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Supplementary Table S2 from A Critical Role for the Inflammatory Response in a Mouse Model of Preneoplastic Progression

Supplementary Figure S1 from A Critical Role for the Inflammatory Response in a Mouse Model of Preneoplastic Progression

The tumor microenvironment, which includes inflammatory cells, vasculature, extracellular matrix, and fibroblasts, is a critical mediator of neoplastic progression and metastasis. Using an inducible transgenic mouse model of preneoplastic progression in the mammary gland, we discovered that activation of inducible fibroblast growth factor receptor-1 (iFGFR1) in the mammary epithelium rapidly increased the expression of several genes involved in the inflammatory response. Further analysis revealed that iFGFR1 activation induced recruitment of macrophages to the epithelium and continued association with the alveolar hyperplasias that developed following long-term activation. Studies using HC-11 mammary epithelial cells showed that iFGFR1-induced expression of the macrophage chemoattractant osteopontin was required for macrophage recruitment in vitro. Finally, conditional depletion of macrophages inhibited iFGFR1-mediated epithelial cell proliferation and lateral budding. These findings show that inflammatory cells, specifically macrophages, are critical for mediating early events in an inducible transgenic mouse model of preneoplastic progression. (Cancer Res 2006; 66(11): 5676-85)

This article reports the results of studying three novel bacteriophages, JL, Shanette, and Basilisk, which infect the pathogen Bacillus cereus and carry genes that may contribute to its pathogenesis. We analyzed host range and superinfection ability, mapped their genomes, and characterized phage structure by mass spectrometry and transmission electron microscopy (TEM). The JL and Shanette genomes were 96% similar and contained 217 open reading frames (ORFs) and 220 ORFs, respectively, while Basilisk has an unrelated genome containing 138 ORFs. Mass spectrometry revealed 23 phage particle proteins for JL and 15 for Basilisk, while only 11 and 4, respectively, were predicted to be present by sequence analysis. Structural protein homology to well-characterized phages suggested that JL and Shanette were members of the family Myoviridae , which was confirmed by TEM. The third phage, Basilisk, was similar only to uncharacterized phages and is an unrelated siphovirus. Cryogenic electron microscopy of this novel phage revealed a T=9 icosahedral capsid structure with the major capsid protein (MCP) likely having the same fold as bacteriophage HK97 MCP despite the lack of sequence similarity. Several putative virulence factors were encoded by these phage genomes, including TerC and TerD involved in tellurium resistance. Host range analysis of all three phages supports genetic transfer of such factors within the B. cereus group, including B. cereus , B. anthracis , and B. thuringiensis . This study provides a basis for understanding these three phages and other related phages as well as their contributions to the pathogenicity of B. cereus group bacteria. IMPORTANCE The Bacillus cereus group of bacteria contains several human and plant pathogens, including B. cereus , B. anthracis , and B. thuringiensis . Phages are intimately linked to the evolution of their bacterial hosts and often provide virulence factors, making the study of B. cereus phages important to understanding the evolution of pathogenic strains. Herein we provide the results of detailed study of three novel B. cereus phages, two highly related myoviruses (JL and Shanette) and an unrelated siphovirus (Basilisk). The detailed characterization of host range and superinfection, together with results of genomic, proteomic, and structural analyses, reveal several putative virulence factors as well as the ability of these phages to infect different pathogenic species.

Unique micromechanisms are required to grasp mouse egg cells while genetic material is inserted into the cell through micro or nanoinjection. To obtain the high aspect ratio needed to fully grasp the 100 μm-diameter cells, carbon-infiltrated vertically aligned carbon nanotube (CNT) forests are fabricated into various designs of compliant cell restraint mechanisms. Six preliminary designs are fabricated and tested, leading to a more effective design that meets the stated design requirements. This improved mechanism is discussed in detail. Finally, as a possible alternative to these more complicated mechanisms, a simple CNT passive cell restraint structure is also presented.

This paper investigates the accumulation and release of deoxyribonucleic acid (DNA) relative to a surface micromachined silicon lance. The lance is a critical element of nanoinjection, a proposed approach for injecting foreign DNA into living cells. The quantity of DNA accumulated on the nanoinjector lance and the speed at which it can be moved on and off the lance are essential to the proposed system's function. Prototype nanoinjector lances were fabricated using a multilayer surface micromachining process. DNA stained with the fluorescent dye 4', 6-diamidino-2-phenylidole dihydrochloride was visualized using fluorescent illumination as the DNA was accumulated on and released from the tips of microelectromechanical systems (MEMS) microlances using a 1.5-V dc source. In 5 min 46 s, the lance accumulated over 32 000 DNA molecules from a dilute DNA solution. The lance then released over 6200 DNA molecules within 6 s. Finally, the nanoinjector lance was used to inject a reporter gene encoding a red fluorescent protein into a mouse embryo, resulting in expression of the gene. The nanoinjector lance represents an important and significant step in the development of a self-contained MEMS-based DNA injection system.

The mammalian cornea contains an extensive network of resident macrophages and dendritic cells. To determine the role of these cells in LPS-induced corneal inflammation, TLR4−/− mice were sublethally irradiated and reconstituted with bone marrow cells from either enhanced GFP (eGFP)+/C57BL/6 or eGFP+/TLR4−/− mice. The corneal epithelium was abraded, LPS was added topically, and cellular infiltration to the corneal stroma and development of corneal haze were examined after 24 h. TLR4−/− mice reconstituted with C57BL/6, but not TLR4−/− bone marrow cells donor cells were found to cause infiltration of eGFP+ cells to the cornea, including neutrophils, and also increased corneal haze compared with saline-treated corneas. In a second experimental approach, corneas of transgenic macrophage Fas induced apoptosis (Mafia) mice were stimulated with LPS. These mice express eGFP and a suicide gene under control of the c-fms promoter, and systemic treatment with the FK506 dimerizer (AP20187) causes Fas-mediated apoptosis of monocytic cells. AP20187-treated mice had significantly fewer eGFP+ cells in the cornea than untreated mice. After stimulation with LPS neutrophil recruitment and development of corneal haze were impaired in AP20187-treated mice compared with untreated controls. Furthermore, LPS induced CXCL1/KC and IL-1α production within 4 h in corneas of untreated Mafia mice, which is before cellular infiltration; however, cytokine production was impaired after AP20187 treatment. Together, results from both experimental approaches demonstrate an essential role for resident corneal monocytic lineage cells (macrophages and dendritic cells) in development of corneal inflammation.

Brevibacillus laterosporus has been isolated from many different environments, including beehives, and produces compounds that are toxic to many organisms. Five B. laterosporus phages have been isolated previously. Here, we announce five additional phages that infect this bacterium, including the first B. laterosporus siphoviruses to be discovered.

Paenibacillus larvae is a pathogen of honeybees that causes American foulbrood (AFB). We isolated bacteriophages from soil containing bee debris collected near beehives in Utah. We announce five high-quality complete genome sequences, which represent the first completed genome sequences submitted to GenBank for any P. larvae bacteriophage.

Background We present a new mouse model for the study of peritoneal adhesions using macrophage Fasinduced apoptosis (Mafia) transgenic mice expressing a Fas-FKBP construct under control of the murine c-fms promoter. Mafia mice allow systemic macrophage depletion by dimerization of Fas with a synthetic dimerizer, AP20187. Results demonstrate that macrophage depletion in Mafia mice induces peritoneal adhesion formation when the peritoneal cavity is also exposed to an irritant. The Mafia mouse model presents a reproducible, non-surgical approach for research in adhesion formation and prevention. Materials and methods Mafia mice were treated with AP20187 using an intravenous (i.v.) or intraperitoneal (i.p.) injection. Control groups included mock-treated Mafia mice and both AP20187 and mock-treated wild type mice. Seven days after treatment, mice were observed for the presence of adhesions. Results After i.p. injection with AP20187, 76% of Mafia mice developed adhesions whereas none of the mock-treated Mafia or wild-type mice developed adhesions, and only one AP20187-treated wild-type mouse (5.8%) developed a mild adhesion. Mafia mice treated with AP20187 i.v. exhibited macrophage depletion not significantly different than i.p. treated mice, but did not develop adhesions. In contrast, Mafia mice treated with AP20187 i.v. developed adhesions when diluent was also injected into the peritoneal cavity, whereas i.p diluent alone had no effect. Conclusion Macrophage depletion, combined with a peritoneal irritant, results in peritoneal adhesion formation in transgenic Mafia mice. Macrophages appear to play a protective role in the development and/or repair of peritoneal adhesions.

Transgenic mice expressing an inducible suicide gene, which allows systemic and reversible elimination of macrophages, were developed. A macrophage-specific c-fms promoter was used to express enhanced green fluorescent protein and a drug-inducible suicide gene that leads to Fas-mediated apoptosis in resting and cycling cells of the macrophage lineage. Transgenic mice were fertile, of normal weight, and showed no abnormal phenotype before drug exposure. The transgene was expressed constitutively in macrophages and dendritic cells (DC) but not significantly in T cells or B cells. Induction of the suicide gene led to depletion of 70–95% of macrophages and DC in nearly all tissues examined. Depletion reduced the ability to clear bacteria from the blood and led to increased bacterial growth in the liver. Depleted mice displayed several abnormalities, including splenomegaly, lymphadenopathy, thymic atrophy, extramedullary hematopoiesis, and development of peritoneal adhesions. This new, transgenic line will be useful in investigating the role of macrophages and DC.

Mycobacteriophages – viruses of mycobacterial hosts – are genetically diverse but morphologically are all classified in the Caudovirales with double-stranded DNA and tails. We describe here a group of five closely related mycobacteriophages – Corndog, Catdawg, Dylan, Firecracker, and YungJamal – designated as Cluster O with long flexible tails but with unusual prolate capsids. Proteomic analysis of phage Corndog particles, Catdawg particles, and Corndog-infected cells confirms expression of half of the predicted gene products and indicates a non-canonical mechanism for translation of the Corndog tape measure protein. Bioinformatic analysis identifies 8–9 strongly predicted SigA promoters and all five Cluster O genomes contain more than 30 copies of a 17 bp repeat sequence with dyad symmetry located throughout the genomes. Comparison of the Cluster O phages provides insights into phage genome evolution including the processes of gene flux by horizontal genetic exchange.

Background The Bacillus genus of Firmicutes bacteria is ubiquitous in nature and includes one of the best characterized model organisms, B. subtilis, as well as medically significant human pathogens, the most notorious being B. anthracis and B. cereus. As the most abundant living entities on the planet, bacteriophages are known to heavily influence the ecology and evolution of their hosts, including providing virulence factors. Thus, the identification and analysis of Bacillus phages is critical to understanding the evolution of Bacillus species, including pathogenic strains. Results Whole genome nucleotide and proteome comparison of the 93 extant Bacillus phages revealed 12 distinct clusters, 28 subclusters and 14 singleton phages. Host analysis of these clusters supports host boundaries at the subcluster level and suggests phages as vectors for genetic transfer within the Bacillus cereus group, with B. anthracis as a distant member of the group. Analysis of the proteins conserved among these phages reveals enormous diversity and the uncharacterized nature of these phages, with a total of 4,922 protein families (phams) of which only 951 (19%) had a predicted function. In addition, 3,058 (62%) of phams were orphams (phams containing a gene product from a single phage). The most populated phams were those encoding proteins involved in DNA metabolism, virion structure and assembly, cell lysis, or host function. These included several genes that may contribute to the pathogenicity of Bacillus strains. Conclusions This analysis provides a basis for understanding and characterizing Bacillus phages and other related phages as well as their contributions to the evolution and pathogenicity of Bacillus cereus group bacteria. The presence of sparsely populated clusters, the high ratio of singletons to clusters, and the large number of uncharacterized, conserved proteins confirms the need for more Bacillus phage isolation in order to understand the full extent of their diversity as well as their impact on host evolution.

Being able to deliver molecular loads to the intracellular space of mammalian cells is a key initial step of genetic engineering. In the following work, experimentation with nanoinjection, a non-viral molecular load delivery technique, was examined in regards to transmembrane delivery of propidium iodide (PI), a dye that cannot penetrate the cell membrane and fluoresces when bound to genetic material. Investigation includes two environmental factors: peak pulse amplitude (1.5 to 3, 5, 7, or 9 V) and saline type (HBSS, PBS with potassium, and PBS without potassium). Results indicate that PBS with potassium has significantly higher PI uptake efficiency than the other two saline solutions for pulsed voltages of 3V, 5V, and 7V (with the peak value being 3.352 times greater than the positive control). Also, cell viability analysis indicates that there is a measureable reduction in cell viability for voltage protocol samples in comparison to non-voltage protocol samples. Cell viabilities range from 74.5% to 89.4% for voltage protocol samples. Findings suggest that a possible combination of physical/electrical variables work in concert with biological mechanisms to contribute to overall cell survival and PI uptake efficiency in nanoinjection.

Delivering foreign molecules into human cells is a wide and ongoing area of research. Gene therapy, or delivering nucleic acids into cells via nonviral or viral pathways, is an especially promising area for pharmaceutics. All gene therapy methods have their respective advantages and disadvantages, including limited delivery efficiency and low viability. We present an electromechanical method for delivering foreign molecules into human cells. Nanoinjection, or delivering molecules into cells using a solid lance, has proven to be highly efficient while maintaining high viability levels. This paper describes an array of solid silicon microlances that was tested to determine efficiency and viability when nanoinjecting tens of thousands of HeLa cells simultaneously. Propidium iodide (PI), a dye that fluoresces when bound to nucleic acids and does not fluoresce when unbound, was delivered into cells using the lance array. Results show that the lance array delivers PI into up to 78% of a nanoinjected HeLa cell culture, while maintaining 78–91% viability. With these results, we submit the nanoinjection method using a silicon lance array as another promising particle delivery method for mammalian culture cells.

Engaging large numbers of undergraduates in authentic scientific discovery is desirable but difficult to achieve. We have developed a general model in which faculty and teaching assistants from diverse academic institutions are trained to teach a research course for first-year undergraduate students focused on bacteriophage discovery and genomics. The course is situated within a broader scientific context aimed at understanding viral diversity, such that faculty and students are collaborators with established researchers in the field. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) course has been widely implemented and has been taken by over 4,800 students at 73 institutions. We show here that this alliance-sourced model not only substantially advances the field of phage genomics but also stimulates students’ interest in science, positively influences academic achievement, and enhances persistence in science, technology, engineering, and mathematics (STEM) disciplines. Broad application of this model by integrating other research areas with large numbers of early-career undergraduate students has the potential to be transformative in science education and research training., IMPORTANCE Engagement of undergraduate students in scientific research at early stages in their careers presents an opportunity to excite students about science, technology, engineering, and mathematics (STEM) disciplines and promote continued interests in these areas. Many excellent course-based undergraduate research experiences have been developed, but scaling these to a broader impact with larger numbers of students is challenging. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunting Advancing Genomics and Evolutionary Science (SEA-PHAGES) program takes advantage of the huge size and diversity of the bacteriophage population to engage students in discovery of new viruses, genome annotation, and comparative genomics, with strong impacts on bacteriophage research, increased persistence in STEM fields, and student self-identification with learning gains, motivation, attitude, and career aspirations.

The Bacillus cereus group is an assemblage of highly related firmicute bacteria that cause a variety of diseases in animals, including insects and humans. We announce three high-quality, complete genome sequences of bacteriophages we isolated from soil samples taken at the bases of fruit trees in Utah County, Utah. While two of the phages (Shanette and JL) are highly related myoviruses, the bacteriophage Basilisk is a siphovirus.

Paenibacillus larvae is a pathogen of honeybees that causes American foulbrood (AFB). We isolated bacteriophages from soil containing bee debris collected near beehives in Utah. We announce five high-quality complete genome sequences, which represent the first completed genome sequences submitted to GenBank for any P. larvae bacteriophage.

Mycobacteriophages infect members of the Mycobacterium genus in the phylum Actinobacteria and exhibit remarkable diversity. Genome analysis groups the thousands of known mycobacteriophages into clusters, of which the B1 subcluster is currently the third most populous. We report the complete genome sequences of five additional members of the B1 subcluster.

Nanoinjection lance arrays have been used to inject propidium iodide, a dye, into living cells. The lance arrays consist of approximately four million needle-like structures on a 2 × 2 cm silicon chip, fabricated using standard methods for silicon wafers. A culture of HeLa cancer cells, commonly used in genetic research, has been employed for testing the nanoinjection process. Propidium iodide at several concentrations has been used as the dye for cell injection. The dye binds to nucleic acids after injection, and does not fluoresce when not bound, allowing accurate flow cytometry measurement of successful injections. Over 200 wells were tested to gather reliable testing data, consisting of negative controls (no treatment), positive controls (dye added with no injection), and samples (dye added and injection performed). Tests were performed for dye concentrations of 20, 40, 60, and 80 μL per 1 mL of cell media solution, for two different lance array geometries. The multi-cell nanoinjection process presented in this paper has proven to produce positive dye uptake results in injected cells while maintaining high cell viability, with an average uptake rate of about 52% for cells injected with the highest concentration of dye. Reviewing all data, the average sample success rate is 8 times higher than the rate of dye uptake in the positive controls. Cell viability in these tests is on average 96.2%. The process may be used in a variety of research areas.Copyright © 2013 by ASME

Background Phylogenetic comparison of bacteriophages requires whole genome approaches such as dotplot analysis, genome pairwise maps, and gene content analysis. Currently mycobacteriophages, a highly studied phage group, are categorized into related clusters based on the comparative analysis of whole genome sequences. With the recent explosion of phage isolation, a simple method for phage cluster prediction would facilitate analysis of crude or complex samples without whole genome isolation and sequencing. The hypothesis of this study was that mycobacteriophage-cluster prediction is possible using comparison of a single, ubiquitous, semi-conserved gene. Tape Measure Protein (TMP) was selected to test the hypothesis because it is typically the longest gene in mycobacteriophage genomes and because regions within the TMP gene are conserved. Results A single gene, TMP, identified the known Mycobacteriophage clusters and subclusters using a Gepard dotplot comparison or a phylogenetic tree constructed from global alignment and maximum likelihood comparisons. Gepard analysis of 247 mycobacteriophage TMP sequences appropriately recovered 98.8% of the subcluster assignments that were made by whole-genome comparison. Subcluster-specific primers within TMP allow for PCR determination of the mycobacteriophage subcluster from DNA samples. Using the single-gene comparison approach for siphovirus coliphages, phage groupings by TMP comparison reflected relationships observed in a whole genome dotplot comparison and confirm the potential utility of this approach to another widely studied group of phages. Conclusions TMP sequence comparison and PCR results support the hypothesis that a single gene can be used for distinguishing phage cluster and subcluster assignments. TMP single-gene analysis can quickly and accurately aid in mycobacteriophage classification.

Development of an effective cytoplasmic delivery technique has remained an elusive goal for decades despite the success of pronuclear microinjection. Cytoplasmic injections are faster and easier than pronuclear injection and do not require the pronuclei to be visible; yet previous attempts to develop cytoplasmic injection have met with limited success. In this work we report a cytoplasmic delivery method termed intracellular electroporetic nanoinjection (IEN). IEN is unique in that it manipulates transgenes using electrical forces. The microelectromechanical system (MEMS) uses electrostatic charge to physically pick up transgenes and place them in the cytoplasm. The transgenes are then propelled through the cytoplasm and electroporated into the pronuclei using electrical pulses. Standard electroporation of whole embryos has not resulted in transgenic animals, but the MEMS device allows localized electroporation to occur within the cytoplasm for transgene delivery from the cytoplasm to the pronucleus. In this report we describe the principles which allow localized electroporation of the pronuclei including: the location of mouse pronuclei between 21 and 28 h post-hCG treatment, modeling data predicting the voltages needed for localized electroporation of pronuclei, and data on electric-field-driven movement of transgenes. We further report results of an IEN versus microinjection comparative study in which IEN produced transgenic pups with viability, transgene integration, and expression rates statistically comparable to microinjection. The ability to perform injections without visualizing or puncturing the pronuclei will widely benefit transgenic research, and will be particularly advantageous for the production of transgenic animals with embryos exhibiting reduced pronuclear visibility.

This paper introduces a metamorphic erectable cell restraint (MECR) to provide cell restraint in genetic research. A micro-electromechanical systems (MEMS) metamorphic mechanism with two phases of motion was designed to grasp individual embryos about their midplane. The first phase of motion lifts a compliant gripper approximately 40 μm (about half the diameter of an embryo). The gripper then closes in the second phase to grasp the embryo. The metamorphic mechanism includes compliant mechanism components which are analyzed here. A microscale prototype was fabricated from polysilicon and used to demonstrate the mechanism’s two phase motion.Copyright © 2012 by ASME

Many transgenic animal production techniques require egg cells to be held in place during injection of the transgene. This paper presents a micro-electromechanical systems (MEMS) mechanism that provides cell support, self-centers the cell, and requires a single linear input for actuation. This restraint device uses an innovative spatial mechanism, termed a cylindrical mechanism. The kinematics and design of the restraint are discussed. The MEMS cell restraints were fabricated using a surface micromachining process, after which the mechanism’s cell support, self-centering of the cell, and motion were verified.

Electrophoretic systems commonly use metal electrodes in their construction. This paper explores and reports the differences in the electrophoretic motion of DNA (decomposition voltage, electrical field, etc.) when one electrode is constructed from a semiconductor, silicon, rather than metal. Experimental VI (voltage-current) curves for different electrode configurations (using steel and silicon) are presented. Experimental results are used to update and validate the mathematical model to reflect the differences in material selection. In addition, the model predicts large curved-field motion for DNA motion. The model helps to quantify the effect of parameters on DNA motion in biological microelectromechanical systems in order to improve device designs and protocols.

Nanoinjection is an innovative approach for the electromechanical injection of DNA into cells, in which DNA is electrically attracted to a lance, inserted into a cell, and repelled by reversing the electrical polarity. In previous work, the lance has been micromachined as part of an on-chip microelectromechanical system. This work investigates a Stand-Alone Lance concept, where the lance and other components are independent of a common substrate. The Stand-Alone Lance may make nanoinjection more accessible to researchers and be more compatible with lab equipment commonly available in transgenic facilities. Required parameters for the electrode are investigated using a mathematical computer model. Different materials and fabrication processes for the metal lance are also considered. Additional testing was performed using tungsten probes, including mock injections on mouse egg cells. Based upon the optimistic cell viability rate, it is recommended to further investigate the use of the Stand-Alone Lance to perform nanoinjections.Copyright © 2011 by ASME

We are developing a new technique to insert foreign DNA into a living cell using a microelectromechanical system. This new technique relies on electrical forces to move DNA in a nonuniform electric field. To better understand this phenomenon, we perform integrated modeling and experiments of DNA electrophoresis. This paper describes the protocol and presents the results for DNA motion experiments using fabricated gel electrophoresis devices. We show that DNA motion is strongly correlated with ion transport (current flow) in the system. A better understanding of electrophoretic fundamentals allows for the creation of a mathematical model to predict the motion of DNA during electrophoresis in both uniform and nonuniform electric fields. The mathematical model is validated within 4% through comparison with the experimental results.

Intranasal application of vesicular stomatitis virus (VSV) induces acute encephalitis characterized by a pronounced myeloid and T cell infiltrate. The role of distinct phagocytic populations on VSV encephalitis was therefore examined in this study. Ablation of peripheral macrophages did not impair VSV encephalitis or viral clearance from the brain, whereas, depletion of splenic marginal dendritic cells impaired this response and enhanced morbidity/mortality. Selective depletion of brain perivascular macrophages also suppressed this response without altering viral clearance. Thus, two anatomically distinct phagocytic populations regulate VSV encephalitis in a non-redundant fashion although neither population is essential for viral clearance in the CNS.

This paper describes the protocol and presents the results for DNA motion experiments using fabricated macroscale gel electrophoresis devices. Gel electrophoresis is a process used to separate/move DNA, RNA or protein molecules using an electric field through a gel matrix (electrolytic solution). In electrolytic solutions, the current conduction is due to a transport of ions (anions and cations). A better understanding of electrophoretic fundamentals allows for modeling the motion of DNA during electrophoresis. The model is validated through comparison with the experimental results. The model and experimental validation will be used to improve the process of cellular nanoinjection of DNA, currently in development in our lab.Copyright © 2010 by ASME

The ultimate goal of this work is to develop an automated MEMS-based lab-on-a-chip microinjector. This paper outlines one phase of that work: testing the feasibility of a pumpless, polysilicon MEMS microneedle for use in the proposed MEMS-based lab-on-a-chip microinjector. The pumpless MEMS microneedle operates on the principle of attraction and repulsion of DNA using electrostatic charges. Prototype microneedles were fabricated using a multi-layer surface micromachining process. DNA stained with a fluorescent dye (4‘, 6-DIAMIDINO-2-PHENYLINDOLE DIHYDROCHLORIDE or DAPI) was visualized using fluorescent illumination as the DNA was attracted to and repelled from the tips of MEMS microneedles using a 1.5 V DC source. The pumpless MEMS microneedle represents an important and significant step in the development of a self-contained, automated, MEMS-based microinjection system.Copyright © 2008 by ASME

The tumor microenvironment, which includes inflammatory cells, vasculature, extracellular matrix, and fibroblasts, is a critical mediator of neoplastic progression and metastasis. Using an inducible transgenic mouse model of preneoplastic progression in the mammary gland, we discovered that activation of inducible fibroblast growth factor receptor-1 (iFGFR1) in the mammary epithelium rapidly increased the expression of several genes involved in the inflammatory response. Further analysis revealed that iFGFR1 activation induced recruitment of macrophages to the epithelium and continued association with the alveolar hyperplasias that developed following long-term activation. Studies using HC-11 mammary epithelial cells showed that iFGFR1-induced expression of the macrophage chemoattractant osteopontin was required for macrophage recruitment in vitro. Finally, conditional depletion of macrophages inhibited iFGFR1-mediated epithelial cell proliferation and lateral budding. These findings show that inflammatory cells, specifically macrophages, are critical for mediating early events in an inducible transgenic mouse model of preneoplastic progression. (Cancer Res 2006; 66(11): 5676-85)

The V antigen (LcrV) of the plague bacteriumYersinia pestisis a potent protective antigen that is under development as a vaccine component for humans. LcrV is multifunctional. On the bacterial surface it mediates delivery of a set of toxins called Yops into host cells, and as a released protein it can cause production of the immunosuppressive cytokine interleukin-10 (IL-10) and can inhibit chemotaxis of polymorphonuclear neutrophils. It is not known how these mechanisms of LcrV operate, what their relative importance is, when they function during plague, and which are critical to protection by antibody. This study investigated several of these issues. C57BL/6 mice, mice unable to express IL-10, or mice with the macrophage lineage eliminated were treated with a protective anti-LcrV antibody or a nonprotective antibody against YopM and infected intravenously byY. pestisKIM5 or a strain that lacked the genes encoding all six effector Yops. Viable bacterial numbers were determined at various times. The data indicated that Yops were necessary forYersiniagrowth after the bacteria had seeded liver and spleen. Anti-LcrV antibody prevented this growth, even in IL-10−/−mice, demonstrating that one protective mechanism for anti-LcrV antibody is independent of IL-10. Anti-LcrV antibody had no effect on persistence in organs ofY. pestislacking effector Yops, even though the yersiniae could strongly express LcrV, suggesting that Yops are necessary for building sufficient bacterial numbers to produce enough LcrV for its immunosuppressive effects. In vitro assays showed that anti-LcrV antibody could partially block delivery of Yops and downstream effects of Yops in infected macrophage-like J774A.1 cells. However, cells of the macrophage lineage were found to be dispensable for protection by anti-LcrV antibody in spleen, although they contributed to protection in liver. Taken together, the data support the hypothesis that one protective effect of the antibody is to block delivery of Yops to host cells and prevent early bacterial growth. The findings also identified the macrophage lineage as one host cell type that mediates protection.

This paper presents a surface-micromachined microelectromechanical system nanoinjector designed to inject DNA into mouse zygotes which are ≈90 μm in diameter. The proposed injection method requires that an electrically charged, DNA coated lance be inserted into the mouse zygote. The nanoinjector's principal design requirements are (1) it must penetrate the lance into the mouse zygote without tearing the cell membranes and (2) maintain electrical connectivity between the lance and a stationary bond pad. These requirements are satisfied through a two-phase, self-reconfiguring metamorphic mechanism. In the first motion subphase a change-point six-bar mechanism elevates the lance to ≈45 μm above the substrate. In the second motion subphase, a compliant folded-beam suspension allows the lance to translate in-plane at a constant height as it penetrates the cell membranes. The viability of embryos following nanoinjection is presented as a metric for quantifying how well the nanoinjector mechanism fulfills its design requirements of penetrating the zygote without causing membrane damage. Viability studies of nearly 3000 nanoinjections resulted in 71.9% of nanoinjected zygotes progressing to the two-cell stage compared to 79.6% of untreated embryos.

This paper presents a biological microelectromechanical system for injecting foreign particles into thousands of cells simultaneously. The system inserts an array of microneedles into a monolayer of cells, and the foreign particles enter the cells by diffusion. The needle array is fabricated using a series of deep reactive ion etches and produces about 4 million needles that average 1 μm in diameter and 8 μm in length with 10 μm spacing. The insertion of the needles is controlled through a compliant suspension. The compliant suspension was designed to provide for needle motion into the cells while restraining rotations or transverse motions that could result in tearing of the cell membranes. Testing was performed using propidium iodide, a membrane impermeable dye, injected into HeLa cells. Average cell survivability was found to be 97.7%, and up to 97.9% of the surviving cells received the propidium iodide.

This paper reports the effects of various parameters on the attraction and repulsion of DNA to and from a silicon lance. An understanding of DNA motion is crucial for a new approach to insert DNA, or other foreign microscopic matter, into a living cell. The approach, called nanoinjection, uses electrical forces to attract and repel the desired substance to a micromachined lance designed to pierce the cell membranes. We have developed mathematical models to predict the trajectory of DNA. The mathematical model allows investigation of the attraction/repulsion process by varying specific parameters. We find that the ground electrode placement, lance orientation and lance penetration significantly affect attraction or repulsion efficiency, while the gap, lance direction, lance tip width, lance tip half-angle and lance tip height do not.

The Bacillus genus of Firmicutes bacteria is ubiquitous in nature and includes one of the best characterized model organisms, B. subtilis, as well as medically significant human pathogens, the most notorious being B. anthracis and B. cereus. As the most abundant living entities on the planet, bacteriophages are known to heavily influence the ecology and evolution of their hosts, including providing virulence factors. Thus, the identification and analysis of Bacillus phages is critical to understanding the evolution of Bacillus species, including pathogenic strains. Whole genome nucleotide and proteome comparison of the 83 extant, fully sequenced Bacillus phages revealed 10 distinct clusters, 24 subclusters and 15 singleton phages. Host analysis of these clusters supports host boundaries at the subcluster level and suggests phages as vectors for genetic transfer within the Bacillus cereus group, with B. anthracis as a distant member. Analysis of the proteins conserved among these phages reveals enormous diversity and the uncharacterized nature of these phages, with a total of 4,442 protein families (phams) of which only 894 (20%) had a predicted function. In addition, 2,583 (58%) of phams were orphams (phams containing a single member). The most populated phams were those encoding proteins involved in DNA metabolism, virion structure and assembly, cell lysis, or host function. These included several genes that may contribute to the pathogenicity of Bacillus strains. This analysis provides a basis for understanding and characterizing Bacillus and other related phages as well as their contributions to the evolution and pathogenicity of Bacillus cereus group bacteria. The presence of sparsely populated clusters, the high ratio of singletons to clusters, and the large number of uncharacterized, conserved proteins confirms the need for more Bacillus phage isolation in order to understand the full extent of their diversity as well as their impact on host evolution.

Background Paenibacillus larvae is a Firmicute bacterium that causes American Foulbrood, a lethal disease in honeybees and is a major source of global agricultural losses. Although P. larvae phages were isolated prior to 2013, no full genome sequences of P. larvae bacteriophages were published or analyzed. This report includes an in-depth analysis of the structure, genomes, and relatedness of P. larvae myoviruses Abouo, Davis, Emery, Jimmer1, Jimmer2, and siphovirus phiIBB_Pl23 to each other and to other known phages. Results P. larvae phages Abouo, Davies, Emery, Jimmer1, and Jimmer2 are myoviruses with ~50 kbp genomes. The six P. larvae phages form three distinct groups by dotplot analysis. An annotated linear genome map of these six phages displays important identifiable genes and demonstrates the relationship between phages. Sixty phage assembly or structural protein genes and 133 regulatory or other non-structural protein genes were identifiable among the six P. larvae phages. Jimmer1, Jimmer2, and Davies formed stable lysogens resistant to superinfection by genetically similar phages. The correlation between tape measure protein gene length and phage tail length allowed identification of co-isolated phages Emery and Abouo in electron micrographs. A Phamerator database was assembled with the P. larvae phage genomes and 107 genomes of Firmicute-infecting phages, including 71 Bacillus phages. Phamerator identified conserved domains in 1,501 of 6,181 phamilies (only 24.3%) encoded by genes in the database and revealed that P. larvae phage genomes shared at least one phamily with 72 of the 107 other phages. The phamily relationship of large terminase proteins was used to indicate putative DNA packaging strategies. Analyses from CoreGenes, Phamerator, and electron micrograph measurements indicated Jimmer1, Jimmer2, Abouo and Davies were related to phages phiC2, EJ-1, KC5a, and AQ113, which are small-genome myoviruses that infect Streptococcus, Lactobacillus, and Clostridium, respectively. Conclusions This paper represents the first comparison of phage genomes in the Paenibacillus genus and the first organization of P. larvae phages based on sequence and structure. This analysis provides an important contribution to the field of bacteriophage genomics by serving as a foundation on which to build an understanding of the natural predators of P. larvae. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-745) contains supplementary material, which is available to authorized users.