered antibodies on the surface and the bacterial surface LPS firmly attached to the bacteria. This type of attachment is known as immunoimmobilization. The experiments suggest no noticeable bacterial attachment until the surface antibody concentration reaches ∼70% of a full monolayer of coverage. Above this critical antibody density, a sharp increase in immunoimmobilized bacteria is observed as they populate nearly 80% to 100% of the available surface area, reaching ∼1.2 cells/10 µm(2). This sharp increase in population is tentatively explained in terms of the minimum number of antibody-antigen interactions required per bacterium to immobilize the cell. This critical number is estimated to be ∼6000-8000 antibodies per bacterium (having a 1 µm(2) footprint on the surface) under the assumption that a full monolayer of antibodies is about 1 antibody per ∼100 nm(2). However, the large majority of the 6000-8000 antibodies are not expected to participate in antibody-antigen interactions, in that the loose LPS in solution will saturate many of these antibodies before bacteria have a chance to interact with them. Furthermore, the geometric considerations will further restrict the majority of the active antibodies from interacting with the surface antigens of the cell, reducing its effective contact area with the antibodies considerably.

Role of overexpressed CFA/I fimbriae in bacterial swimming.

Enterotoxigenic Escherichia coli CFA/I is a protective antigen and has been overexpressed in bacterial vectors, such as Salmonella Typhimurium H683, to generate vaccines. Effects that overexpressed CFA/I may engender on the bacterial host remain largely unexplored. To investigate, we constructed a high CFA/I expression strain, H683-pC2, and compared it to a low CFA/I expression strain, H683-pC, and to a non-CFA/I expression strain, H683-pY. The results showed that H683-pC2 was less able to migrate into semisolid agar (0.35%) than either H683-pC or H683-pY. Bacteria that migrated showed motility halo sizes of H683-pC2 < H683-pC < H683-pY. In the liquid culture media, H683-pC2 cells precipitated to the bottom of the tube, while those of H683-pY did not. In situ imaging revealed that H683-pC2 bacilli tended to auto-agglutinate within the semisolid agar, while H683-pY bacilli did not. When the cfaBE fimbrial fiber encoding genes were deleted from pC2, the new plasmid, pC2(-), significantly recovered bacterial swimming capability. Our study highlights the negative impact of overexpressed CFA/I fimbriae on bacterial swimming motility.

Capture efficiency of Escherichia coli in fimbriae-mediated immunoimmobilization.

Capturing pathogens on a sensor surface is one of the most important steps in the design of a biosensor. The efficiency of a biosensor at capturing pathogens has direct bearing on its sensitivity. In this work we investigated the capturing of Escherichia coli on substrates modified with antibodies targeting different types of fimbriae: K88ab (F4), K88ac (F4), K99 (F5), 987P (F6), F41, and CFA/I. The results suggest that all these fimbriae can be used for the efficient immobilization of living E. coli cells. The immobilization efficiency was affected by the purity and clone type of the antibody and the fimbriae expression level of the bacteria. For a specific fimbriae type, a higher immobilization efficiency was often observed with the monoclonal antibodies. Immunoimmobilization was utilized in an antibody microarray immersed in a mixed culture of pathogens to demonstrate the rapid and simultaneous label-free detection of multiple pathogens within less than 1 h using a single test. The capture rate of living pathogens exceeds a single bacterium per 100 × 100 µm(2) area per 0.5 h of incubation for a bulk concentration of 10(5) cfu/mL.

Serum antibodies protect against intraperitoneal challenge with enterotoxigenic Escherichia coli.

To assess whether anticolonization factor antigen I (CFA/I) fimbriae antibodies (Abs) from enterotoxigenic Escherichia coli (ETEC) can protect against various routes of challenge, BALB/c mice were immunized with a live attenuated Salmonella vaccine vector expressing CFA/I fimbriae. Vaccinated mice elicited elevated systemic IgG and mucosal IgA Abs, unlike mice immunized with the empty Salmonella vector. Mice were challenged with wild-type ETEC by the oral, intranasal (i.n.), and intraperitoneal (i.p.) routes. Naïve mice did not succumb to oral challenge, but did to i.n. challenge, as did immunized mice; however, vaccinated mice were protected against i.p. ETEC challenge. Two intramuscular (i.m.) immunizations with CFA/I fimbriae without adjuvant conferred 100% protection against i.p. ETEC challenge, while a single 30 µg dose conferred 88% protection. Bactericidal assays showed that ETEC is highly sensitive to anti-CFA/I sera. These results suggest that parenteral immunization with purified CFA/I fimbriae can induce protective Abs and may represent an alternative method to elicit protective Abs for passive immunity to ETEC.

Challenges for physical characterization of silver nanoparticles under pristine and environmentally relevant conditions.

The reported size distribution of silver nanoparticles (AgNPs) is strongly affected by the underlying measurement method, agglomeration state, and dispersion conditions. A selection of AgNP materials with vendor-reported diameters ranging from 1 nm to 100 nm, various size distributions, and biocompatible capping agents including citrate, starch and polyvinylpyrrolidone were studied. AgNPs were diluted with either deionized water, moderately hard reconstituted water, or moderately hard reconstituted water containing natural organic matter. Rigorous physico-chemical characterization by consensus methods and protocols where available enables an understanding of how the underlying measurement method impacts the reported size measurements, which in turn provides a more complete understanding of the state (size, size distribution, agglomeration, etc.) of the AgNPs with respect to the dispersion conditions. An approach to developing routine screening is also presented.

Antibody selection for immobilizing living bacteria.

We report a comparative study of the efficacy of immobilizing living bacteria by means of seven antibodies against bacterial surface antigens associated with Salmonella enterica Serovar Typhimurium. The targeted bacterial antigens were CFA/I fimbriae, flagella, lipopolysaccharides (LPS), and capsular F1 antigen. The best immobilization of S. Typhimurium was achieved with the antibody against CFA/I fimbriae. The immobilization of bacteria using antiflagellin showed significant enhancement if the flagella rotary motion was paralyzed. Of the four antibodies targeting LPS structures, only one, the antibody against the O-antigen polysaccharides, showed a relatively efficient bacterial immobilization. No bacterial immobilization was achieved using the antibody against F1 antigen, presumably because F1 protein can detach from the bacterial surface easily. The results suggest that an antibody for bacterial immunoimmobilization should target a surface antigen which extends out from the bacterial surface and is tightly attached to the bacterial cell wall. The microarrays of living S. Typhimurium cells immobilized in this manner remained viable and effective for at least 2 weeks in growth medium before a thick biofilm covered the whole surface.

Porphyrin as an ideal biomarker in the search for extraterrestrial life.

A key issue in astrobiological research is identifying target molecules that are unambiguously biological in origin and can be easily detected and recognized. We suggest porphyrin derivatives as an ideal target, because these chromophores are global in distribution and found in virtually all living organisms on Earth, including microorganisms that may approximate the early evolution of life on Earth. We discuss the inherent qualities that make porphyrin ideally suited for astrobiological research and discuss methods for detecting porphyrin molecules in terrestrial sedimentary environments. We present preliminary data to support the use of ToFSIMS as a powerful technique in the identification of porphyrins.

New fluorophores based on trifluorenylamine with very large intrinsic three-photon absorption cross sections.

[structure: see text] A new fluorophore, tri(9,9-diethyl-9H-fluorenyl)amine, was synthesized by the Buchwald-Hartwig reaction of 2-aminofluorene, and based on this molecule three more fluorophores were prepared that exhibit a very large intrinsic three-photon absorption in the near-IR region, which scales as a third power of the bridge length.

Attenuating gene expression (AGE) for vaccine development.

Live attenuated vaccines are adept in stimulating protective immunity. Methods for generating such vaccines have largely adopted strategies used with Salmonella enterica. Yet, when similar strategies were tested in other gram-negative bacteria, the virulence factors or genes responsible to incapacitate Salmonella often failed in providing the desired outcome. Consequently, conventional live vaccines rely on prior knowledge of the pathogen's virulence factors to successfully attenuate them. This can be problematic since such bacterial pathogens normally harbor thousands of genes. To circumvent this problem, we found that overexpression of bacterial appendages, e.g., fimbriae, capsule, and flagella, could successfully attenuate wild-type (wt) Salmonella enterica serovar Typhimurium. Further analysis revealed these attenuated Salmonella strains conferred protection against wt S. Typhimurium challenge as effectively as genetically defined Salmonella vaccines. We refer to this strategy as attenuating gene expression (AGE), a simple efficient approach in attenuating bacterial pathogens, greatly facilitating the construction of live vaccines.

Expression of Escherichia coli virulence usher protein attenuates wild-type Salmonella.

Generation of a live attenuated vaccine for bacterial pathogens often requires prior knowledge of the pathogen's virulence factors. We hypothesized an alternative approach of heterologous gene expression would make a wild-type (wt) pathogen more susceptible to host cell killing, thus, resulting in immunization. As proof of concept, the heterologous expression of enterotoxigenic E. coli (ETEC) colonization factor antigen I (CFA/I) was tested to attenuate Salmonella. The overexpression of CFA/I resulted in significant attenuation of wt Salmonella. In-depth studies revealed the attenuation depended on the co-expression of chaperone (CfaA) and usher (CfaC) proteins. Remarkably, the CfaAC-attenuated Salmonella conferred protection against wt Salmonella challenge. Mechanistic study indicated CfaAC made Salmonella outer membranes permeable, causing Salmonella to be vulnerable to host destruction. Thus, enhancing bacterial permeability via CfaAC represents an alternative method to attenuate pathogens despite the presence of unknown virulence factors.

Flagella overexpression attenuates Salmonella pathogenesis.

Flagella are cell surface appendages involved in a number of bacterial behaviors, such as motility, biofilm formation, and chemotaxis. Despite these important functions, flagella can pose a liability to a bacterium when serving as potent immunogens resulting in the stimulation of the innate and adaptive immune systems. Previous work showing appendage overexpression, referred to as attenuating gene expression (AGE), was found to enfeeble wild-type Salmonella. Thus, this approach was adapted to discern whether flagella overexpression could induce similar attenuation. To test its feasibility, flagellar filament subunit FliC and flagellar regulon master regulator FlhDC were overexpressed in Salmonella enterica serovar Typhimurium wild-type strain H71. The results show that the expression of either FliC or FlhDC alone, and co-expression of the two, significantly attenuates Salmonella. The flagellated bacilli were unable to replicate within macrophages and thus were not lethal to mice. In-depth investigation suggests that flagellum-mediated AGE was due to the disruptive effects of flagella on the bacterial membrane, resulting in heightened susceptibilities to hydrogen peroxide and bile. Furthermore, flagellum-attenuated Salmonella elicited elevated immune responses to Salmonella presumably via FliC's adjuvant effect and conferred robust protection against wild-type Salmonella challenge.

Nanoparticles to increase adhesive properties of biologically secreted materials for surface affixing.

Surface adhesion in nature has been the focus of intense study over the past few years. Nevertheless, research in this field has primarily concentrated on understanding the chemical aspects of adhesion. While scientists have been able to determine some of the molecular structures present in the adhesives secreted by surface climbing or surface affixing biological systems such as mussels and barnacles, the fundamental adhesion mechanisms used by these systems are still unknown. This research paper focuses on the nano-scale morphological similarities of adhesive materials secreted from marine mussels, barnacles and ivy. We discovered that marine mussels secrete large amounts of adhesive materials in the form of nanoparticles for surface adhesion. This is in keeping with our previous work, which indicated a similar phenomenon for ivy. Both studies concur with earlier research on marine barnacles, polychaetes and sea stars. Taken together, these results indicate that nanoparticles are used by natural, biological systems to increase surface adhesion. These nanoparticle surface adhesion mechanisms have important implications in terms of engineering surface adhesive materials and devices.

Bacteria survive multiple puncturings of their cell walls.

A bacterial cell wall is a highly dynamic multilayer structure interfacing the cytoplasm to the outside environment. It supports a multitude of chemical and biological processes necessary for life. It is therefore postulated that damage to the structure of bacterial cell wall would threaten cell integrity and result in cell death. We tested this hypothesis by repeatedly puncturing the cell wall of a live Gram negative bacterium Salmonella typhimurium at different locations using a sharp atomic force microscope nanotip and conducting multiple viability tests. Our study demonstrated that a S. typhimurium survives repeated puncturings of its cell wall and retains its integrity, viability, and ability to divide. The results are explained on the basis of the concept of the self-repairing of lipid bilayers and the peptidoglycan layer.

Biomolecular characterization and protein sequences of the Campanian hadrosaur B. canadensis.

Molecular preservation in non-avian dinosaurs is controversial. We present multiple lines of evidence that endogenous proteinaceous material is preserved in bone fragments and soft tissues from an 80-million-year-old Campanian hadrosaur, Brachylophosaurus canadensis [Museum of the Rockies (MOR) 2598]. Microstructural and immunological data are consistent with preservation of multiple bone matrix and vessel proteins, and phylogenetic analyses of Brachylophosaurus collagen sequenced by mass spectrometry robustly support the bird-dinosaur clade, consistent with an endogenous source for these collagen peptides. These data complement earlier results from Tyrannosaurus rex (MOR 1125) and confirm that molecular preservation in Cretaceous dinosaurs is not a unique event.

Efficient immobilization and patterning of live bacterial cells.

A monolayer of live bacterial cells has been patterned onto substrates through the interaction between CFA/I fimbriae and the corresponding antibody. Patterns of live bacteria have been prepared with cellular resolution on silicon and gold substrates for Salmonella enterica serovar Typhimurium as a model with high specificity and efficiency. The immobilized cells are capable of dividing in growth medium to form a self-sustaining bacterial monolayer on the patterned areas. Interestingly, the immobilized cells can alter their orientation on the substrate, from lying-down to standing-up, as a response to the cell density increase during incubation. This method was successfully used to sort a targeted bacterial species from a mixed culture within 2 h.

HEPES-stabilized encapsulation of Salmonella typhimurium.

Most bacteria, planktonic and sessile, are encapsulated inside loosely bound extracellular polymeric substance (EPS) in their physiological environment. Imaging a bacterium with its capsule requires lengthy sample preparation to enhance the capsular contrast. In this study, Salmonella typhimurium was investigated using atomic force microscopy for a practical means of imaging an encapsulated bacterium in air. The investigation further aimed to determine the relation between the buffers used for preparing the bacterium and the preservation of the capsular material surrounding it. It was observed that rinsing bacteria with HEPES buffer could stabilize and promote capsule formation, while rinsing with PBS, Tris, or glycine removes most of the capsular EPS. For bacteria rinsed with HEPES and air-dried, the height images showed only the contour of the capsular material, while the phase and amplitude images presented the detailed structures of the bacterial surface, including the flagella encapsulated inside the capsular EPS. The encapsulation was attributed to the cross-linking of the acidic exopolysaccharides mediated by the piperazine moiety of HEPES through electrostatic attraction. This explanation is supported by encapsulated bacteria observed for samples rinsed with N,N'-bis(2-hydroxyethyl)-piperazine solution and by the presence of entrapped HEPES within the dry capsular EPS suggested by micro-Raman spectroscopy.

Analyses of soft tissue from Tyrannosaurus rex suggest the presence of protein.

We performed multiple analyses of Tyrannosaurus rex (specimen MOR 1125) fibrous cortical and medullary tissues remaining after demineralization. The results indicate that collagen I, the main organic component of bone, has been preserved in low concentrations in these tissues. The findings were independently confirmed by mass spectrometry. We propose a possible chemical pathway that may contribute to this preservation. The presence of endogenous protein in dinosaur bone may validate hypotheses about evolutionary relationships, rates, and patterns of molecular change and degradation, as well as the chemical stability of molecules over time.

Oral vaccination with salmonella simultaneously expressing Yersinia pestis F1 and V antigens protects against bubonic and pneumonic plague.

The gut provides a large area for immunization enabling the development of mucosal and systemic Ab responses. To test whether the protective Ags to Yersinia pestis can be orally delivered, the Y. pestis caf1 operon, encoding the F1-Ag and virulence Ag (V-Ag) were cloned into attenuated Salmonella vaccine vectors. F1-Ag expression was controlled under a promoter from the caf1 operon; two different promoters (P), PtetA in pV3, PphoP in pV4, as well as a chimera of the two in pV55 were tested. F1-Ag was amply expressed; the chimera in the pV55 showed the best V-Ag expression. Oral immunization with Salmonella-F1 elicited elevated secretory (S)-IgA and serum IgG titers, and Salmonella-V-Ag(pV55) elicited much greater S-IgA and serum IgG Ab titers than Salmonella-V-Ag(pV3) or Salmonella-V-Ag(pV4). Hence, a new Salmonella vaccine, Salmonella-(F1+V)Ags, made with a single plasmid containing the caf1 operon and the chimeric promoter for V-Ag allowed the simultaneous expression of F1 capsule and V-Ag. Salmonella-(F1+V)Ags elicited elevated Ab titers similar to their monotypic derivatives. For bubonic plague, mice dosed with Salmonella-(F1+V)Ags and Salmonella-F1-Ag showed similar efficacy (>83% survival) against approximately 1000 LD(50) Y. pestis. For pneumonic plague, immunized mice required immunity to both F1- and V-Ags because the mice vaccinated with Salmonella-(F1+V)Ags protected against 100 LD(50) Y. pestis. These results show that a single Salmonella vaccine can deliver both F1- and V-Ags to effect both systemic and mucosal immune protection against Y. pestis.