Whole-cell biochips for bio-sensing: integration of live cells and inanimate surfaces

Recent advances in the convergence of the biological, chemical, physical, and engineering sciences have opened new avenues of research into the interfacing of diverse biological moieties with inanimate platforms. A main aspect of this field, the integration of live cells with micro-machined platforms for high throughput and bio-sensing applications, is the subject of the present review. These unique hybrid systems are configured in a manner that ensures positioning of the cells in designated patterns, and enables cellular viability maintenance, and monitoring of cellular functionality. Here we review both animate and inanimate surface properties and how they affect cellular attachment, describe relevant modifications of both types of surfaces, list technologies for platform engineering and for cell deposition in the desired configurations, and discuss the influence of various deposition and immobilization methods on the viability and performance of the immobilized cells.     

Involvement of ligninolytic enzymes and Fenton-like reaction in humic acid degradation by Trametes sp

Trametes sp. M23, isolated from biosolids compost was found to decompose humic acids (HA). A low N (LN) medium (C/N, 53) provided suitable conditions for HA degradation, whereas in a high N (HN) medium (C/N, 10), HA was not degraded. In the absence of Mn²⁺, HA degradation was similar to that in Mn²⁺-containing medium. In contrast, MnP activity was significantly affected by Mn²⁺. Laccase activity exhibited a negative correlation to HA degradation, while LiP activity was not detected. Thus, ligninolytic enzymes activity could provide only a partial explanation for the HA-degradation mechanism. The decolorization of two dyes, Orange II and Brilliant Blue R250, was also determined. Similar to HA degradation, under LN conditions, decolorization occurred independently of the presence of Mn²⁺. We investigated the possible involvement of a Fenton-like reaction in HA degradation. The addition of DMSO, an OH-radical scavenger, to LN media resulted in a significant decrease in HA bleaching. The rate of extracellular Fe³⁺ reduction was much higher in the LN vs. HN medium. In addition, the rate of reduction was even higher in the presence of HA in the medium. In vitro HA bleaching in non-inoculated media was observed with H₂O₂ amendment to a final concentration of 200 mM (obtained by 50 mM amendments for 4 days) and Fe²⁺ (36 mM). After 4 days of incubation, HA decolorization was similar to the biological treatment. These results support our hypothesis that a Fenton-like reaction is involved in HA degradation by Trametes sp. M23.     

Bio-Imaging of Colorectal Cancer Models Using Near Infrared Labeled Epidermal Growth Factor

Novel strategies that target the epidermal growth factor receptor (EGFR) have led to the clinical development of monoclonal antibodies, which treat metastatic colorectal cancer (mCRC) but only subgroups of patients with increased wild type KRAS and EGFR gene copy, respond to these agents. Furthermore, resistance to EGFR blockade inevitably occurred, making future therapy difficult. Novel bio-imaging (BOI) methods may assist in quantization of EGFR in mCRC tissue thus complementing the immunohistochemistry methodology, in guiding the future treatment of these patients. The aim of the present study was to explore the usefulness of near infrared-labeled EGF (EGF-NIR) for bio-imaging of CRC using in vitro and in vivo orthotopic tumor CRC models and ex vivo human CRC tissues. We describe the preparation and characterization of EGF-NIR and investigate binding, using BOI of a panel of CRC cell culture models resembling heterogeneity of human CRC tissues. EGF-NIR was specifically and selectively bound by EGFR expressing CRC cells, the intensity of EGF-NIR signal to background ratio (SBR) reflected EGFR levels, dose-response and time course imaging experiments provided optimal conditions for quantization of EGFR levels by BOI. EGF-NIR imaging of mice with HT-29 orthotopic CRC tumor indicated that EGF-NIR is more slowly cleared from the tumor and the highest SBR between tumor and normal adjacent tissue was achieved two days post-injection. Furthermore, images of dissected tissues demonstrated accumulation of EGF-NIR in the tumor and liver. EGF-NIR specifically and strongly labeled EGFR positive human CRC tissues while adjacent CRC tissue and EGFR negative tissues expressed weak NIR signals. This study emphasizes the use of EGF-NIR for preclinical studies. Combined with other methods, EGF-NIR could provide an additional bio-imaging specific tool in the standardization of measurements of EGFR expression in CRC tissues.     

Met Kinetic Signature Derived from the Response to HGF/SF in a Cellular Model Predicts Breast Cancer Patient Survival

To determine the signaling pathways leading from Met activation to metastasis and poor prognosis, we measured the kinetic gene alterations in breast cancer cell lines in response to HGF/SF. Using a network inference tool we analyzed the putative protein-protein interaction pathways leading from Met to these genes and studied their specificity to Met and prognostic potential. We identified a Met kinetic signature consisting of 131 genes. The signature correlates with Met activation and with response to anti-Met therapy (p<0.005) in in-vitro models. It also identifies breast cancer patients who are at high risk to develop an aggressive disease in six large published breast cancer patient cohorts (p<0.01, N>1000). Moreover, we have identified novel putative Met pathways, which correlate with Met activity and patient prognosis. This signature may facilitate personalized therapy by identifying patients who will respond to anti-Met therapy. Moreover, this novel approach may be applied for other tyrosine kinases and other malignancies.     

Modification of protein crystal packing by systematic mutations of surface residues: Implications on biotemplating and crystal porosity

Bioinspired nano‐scale biotemplating for the development of novel composite materials has recently culminated in several demonstrations of nano‐structured hybrid materials. Protein crystals, routinely prepared for the elucidation of protein 3D structures by X‐ray crystallography, present an ordered and highly accurate 3D array of protein molecules. Inherent to the 3D arrangement of the protein “building blocks” in the crystal, a complementary 3D array of interconnected cavities—voids array, exhibiting highly ordered porosity is formed. The porous arrays of protein crystal may serve as a nano‐structured, accurate biotemplate by a “filling” process. These cavities arrays are shaped by the mode of protein packing throughout the crystallization process. Here we propose and demonstrate feasibility of targeting site specific mutations to modify protein's surface to affect protein crystal packing, enabling the generation of a series of protein crystal “biotemplates” all originating from same parent protein. The selection of these modification sites was based on in silico analysis of protein–protein interface contact areas in the parent crystal. The model protein selected for this study was the N‐terminal type II cohesin from the cellulosomal scaffold in ScaB subunit of Acetivibrio cellulolyticus and mutations were focused on lysine residues involved in protein packing as prime target. The impact of systematically mutating these lysine residues on protein packing and its resulting interconnected cavities array were found to be most significant when surface lysine residues were substituted to tryptophan residues. Our results demonstrate the feasibility of using pre‐designed site directed mutations for the generation of a series of protein crystal biotemplates from a “parent” protein. Biotechnol. Bioeng. 2009; 104: 444–457 © 2009 Wiley Periodicals, Inc.     

Fungal activities involved in lignocellulose degradation by Pleurotus

Summary During growth of Pleurotus on cotton straw both the straw in general and the lignin in particular were degraded. After 4 days of fungal growth, activity of laccase, catechol oxidase, peroxidase, and cellulase were detected. This activity, however, declined rapidly after 8–10 days of growth.Lignin degradation began after 10 days and reached a maximum after 21 days. It would seem that the preliminary action of laccase is a prerequisite for lignin degradation.The Pleurotus ostreatus strain P₃ had no detectable laccase activity and showed very poor ability to degrade cotton straw and lignin.Water extract of cotton straw was found to be a potent inducer of laccase in liquid medium and had an effect much stronger than several small phenolic compounds. The degradation of washed cotton straw and lignin from this straw was lower than native straw, so was laccase activity on this medium. High carbon dioxide concentrations encouraged straw degradation by P. ostreatus florida but severly limited lignin degradation. Other fungi including the known lignin degrader Phanarochaete chrysosporium were able to degrade up to 40% of cotton straw dry weight within 21 days of fungal growth. The percentage degradation of lignin, however, was very low (only 10% in 21 days). Pleurotus ostreatus florida was able to degrade up to 56% of the lignin within this time.After treatment with P. ostreatus florida almost four times as much glucose was released when the straw was treated with commercial cellulases, showing increased availability of cellulose.It is suggested that treatment with P. ostreatus florida may be used to enrich low value food materials for ruminant animals.     

Inhibition of polyamine synthesis reduces the growth rate and delays the expression of differentiated phenotypes in primary cultures of embryonic mesoderm from chick

Summary Inhibition of polyamine synthesis in early chick embryos blocks their development at gastrulation. Analyses of arrested embryos show that mesodermal outgrowth and differentiation are drastically impaired. To study these effects in greater detail, we have used primary cultures of embryonic mesoderm from chick. The cultures were treated with -difluoromethylornithine (DFMO), an enzyme-activated irreversible inhibitor of ornithine decarboxylase, the first and rate-limiting enzyme in polyamine synthesis. In control culture medium, mesodermal cells retained their in ovo outgrowth behavior and differentiation pattern. Addition of 10 mM DFMO to the culture medium, however, retarded attachment and outgrowth, and reduced the rate of proliferation of the mesodermal cells. Furthermore, the expression of differentiated phenotypes, such as beating heart tissue, erythroid cells, and adipocyte-like cells, was delayed. Simultaneous addition of 100 M putrescine prevented or reduced the effects of DFMO, showing that these were indeed caused by polyamine deficiency. In the DFMO-treated mesoderm, DNA synthesis was markedly suppressed by the first day. Similar effects on RNA and protein synthesis developed at a later time. Our data suggest that a reduction in the concentrations of the polyamines decreases the rate of mesodermal cell proliferation, and as a conseqence delays the expression of differentiated phenotypes.     

Uptake of putrescine by Tetrahymena

Summary The uptake of the diamine ³H-putrescine by Tetrahymena pyriformis GL was studied in cultures which were synchronized by heat shocks. An inverse correlation was found between the uptake of putrescine and the acid stability of DNA, but there was also a parallelism between putrescine uptake and the intracellular amount of putrescine. There was no evidence for a transformation of the labeled putrescine to other amino compounds within the cells. Electronmicroscopical autoradiography showed a structure-bound radioactivity localized to nuclear and mitochondrial structures. In the nucleus, both the chromatin and the nucleoli showed labeling.The authors are indebted to fil. kand. Per Arlock, who participated in some preliminary experiments, and to Mrs Siv Nilsson and Mrs Annagreta Petersen for skilful technical assistance. The investigation was financially supported by the Swedish Natural Science Research Council, the Swedish Cancer Society and the C.-B. Nathhorst Scientific Foundation.