RNA interference in adult Ascaris suum - an opportunity for the development of a functional genomics platform that supports organism-, tissue- and cell-based biology in a nematode parasite

The sustainable control of animal parasitic nematodes requires the development of efficient functional genomics platforms to facilitate target validation and enhance anthelmintic discovery. Unfortunately, the utility of RNA interference (RNAi) for the validation of novel drug targets in nematode parasites remains problematic. Ascaris suum is an important veterinary parasite and a zoonotic pathogen. Here we show that adult A. suum is RNAi competent, and highlight the induction, spread and consistency of RNAi across multiple tissue types. This platform provides a new opportunity to undertake whole organism-, tissue- and cell-level gene function studies to enhance target validation processes for nematode parasites of veterinary/medical significance.

Refresh-free dynamic standard-cell based memories: Application to a QC-LDPC decoder

The area and power consumption of low-density parity check (LDPC) decoders are typically dominated by embedded memories. To alleviate such high memory costs, this paper exploits the fact that all internal memories of a LDPC decoder are frequently updated with new data. These unique memory access statistics are taken advantage of by replacing all static standard-cell based memories (SCMs) of a prior-art LDPC decoder implementation by dynamic SCMs (D-SCMs), which are designed to retain data just long enough to guarantee reliable operation. The use of D-SCMs leads to a 44% reduction in silicon area of the LDPC decoder compared to the use of static SCMs. The low-power LDPC decoder architecture with refresh-free D-SCMs was implemented in a 90nm CMOS process, and silicon measurements show full functionality and an information bit throughput of up to 600 Mbps (as required by the IEEE 802.11n standard).

The construction of a whole-cell biosensor for phosphonoacetate, based on the LysR-like transcriptional regulator PhnR from Pseudomonas fluorescens 23F

The phnA gene that encodes the carbon-phosphorus bond cleavage enzyme phosphonoacetate hydrolase is widely distributed in the environment, suggesting that its phosphonate substrate may play a significant role in biogeochemical phosphorus cycling. Surprisingly, however, no biogenic origin for phosphonoacetate has yet been established. To facilitate the search for its natural source we have constructed a whole-cell phosphonoacetate biosensor. The gene encoding the LysR-type transcriptional activator PhnR, which controls expression of the phosphonoacetate degradative operon in Pseudomonas fluorescens 23F, was inserted in the broad-host-range promoter probe vector pPROBE-NT, together with the promoter region of the structural genes. Cells of Escherichia coli DH5a that contained the resultant construct, pPANT3, exhibited phosphonoacetate-dependent green fluorescent protein fluorescence in response to threshold concentrations of as little as 0.5 µM phosphonoacetate, some 100 times lower than the detection limit of currently available non-biological analytical methods; the pPANT3 biosensor construct in Pseudomonas putida KT2440 was less sensitive, although with shorter response times. From a range of other phosphonates and phosphonoacetate analogues tested, only phosphonoacetaldehyde and arsonoacetate induced green fluorescent protein fluorescence in the E. coli DH5a (pPANT3) biosensor, although at much-reduced sensitivities (50 µM phosphonoacetaldehyde and 500 µM arsonoacetate).

Recombinant cathepsin S propeptide attenuates cell invasion by inhibition of cathepsin L-like proteases in tumor microenvironment

Human cathepsin L along with cathepsin S, K, and V are collectively known as cathepsin L-like proteases due to their high homology. The overexpression and aberrant activity of each of these proteases has been implicated in tumorigenesis. These proteases contain propeptide domains that can potently inhibit both their cognate protease and other proteases within the cathepsin L-like subfamily. In this investigation, we have produced the cathepsin S propeptide recombinantly and have shown that it is a potent inhibitor of the peptidolytic, elastinolytic, and gelatinolytic activities of the cathepsin L-like proteases. In addition, we show that this peptide is capable of significantly attenuating tumor cell invasion in a panel of human cancer cell lines. Furthermore, fusion of an IgG Fc-domain to the COOH terminus of the propeptide resulted in a chimeric protein with significantly enhanced ability to block tumor cell invasion. This Fc fusion protein exhibited enhanced stability in cell-based assays in comparison with the unmodified propeptide species. This approach for the combined inhibition of the cathepsin L-like proteases may prove useful for the further study in cancer and other conditions where their aberrant activity has been implicated. Furthermore, this strategy for simultaneous inhibition of multiple cysteine cathepsins may represent the basis for novel therapeutics to attenuate tumorigenesis.

6-T SRAM cell design with nanoscale double-gate SOI MOSFETs: impact of source/drain engineering and circuit topology

The impact of source/drain engineering on the performance of a six-transistor (6-T) static random access memory (SRAM) cell, based on 22 nm double-gate (DG) SOI MOSFETs, has been analyzed using mixed-mode simulation, for three different circuit topologies for low voltage operation. The trade-offs associated with the various conflicting requirements relating to read/write/standby operations have been evaluated comprehensively in terms of eight performance metrics, namely retention noise margin, static noise margin, static voltage/current noise margin, write-ability current, write trip voltage/current and leakage current. Optimal design parameters with gate-underlap architecture have been identified to enhance the overall SRAM performance, and the influence of parasitic source/drain resistance and supply voltage scaling has been investigated. A gate-underlap device designed with a spacer-to-straggle (s/sigma) ratio in the range 2-3 yields improved SRAM performance metrics, regardless of circuit topology. An optimal two word-line double-gate SOI 6-T SRAM cell design exhibits a high SNM similar to 162 mV, I-wr similar to 35 mu A and low I-leak similar to 70 pA at V-DD = 0.6 V, while maintaining SNM similar to 30% V-DD over the supply voltage (V-DD) range of 0.4-0.9 V.

Reduction of severe bovine serum associated matrix effects on carboxymethylated dextran coated biosensor surfaces

Surface plasmon resonance (SPR) based biosensor technology has been widely used in life science research for many applications. While the advantages of speed, ruggedness, versatility, sensitivity and reproducibility are often quoted, many researchers have experienced severe problem of non-specific binding (NSB) to chip surfaces when performing analysis of biological samples Such as bovine serum. Using the direct measurement of the bovine protein leptin, present in bovine serum samples as a model, a unique buffering system has been developed and optimised which was able to significantly reduce the non-specific interactions of bovine serum components with the carboxymethyl dextran chip (CM5) surface on a Biacore SPR The developed NSB buffering system comprised of HBS-EP buffer, containing 0.5 M NaCl, 0.005% CM-dextran pH 9.0. An average NSB reduction (n = 20) of 85.9% and 87.3% was found on an unmodified CM5 surface and a CM5 with bovine leptin immobilised on the chip surface, respectively. A reduction in NSB of up to 94% was observed on both surfaces. The concentration of the constitutive components and pH of the buffer were crucial in achieving this outcome. (C) 2008 Elsevier B.V. All rights reserved.

Body Mass Index Is More Predictive of Progenitor Number in Bone Marrow Stromal Cell Population Than Age in Men: Expanding the Predictors of the Progenitor Compartment

Research has focused on in vitro expansion of bone marrow stromal cells with the aim of developing cell-based therapies or tissue-engineered constructs. There is debate over whether there is a reduction in stem cells/osteoprogenitors in the bone marrow compartment with increasing age. The aim of this study was to investigate patient factors that affect the progenitor pool in bone marrow samples. Six milliliters of marrow aspirate was obtained from the femoral canal of 38 primary hip replacement patients (aged 28-91). Outcome measures were total nucleated cell count, colony-forming efficiency, alkaline phosphatase expression, and expression of stem cell markers. There was a nonsignificant negative correlation between age and both colony-forming efficiency and stem cell marker expression. However, body mass index showed a positive, significant correlation with colony area and number in men-accounting for up to 75% of the variation. In conclusion, body mass index, not age, was highly predictive of the number of progenitors found in bone marrow, and this relationship was sex specific. These results may inform the clinician's treatment choice when considering bone marrow-based therapies. Further, it highlights the need to widen research into patient factors that affect the adult stem cell population beyond age and reinforces the need to consider sexes separately.

Eyes open to stem cells: safety trial may pave the way for cell therapy to treat retinal disease in patients

A clinical trial using human embryonic stem cell (hESC) therapy for an inherited retinal degenerative disease is about to commence. The Advanced Cell Technology (ACT) trial will treat patients with Stargardt's macular dystrophy using transplanted retinal pigment epithelium derived from hESCs. Currently, no effective treatment is available for Stargardt's disease so a stem cell-based therapy that can slow progression of this blinding condition could represent a significant breakthrough. While there are some hurdles to clear, the ACT trial is a fine example of translational research that could eventually pave the way for a range of stem cell therapies for the retina and other tissues.

Potentiation of Inflammatory CXCL8 Signalling Sustains Cell Survival in PTEN-deficient Prostate Carcinoma

Background: Inflammation and genetic instability are enabling characteristics of prostate carcinoma (PCa). Inactivation of the tumour suppressor gene phosphatase and tensin homolog (PTEN) is prevalent in early PCa. The relationship of PTEN deficiency to inflammatory signalling remains to be characterised.

Objective: To determine how loss of PTEN functionality modulates expression and efficacy of clinically relevant, proinflammatory chemokines in PCa.

Design, setting and participants: Experiments were performed in established cell-based PCa models, supported by pathologic analysis of chemokine expression in prostate tissue harvested from PTEN heterozygous (Pten(+/-)) mice harbouring inactivation of one PTEN allele.

Interventions: Small interfering RNA (siRNA)- or small hairpin RNA (shRNA)-directed strategies were used to repress PTEN expression and resultant interleukin-8 (CXCL8) signalling, determined under normal and hypoxic culture conditions.

Outcome measurements and statistical analysis: Changes in chemokine expression in PCa cells and tissue were analysed by real-time polymerase chain reaction (PCR), immunoblotting, enzyme-linked immunosorbent assay (ELISA), and immunohistochemistry; effects of chemokine signalling on cell function were assessed by cell cycle analysis, apoptosis, and survival assays.

Results and limitations: Transient (siRNA) or prolonged (shRNA) PTEN repression increased expression of CXCL8 and its receptors, chemokine (C-X-C motif) receptor (CXCR) 1 and CXCR2, in PCa cells. Hypoxia-induced increases in CXCL8, CXCR1, and CXCR2 expression were greater in magnitude and duration in PTEN-depleted cells. Autocrine CXCL8 signalling was more efficacious in PTEN-depleted cells, inducing hypoxia-inducible factor-1 (HIF-1) and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-?B) transcription and regulating genes involved in survival and angiogenesis. Increased expression of the orthologous chemokine KC was observed in regions displaying atypical cytologic features in Pten(+/-) murine prostate tissue relative to normal epithelium in wild-type PTEN (Pten(WT)) glands. Attenuation of CXCL8 signalling decreased viability of PCa cells harbouring partial or complete PTEN loss through promotion of G1 cell cycle arrest and apoptosis. The current absence of clinical validation is a limitation of the study.

Conclusions: PTEN loss induces a selective upregulation of CXCL8 signalling that sustains the growth and survival of PTEN-deficient prostate epithelium.

Development of a rapid low cost fluorescent biosensor for the detection of food contaminants

A prototype fluorescent based biosensor has been developed for the antibody based detection of food related contaminants. Its performance was characterised and showed a typical antibody binding signal of 200-2000 mV, a short term noise of 9.1 mV, and baseline slope of -0.016 mV/s over 4 h. Bulk signal detection repeatability (n=23) and reproducibility (n=3) were less than 2.4%CV. The biosensor detection unit was evaluated using two food related model systems proving its ability to monitor both binding using commercial products and inhibition through the development of an assay. This assay development potential was evaluated by observing the biosensor's performance whilst appraising several labelled antibody and glass slide configurations. The molecular interaction between biotin and an anti-biotin antibody was shown to be inhibited by 41% due to the presence of biotin in a sample. A food toxin (domoic acid) calibration curve was produced, with %CVs ranging from 2.7 to 7.8%, and a midpoint of approximately 17 ng/ml with further optimisation possible. The ultimate aim of this study was to demonstrate the working principles of this innovative biosensor as a potential portable tool with the opportunity of interchangeable assays. The biosensor design is applicable for the requirements of routine food contaminant analysis, with respect to performance, functionality and cost. (C) 2012 Elsevier B.V. All rights reserved.

Development of M13 bacteriophage-based SPR detection using Salmonella detection as a case study

Surface plasmon resonance (SPR)-based biosensor is a popular platform for real-time monitoring and sensitive detection for a myriad of targets. However, only a few studies have reported the use of bacteriophages as specific binders for SPR-based detection. This study aimed to demonstrate how filamentous M13 bacteriophages expressing 12-mer peptides can be employed in an SPR-based assay, using a Salmonella-specific bacteriophage as a model binder to detect the foodborne bacterium Salmonella. Several important factors (immobilization buffers and methods, and interaction buffers) for a successful bacteriophage-based SPR assay were optimized. As a result, a Salmonella-specific bacteriophage-based SPR assay was achieved, with very low cross reactivity with other non-target foodborne pathogens and detection limits of 8.0 × 10⁷ and 1.3 × 10⁷ CFU/mL for one-time and five-time immobilized sensors, respectively. This proof-of-concept study demonstrates the feasibility of using M13 bacteriophages expressing target-specific peptides as a binder in a rapid and label-free SPR assay for pathogen detection.

Cell Coverage Optimization for the Multicell Massive MIMO Uplink

We investigate the cell coverage optimization problem for the massive multiple-input multiple-output (MIMO) uplink. By deploying tilt-adjustable antenna arrays at the base stations, cell coverage optimization can become a promising technique which is able to strike a compromise between covering cell-edge users and pilot contamination suppression. We formulate a detailed description of this optimization problem by maximizing the cell throughput, which is shown to be mainly determined by the user distribution within several key geometrical regions. Then, the formulated problem is applied to different example scenarios: for a network with hexagonal shaped cells and uniformly distributed users, we derive an analytical lower bound of the ergodic throughput in the objective cell, based on which, it is shown that the optimal choice for the cell coverage should ensure that the coverage of different cells does not overlap; for a more generic network with sectoral shaped cells and non-uniformly distributed users, we propose an analytical approximation of the ergodic throughput. After that, a practical coverage optimization algorithm is proposed, where the optimal solution can be easily obtained through a simple one-dimensional line searching within a confined searching region. Our numerical results show that the proposed coverage optimization method is able to greatly increase the system throughput in macrocells for the massive MIMO uplink transmission, compared with the traditional schemes where the cell coverage is fixed.