Commentary : Biomaterials offer cancer research the third dimension

In a mini review from 2002, Tyler Jacks and Robert Weinberg commented on the pioneering three-dimensional (3D) culture work from Bissell laboratories and concluded: “Suddenly the study of cancer cells in two dimensions seems quaint if not archaic.” The relevance of this statement for planning and executing mechanistic biological studies and advanced drug testing has been largely disregarded by both academic researchers and the pharmaceutical and biomedical industry in the twenty-first century.

High-throughput indentational elasticity measurements of hydrogel extracellular matrix substrates

Much interest surrounds the effect of extracellular matrix (ECM) elasticity on cell behavior. Here we present a rapid method for measuring the elasticity of synthetic ECM substrates based on indentation of the substrate with a ferromagnetic sphere and optical tracking of the resulting deformation. We find that this method yields order-of-magnitude agreement with atomic force microscopy elasticity measurements, but that the degree of this agreement depends strongly on sphere density and gel elasticity. In its regime of greatest accuracy, we envision that this method may be used for high-throughput characterization of ECM substrates in cell biological studies.

Wearable neuroimaging and emotion : investigating emotional responses to architectural environments with functional near-infrared spectroscopy (fNIRS)

Supported by contemporary theories of architectural aesthetics and neuro-aesthetics this paper presents a case for the use of portable fNIRS imaging in the assessment of emotional responses to spatial environments experienced by both blind and sighted. The aim of the paper is to outline the implications of fNIRS for spatial research and practice within the field of architecture, thereby suggesting a potential taxonomy of particular formations of space and affect. Empirical neurological study of affect and spatial experience from an architectural design perspective remains in many instances unchartered. Clinical research using the portable non-invasive neuro-imaging device, functional near infrared spectroscopy (fNIRS) is proving convincing in its ability to detect emotional responses to visual, spatio-auditory and task based stimuli, providing a firm basis to potentially track cortical activity in the appraisal of architectural environments. Additionally, recent neurological studies have sought to explore the manifold sensory abilities of the visually impaired to better understand spatial perception in general. Key studies reveal that early blind participants perform as well as sighted due to higher auditory and somato-sensory spatial acuity. For instance, face vision enables the visually impaired to detect environments through skin pressure, enabling at times an instantaneous impression of the layout of an unfamiliar environment. Studies also report pleasant and unpleasant emotional responses such as ‘weightedness’ or ‘claustrophobia’ within certain interior environments, revealing a deeper perceptual sensitivity then would be expected. We conclude with justification that comparative fNIRS studies between the sighted and blind concerning spatial experience have the potential to provide greater understanding of emotional responses to architectural environments.

Large-scale interlaboratory study to develop, analytically validate and apply highly multiplexed, quantitative peptide assays to measure cancer-relevant proteins in plasma

There is an increasing need in biology and clinical medicine to robustly and reliably measure tens-to-hundreds of peptides and proteins in clinical and biological samples with high sensitivity, specificity, reproducibility and repeatability. Previously, we demonstrated that LC-MRM-MS with isotope dilution has suitable performance for quantitative measurements of small numbers of relatively abundant proteins in human plasma, and that the resulting assays can be transferred across laboratories while maintaining high reproducibility and quantitative precision. Here we significantly extend that earlier work, demonstrating that 11 laboratories using 14 LC-MS systems can develop, determine analytical figures of merit, and apply highly multiplexed MRM-MS assays targeting 125 peptides derived from 27 cancer-relevant proteins and 7 control proteins to precisely and reproducibly measure the analytes in human plasma. To ensure consistent generation of high quality data we incorporated a system suitability protocol (SSP) into our experimental design. The SSP enabled real-time monitoring of LC-MRM-MS performance during assay development and implementation, facilitating early detection and correction of chromatographic and instrumental problems. Low to sub-nanogram/mL sensitivity for proteins in plasma was achieved by one-step immunoaffinity depletion of 14 abundant plasma proteins prior to analysis. Median intra- and inter-laboratory reproducibility was <20%, sufficient for most biological studies and candidate protein biomarker verification. Digestion recovery of peptides was assessed and quantitative accuracy improved using heavy isotope labeled versions of the proteins as internal standards. Using the highly multiplexed assay, participating laboratories were able to precisely and reproducibly determine the levels of a series of analytes in blinded samples used to simulate an inter-laboratory clinical study of patient samples. Our study further establishes that LC-MRM-MS using stable isotope dilution, with appropriate attention to analytical validation and appropriate quality c`ontrol measures, enables sensitive, specific, reproducible and quantitative measurements of proteins and peptides in complex biological matrices such as plasma.

The search for genes contributing to endometriosis risk

BACKGROUND: Genetic variation contributes to the risk of developing endometriosis. This review summarizes gene mapping studies in endometriosis and the prospects of finding gene pathways contributing to disease using the latest genome-wide strategies. METHODS: To identify candidate-gene association studies of endometriosis, a systematic literature search was conducted in PubMed of publications up to 1 April 2008, using the search terms 'endometriosis' plus 'allele' or 'polymorphism' or 'gene'. Papers included were those with information on both case and control selection, showed allelic and/or genotypic results for named germ-line polymorphisms and were published in the English language. RESULTS: Genetic variants in 76 genes have been examined for association, but none shows convincing evidence of replication in multiple studies. There is evidence for genetic linkage to chromosomes 7 and 10, but the genes (or variants) in these regions contributing to disease risk have yet to be identified. Genome-wide association is a powerful method that has been successful in locating genetic variants contributing to a range of common diseases. Several groups are planning these studies in endometriosis. For this to be successful, the endometriosis research community must work together to genotype sufficient cases, using clearly defined disease classifications, and conduct the necessary replication studies in several thousands of cases and controls. CONCLUSIONS: Genes with convincing evidence for association with endometriosis are likely to be identified in large genome-wide studies. This will provide a starting point for functional and biological studies to develop better diagnosis and treatment for this debilitating disease.

Laboratory-rearing Techniques for Tephritid Fruit Flies in the South Pacific

Laboratory colonies of 15 economically important species of multi-host fruit flies (Diptera:Tephritidae) have been established in eight South Pacific island countries for the purpose of undertaking biological studies, particularly host status testing and research on quarantine treatments. Laboratory rearing techniques are based on the development of artificial diets for larvae consisting predominately of the pulp of locally available fruits including pawpaw, breadfruit and banana. The pawpaw diet is the standard diet and is used in seven countries for rearing 11 species. Diet ingredients are standard proportions of fruit pulp, hydrolysed protein and a bacterial and fungal inhibitor. The diet is particularly suitable for post-harvest treatment studies when larvae of known age are required. Another major development in the laboratory rearing system is the use of pure strains of Enterobacteriaceae bacterial cultures as important adult-feeding supplements. These bacterial cultures are dissected out of the crop of wild females, isolated by sub-culturing, and identified before supply to adults on peptone yeast extract agar plates. Most species are egged using thin, plastic receptacles perforated with 1 mm oviposition holes, with fruit juice or larval diet smeared internally as an oviposition stimulant. Laboratory rearing techniques have been standardised for all of the Pacific countries. Quality control monitoring is based on acceptable ranges in per cent egg hatch, pupal weight and pupal mortality. Colonies are rejuvenated every 6 to 12 months by crossing wild males with laboratory-reared females and vice versa. The standard rearing techniques, equipment and ingredients used in collecting, establishment, maintenance and quality control of these fruit fly species are detailed in this paper.

The Science and Art of Light

Architecture today often is praised for its tectonics, floating volumes, and sensational, gravity-defying stunts of “starchitecture.” Yet, very so often there is a building that inspires descriptions of the sublime, the experiential, and the power of light and architecture to transcend our expectations. The new Meinel Optical Sciences Research Building, designed by Phoenix-based Richärd+Bauer for the University of Arizona, Tucson, is one of these architectural rarities. Already drawing comparisons to Louis Kahn's 1965 Salk Institute for Biological Studies in La Jolla, California, the indescribable quality of light that characterizes the best of Kahn's work also resonates in Richärd+Bauer's new building. Both an expansion and renovation of the existing College of Optical Sciences facilities, the Meinel building includes teaching and research laboratories, six floors of offices, discussion areas, conference rooms, and an auditorium. The new 47,000 square-foot cast-in-place concrete structure, wrapped on three-sides in copper-alloy panels, harmonizes with the largely brick vocabulary of the campus while reflecting the ethereal quality of the wide Arizona sky. The façade, however, is merely a prelude for what awaits inside—where light and architecture seamlessly combine to create moments of pure awe.

A novel zinc bis(thiosemicarbazone) complex for live cell imaging

Fluorescent zinc complexes have recently attracted a lot of interest owing to their vast applications in cellular imaging. We report the synthesis as well as physical, chemical and biological studies of a novel zinc glyoxalbis(4-methyl-4-phenyl-3-thiosemicarbazone), Zn (GTSC)](3), complex. As compared with the well-studied zinc biacetylbis(4-methyl-3-thiosemicarbazone), Zn(ATSM), complex, which was used as a reference, Zn(GTSC)](3) had 2.5-fold higher fluorescence. When cellular fluorescence was measured using flow cytometry, we observed that Zn(GTSC)](3) had 3.4-fold to 12-fold higher fluorescence than Zn(ATSM) in various cell lines (n = 9) of different tissue origin. Confocal fluorescence microscopy results showed that Zn(GTSC)](3) appeared to have a nuclear localization within 30 mm of addition to MCF7 cells. Moreover, Zn(GTSC)](3) showed minimal cytotoxicity compared with Zn(ATSM), suggesting that Zn(GTSC)](3) may be less deleterious to cells when used as an imaging agent. Our data suggest that the novel Zn(GTSC)](3) complex can potentially serve as a biocompatible fluorescent imaging agent for live cells.

Photoresist functionalisation method for high-density protein microarrays using photolithography

Since the last decade, there is a growing need for patterned biomolecules for various applications ranging from diagnostic devices to enabling fundamental biological studies with high throughput. Protein arrays facilitate the study of protein-protein, protein-drug or protein-DNA interactions as well as highly multiplexed immunosensors based on antibody-antigen recognition. Protein microarrays are typically fabricated using piezoelectric inkjet printing with resolution limit of similar to 70-100 mu m limiting the array density. A considerable amount of research has been done on patterning biomolecules using customised biocompatible photoresists. Here, a simple photolithographic process for fabricating protein microarrays on a commercially available diazo-naphthoquinone-novolac-positive tone photoresist functionalised with 3-aminopropyltriethoxysilane is presented. The authors demonstrate that proteins immobilised using this procedure retain their activity and therefore form functional microarrays with the array density limited only by the resolution of lithography, which is more than an order of magnitude compared with inkjet printing. The process described here may be useful in the integration of conventional semiconductor manufacturing processes with biomaterials relevant for the creation of next-generation bio-chips.

How Does the Spacer Length of Cationic Gemini Lipids Influence the Lipoplex Formation with Plasmid DNA? Physicochemical and Biochemical Characterizations and their Relevance in Gene Therapy

Lipoplexes formed by the pEGFP-C3 plasmid DNA (pDNA) and lipid mixtures containing cationic gemini surfactant of the 1,2-bis(hexadecyl dimethyl ammonium) Acmes family referred to as C16CnC16, where n = 2 3, 5, or 12, and the zwitterionic helper lipid, 1,2-dioleoyl-sn-glycero-3-phosphatidylethanolamine (DOPE) have been studied from a wide variety of physical, chemical, and biological standpoints. The study has been carried out using several experimental methods, such as zeta potential, gel electrophoresis, small-angle X-ray scattering (SAXS), cryo-TEM, gene transfection, cell viability/cytotoxicity, and confocal fluorescence microscopy. As reported recently in a communication (J. Am. Chem. Soc. 2011, 133, 18014), the detailed physicochemical and biological studies confirm that, in the presence of the studied series lipid mixtures, plasmid DNA is compacted with a large number of its associated Na+ counterions. This in turn yields a much lower effective negative charge, q(pDNA)(-), a value that has been experimentally obtained for each mixed lipid mixture. Consequently, the cationic lipid (CL) complexes prepared with pDNA and CL/DOPE mixtures to be used in gene transfection require significantly less amount of CL than the one estimated assuming a value of q(DNA)(-) = -2. This drives to a considerably lower cytotoxicity of the gene vector. Depending on the CL molar composition, alpha, of the lipid mixture, and the effective charge ratio of the lipoplex, rho(eff), the reported SAXS data indicate the presence of two or three structures in the same lipoplex, one in the DOPE-rich region, other in the CL-rich region, and another one present at any CL composition. Cryo-TEM and SAXS studies with C16CnC16/DOPE-pDNA lipoplexes indicate that pDNA is localized between the mixed lipid bilayers of lamellar structures within a monolayer of similar to 2 nm. This is consistent with a highly compacted supercoiled pDNA conformation compared with that of linear DNA. Transfection studies were carried out with HEK293T, HeLa, CHO, U343, and H460 cells. The alpha and rho(eff) values for each lipid mixture were optimized on HEK293T cells for transfection, and using these values, the remaining cells were also transfected in absence (-FBS-FBS) and presence (-FBS+FBS) of serum. The transfection efficiency was higher with the CLs of shorter gemini spacers (n = 2 or 3). Each formulation expressed GFP on pDNA transfection and confocal fluorescence microscopy corroborated the results. C16C2C16/DOPE mixtures were the most efficient toward transfection among all the lipid mixtures and, in presence of serum, even better than the Lipofectamine2000, a commercial transfecting agent Each lipid combination was safe and did not show any significant levels of toxicity. Probably, the presence of two coexisting lamellar structures in lipoplexes synergizes the transfection efficiency of the lipid mixtures which are plentiful in the lipoplexes formed by CLs with short spacer (n = 2, 3) than those with the long spacer (n = 5, 12).

Cationic gemini lipids containing polyoxyethylene spacers as improved transfecting agents of plasmid DNA in cancer cells

Lipoplex nano-aggregates have been analyzed through biophysical characterization (electrostatics, structure, size and morphology), and biological studies (transfection efficiency and cell viability) in five cancer cell lines. Lipoplexes were prepared from pEGFP-C3 plasmid DNA (pDNA) and mixed liposomes, constituted by a zwitterionic lipid (DOPE) and a gemini cationic lipid (GCL) synthesized in this work, bis(hexadecyl dimethyl ammonium) oxyethylene], referred to as (C16Am)(2)(C2O)(n), (where n is the oxyethylene spacer length, n = 1, 2 or 3, between the ammonium heads). Cryo-TEM micrographs show nano-aggregates with two multilamellar structures, a cluster-type (at low-to-medium GCL composition) and a fingerprint-type that coexists with the cluster-type at medium GCL composition and appears alone at high GCL composition. SAXS diffractograms show that these lipoplexes present three lamellar structures, two of them coexisting at low and high GCL composition. The optimized transfection efficiency (TE) of pDNA was higher for lipoplexes containing GCLs with a longer (n = 3) or shorter (n = 1) polyoxyethylene spacer, at high GCL composition (alpha - 0.7) with low charge ratio (rho(eff) 2). In the all cancer cell lines studied, the TE of the optimized formulations was much better than those of both lipofectamine 2000 and lipoplexes with GCLs of the bis(hexadecyl dimethyl ammonium) alkane series recently reported. Probably, (a) the coexistence of two lamellar structures at high GCL composition synergizes the TE of these lipid vectors, (b) the orientation of the polyoxyethylene region in (C16Am)(2)(C2O)(3)/DOPE may occur in such a way that the spacing between two cationic heads becomes smaller than that in (C16Am)(2)(C2O)(2)/DOPE which is poor in terms of TE, and (c) the synergistic interactions between serum proteins and (C16Am)(2)(C2O)(n)/DOPE-pDNA lipoplexes containing a polyoxyethylene spacer improve TE, especially at high GCL content. Lipoplexes studied here show very low levels of toxicity, which confirm them as improved vectors of pDNA in gene therapy.

A novel benzimidazole derivative binds to the DNA minor groove and induces apoptosis in leukemic cells

DNA minor groove binders are an important class of chemotherapeutic agents. These small molecule inhibitors interfere with various cellular processes like DNA replication and transcription. Several benzimidazole derivatives showed affinity towards the DNA minor groove. In this study we show the synthesis and biological studies of a novel benzimidazole derivative (MH1), that inhibits topoisomerase II activity and in vitro transcription. UV-visible and fluorescence spectroscopic methods in conjunction with Hoechst displacement assay demonstrate that MH1 binds to DNA at the minor groove. Cytotoxic studies showed that leukemic cells are more sensitive to MH1 compared to cancer cells of epithelial origin. Further, we find that MH1 treatment leads to cell cycle arrest at G2/M, at early time points in Molt4 cells. Finally multiple cellular assays demonstrate that MH1 treatment leads to reduction in MMP, induction of apoptosis by activating CASPASE 9 and CASPASE 3. Thus our study shows MH1, a novel DNA minor groove binder, induces cytotoxicity efficiently in leukemic cells by activating the intrinsic pathway of apoptosis.

An oceanographic atlas of the Eastern Tropical Pacific Ocean, based on data from EASTROPIC Expedition, October-December 1955.

ENGLISH: EASTROPIC Expedition was a cooperative oceanographic study of the eastern tropical Pacific Ocean conducted during the period 2 October through 16 December 1955. The five participating agencies and the ships they operated were: Scripps Institution of Oceanography (SIO), Spencer F. Baird and Horizon; Pacific Oceanic Fisheries Investigations (POFI) of the U. S. Fish and Wildlife Service, now Honolulu Biological Laboratory (HBL) of the U. S. Bureau of Commercial Fisheries, Hugh M. Smith; California Department of Fish and Game, N. B. Scofield; the Peruvian Navy, Bondu; and the Inter-American Tropical Tuna Commission which operated no vessels but supplied equipment and personnel. In addition to these planned participations in EASTROPIC Expedition, valuable information was provided by CCOFI Cruise 5512 of the California Cooperative Oceanic Fisheries Investigations, conducted during the period 29 November -16 December 1955 with the two vessels Stranger and Black Douglas. While the observational programs of most of the agencies involved, in part, special hydrographic-biological studies of known features and processes in the region (see reports listed under Data Sources) the deployment of ships and therefore of observations was sufficient that EASTROPIC Expedition could be considered a survey of the eastern tropical Pacific. This report is concerned with that aspect of the Expedition and is a presentation in atlas form of most of the hydrographic data collected. For reasons given below, emphasis has been placed on the upper 300 m of the water column. SPANISH: La Expedición EASTROPIC es un estudio oceanográfico cooperativo del Océano Pacífico Oriental Tropical llevado a cabo durante el período del 2 de octubre al 16 de dícíembre de 1955. Las cinco agencias participantes y los barcos operados por ellas son los siguientes: Scrípps Instítutíon of Oceanography (SIO) , Spencer F. Baird y Horizon; Pacific Oceanic Fisheries Investigatíons (PO'FI) del U. S. Fish and Wildlife Service, ahora Honolulu Biological Laboratory (BHL) del U. S. Bureau of Commercial Fisheries, Hugh M. Smith; California Department of Fish and Game, N. B. Scofield; la Marina Peruana, Bondu; y la Comisión Interamericana del Atún Tropical que no dirigió ningún barco pero proporcionó equipo y personal. Además de estas participaciones planeadas en la Expedición EASTROPIC, fué suministrada información de valor por el Crucero CCOFI 5512 del California Cooperative Fisheries Investigatíons, llevado a cabo durante el período del 29 de noviembre al 16 de diciembre de 1955 con los barcos Stranger y Black Douglas. Aunque los programas de observación de la mayoría de las agencias, comprendieron en parte estudios especiales hidrográficos y biológicos de las características y de los procesos conocidos de la región (véase los informes indicados bajo Fuente de Datos), el despliegue de los barcos, y por lo tanto, de las observaciones, fué suficiente para que la Expedición EASTROPIC pudiera ser considerada como una encuesta del Pacífico Oriental Tropical. Este informe se refiere a este aspecto de la Expedición y es una presentación, en forma de un atlas, de la mayoría de los datos hidrográficos recolectados. Por las razones que se dan a continuación, se le dió énfasis a los 300 m., superiores de la columna de agua. (PDF contains 136 pages.)

Age and growth of Heterotis niloticus around Pategi in the middle River Niger, Kwara State

Biological studies of Heterotis niloticus were conducted for three years in the middle River Niger. Scales were found to be the most suitable structure in ageing Heterotis which was validated by length/histogram curve. Annual rings were found to be formed between March to June. Growth was rapid in the first two years and they reached sexual maturity at 2 years. The male grow longer while the female are bulkier. The length-weight relationship of male and female Heterotis did not differ significantly and the resulting equation for male was W = 1.25L super(2.5) and W = 1.6L super(2.7) for females respectively where W = weight (g) and L = total length. The total length to body scale relationship was found to be L = 14.3R super(2.6) where (R = oral radius of scale Heterotis growth was found to be allometric

Developing A Microfluidic-Based System To Quantify Cell Capture Efficiency

Micro-fabrication technology has substantial potential for identifying molecular markers expressed on the surfaces of tissue cells and viruses. It has been found in several conceptual prototypes that cells with such markers are able to be captured by their antibodies immobilized on microchannel substrates and unbound cells are flushed out by a driven flow. The feasibility and reliability of such a microfluidic-based assay, however, remains to be further tested. In the current work, we developed a microfluidic-based system consisting of a microfluidic chip, an image grabbing unit, data acquisition and analysis software, as well as a supporting base. Specific binding of CD59-expressed or BSA-coupled human red blood cells (RBCs) to anti-CD59 or anti-BSA antibody-immobilized chip surfaces was quantified by capture efficiency and by the fraction of bound cells. Impacts of respective flow rate, cell concentration, antibody concentration and site density were tested systematically. The measured data indicated that the assay was robust. The robustness was further confirmed by capture efficiencies measured from an independent ELISA-based cell binding assay. These results demonstrated that the system developed provided a new platform to effectively quantify cellular surface markers effectively, which promoted the potential applications in both biological studies and clinical diagnoses.