Mouth Function Determines the Shape Oscillation Pattern in Regenerating Hydra Tissue Spheres.

Hydra is a small freshwater polyp capable of regeneration from small tissue pieces and from aggregates of cells. During regeneration, a hollow bilayered sphere is formed that undergoes osmotically driven shape oscillations of inflation and rupture. These oscillations are necessary for successful regeneration. Eventually, the oscillating sphere breaks rotational symmetry along the future head-foot axis of the animal. Notably, the shape oscillations show an abrupt shift from large-amplitude, long-period oscillations to small-amplitude, short-period oscillations. It has been widely accepted that this shift in oscillation pattern is linked to symmetry breaking and axis formation, and current theoretical models of Hydra symmetry breaking use this assumption as a model constraint. However, a mechanistic explanation for the shift in oscillation pattern is lacking. Using in vivo manipulation and imaging, we quantified the shape oscillation dynamics and dissected the timing and triggers of the pattern shift. Our experiments demonstrate that the shift in the shape oscillation pattern in regenerating Hydra tissue pieces is caused by the formation of a functional mouth and not by shape symmetry breaking as previously assumed. Thus, model assumptions must be revised in light of these new experimental data, which can be used to constrain and validate improved theoretical models of pattern formation in Hydra.

Systematic chemical and molecular profiling of MLL-rearranged infant acute lymphoblastic leukemia reveals efficacy of romidepsin.

To address the poor prognosis of mixed lineage leukemia (MLL)-rearranged infant acute lymphoblastic leukemia (iALL), we generated a panel of cell lines from primary patient samples and investigated cytotoxic responses to contemporary and novel Food and Drug Administration-approved chemotherapeutics. To characterize representation of primary disease within cell lines, molecular features were compared using RNA-sequencing and cytogenetics. High-throughput screening revealed variable efficacy of currently used drugs, however identified consistent efficacy of three novel drug classes: proteasome inhibitors, histone deacetylase inhibitors and cyclin-dependent kinase inhibitors. Gene expression of drug targets was highly reproducible comparing iALL cell lines to matched primary specimens. Histone deacetylase inhibitors, including romidepsin (ROM), enhanced the activity of a key component of iALL therapy, cytarabine (ARAC) in vitro and combined administration of ROM and ARAC to xenografted mice further reduced leukemia burden. Molecular studies showed that ROM reduces expression of cytidine deaminase, an enzyme involved in ARAC deactivation, and enhances the DNA damage-response to ARAC. In conclusion, we present a valuable resource for drug discovery, including the first systematic analysis of transcriptome reproducibility in vitro, and have identified ROM as a promising therapeutic for MLL-rearranged iALL.

Micro scale self-interaction chromatography of proteins: A mAb case-study.

Self-interaction chromatography is known to be a fast, automated and promising experimental technique for determination of B22, but with the primary disadvantage of needing a significant amount of protein (>50 mg). This requirement compromises its usage as a technique for the early screening of new biotherapeutic candidates. A new scaled down SIC method has been evaluated here using a number of micro LC columns of different diameters and lengths, using typically 10 times less stationary phase than traditional SIC. Scale-down was successfully accomplished using these micro-columns, where the SIC results for a range of differing columns sizes were in agreement, as reflected by k', B22 and column volumes data. The results reported here demonstrate that a scaled down version of SIC can be easily implemented using conventional liquid chromatography system where the final amount of mAbs used was 10 times less than required by conventional SIC methodologies.

High expression of connective tissue growth factor accelerates dissemination of leukaemia.

To improve treatment of acute lymphoblastic leukaemia (ALL), a better understanding of disease development is needed to tailor new therapies. Connective tissue growth factor (CTGF/CCN2) is highly expressed in leukaemia cells from the majority of paediatric patients with B-lineage ALL (pre-B ALL). CTGF is a matricellular protein and plays a role in aggressive cancers. Here we have genetically engineered leukaemia cells to modulate CTGF expression levels. Elevated CTGF levels accelerated disease dissemination and reduced survival in NOD/SCID mice. In vitro studies showed that CTGF protein induces stromal cell proliferation, promotes adhesion of leukaemia cells to stromal cells and leads to overexpression of genes associated with cell cycle and synthesis of extracellular matrix (ECM). Corresponding data from our leukaemia xenograft models demonstrated that CTGF leads to increased proliferation of non-leukaemia cells and deposition of ECM in the bone marrow. We document for the first time a functional role of CTGF in altering disease progression in a lymphoid malignancy. The findings provide support for targeting the bone marrow microenvironment in aggressive forms of leukaemia.

Self-Interaction Chromatography of mAbs: Accurate Measurement of Dead Volumes.

PURPOSE: Measurement of the second virial coefficient B22 for proteins using self-interaction chromatography (SIC) is becoming an increasingly important technique for studying their solution behaviour. In common with all physicochemical chromatographic methods, measuring the dead volume of the SIC packed column is crucial for accurate retention data; this paper examines best practise for dead volume determination. METHOD: SIC type experiments using catalase, BSA, lysozyme and a mAb as model systems are reported, as well as a number of dead column measurements. RESULTS: It was observed that lysozyme and mAb interacted specifically with Toyopearl AF-Formyl dead columns depending upon pH and [NaCl], invalidating their dead volume usage. Toyopearl AF-Amino packed dead columns showed no such problems and acted as suitable dead columns without any solution condition dependency. Dead volume determinations using dextran MW standards with protein immobilised SIC columns provided dead volume estimates close to those obtained using Toyopearl AF-Amino dead columns. CONCLUSION: It is concluded that specific interactions between proteins, including mAbs, and select SIC support phases can compromise the use of some standard approaches for estimating the dead volume of SIC columns. Two other methods were shown to provide good estimates for the dead volume.

Biomechanical analysis of fracture risk associated with tibia deformity in children with osteogenesis imperfecta: a finite element analysis.

OBJECTIVES: Osteogenesis imperfecta (OI) frequently leads to long-bone bowing requiring a surgical intervention in severe cases to avoid subsequent fractures. However, there are no objective criteria to decide when to perform such intervention. The objective is to develop a finite element model to predict the risk of tibial fracture associated with tibia deformity in patients with OI. METHODS: A comprehensive FE model of the tibia was adapted to match bi-planar radiographs of a 7 year-old girl with OI. Ten additional models with different deformed geometries (from 2° to 24°) were created and the elasto-plastic mechanical properties were adapted to reflect OI conditions. Loads were obtained from mechanography of two-legged hopping. Two additional impact cases (lateral and torsion) were also simulated. Principal strain levels were used to define a risk criterion. RESULTS: Fracture risks for the two-legged hopping load case remained low and constant until tibia bowing reached 15° and 16° in sagittal and coronal planes respectively. Fracture risks for lateral and torsion impact were equivalent whatever the level of tibial bowing. CONCLUSIONS: The finite element model of OI tibia provides an objective means of assessing the necessity of surgical intervention for a given level of tibia bowing in OI-affected children.

The accurate measurement of second virial coefficients using self-interaction chromatography: experimental considerations.

Measurement of B22, the second virial coefficient, is an important technique for describing the solution behaviour of proteins, especially as it relates to precipitation, aggregation and crystallisation phenomena. This paper describes the best practise for calculating B22 values from self-interaction chromatograms (SIC) for aqueous protein solutions. Detailed analysis of SIC peak shapes for lysozyme shows that non-Gaussian peaks are commonly encountered for SIC, with typical peak asymmetries of 10%. This asymmetry reflects a non-linear chromatographic retention process, in this case heterogeneity of the protein-protein interactions. Therefore, it is important to use the centre of mass calculations for determining accurate retention volumes and thus B22 values. Empirical peak maximum chromatogram analysis, often reported in the literature, can result in errors of up to 50% in B22 values. A methodology is reported here for determining both the mean and the variance in B22 from SIC experiments, includes a correction for normal longitudinal peak broadening. The variance in B22 due to chemical effects is quantified statistically and is a measure of the heterogeneity of protein-protein interactions in solution. In the case of lysozyme, a wide range of B22 values are measured which can vary significantly from the average B22 values.

Effect of processing route on the surface properties of amorphous indomethacin measured by inverse gas chromatography.

The aim of this study was to investigate the effect of processing route (i.e., quench cooling and ball milling) on the surface energy heterogeneity and surface chemistry of indomethacin (IMC). Recently developed inverse gas chromatography (IGC) methodology at finite concentrations was employed to determine the surface energy distributions of crystalline, quench cooled and milled IMC samples. Surface properties of crystalline and processed IMC were measurably different as determined by the IGC and other conventional characterization techniques: differential scanning calorimetry and powder X-ray diffraction. Quench cooled IMC was in fully amorphous form. Milled IMC showed no amorphous character by calorimetric or X-ray diffraction studies. It was demonstrated that both processed IMC samples were energetically more active than the crystalline IMC. In particular, milled IMC exhibited a relatively higher dispersive surface energy and higher surface basicity (electron donor capability). This may be attributed to the creation of surface defect sites or exposure of higher energy crystal facets during the milling process. This study confirms that processing route has notable influence on the surface energy distribution and surface acid-base character. IGC was demonstrated as a powerful technique for investigating surface properties of real-world, heterogeneous pharmaceutical materials.

Myeloid differentiation factor 88 gene is involved in antiviral immunity in grass carp Ctenopharyngodon idella.

A full-length MyD88 cDNA (CiMyD88) was cloned and characterized from grass carp Ctenopharyngodon idella. CiMyD88 was found to be broadly expressed and was up-regulated by grass carp reovirus (GCRV) and CiMyD88 transcripts in vitro were rapidly elevated in C. idella kidney (CIK) cells after challenge with poly(I:C). These results suggest that CiMyD88 may be involved in the antiviral immune defence in C. idella.

FUBP3 interacts with FGF9 3' microsatellite and positively regulates FGF9 translation.

A TG microsatellite in the 3'-untranslated region (UTR) of FGF9 mRNA has previously been shown to modulate FGF9 expression. In the present study, we investigate the possible interacting protein that binds to FGF9 3'-UTR UG-repeat and study the mechanism underlying this protein-RNA interaction. We first applied RNA pull-down assays and LC-MS analysis to identify proteins associated with this repetitive sequence. Among the identified proteins, FUBP3 specifically bound to the synthetic (UG)(15) oligoribonucleotide as shown by supershift in RNA-EMSA experiments. The endogenous FGF9 protein was upregulated in response to transient overexpression and downregulated after knockdown of FUBP3 in HEK293 cells. As the relative levels of FGF9 mRNA were similar in these two conditions, and the depletion of FUBP3 had no effect on the turn-over rate of FGF9 mRNA, these data suggested that FUBP3 regulates FGF9 expression at the post-transcriptional level. Further examination using ribosome complex pull-down assay showed overexpression of FUBP3 promotes FGF9 expression. In contrast, polyribosome-associated FGF9 mRNA decreased significantly in FUBP3-knockdown HEK293 cells. Finally, reporter assay suggested a synergistic effect of the (UG)-motif with FUBP3 to fine-tune the expression of FGF9. Altogether, results from this study showed the novel RNA-binding property of FUBP3 and the interaction between FUBP3 and FGF9 3'-UTR UG-repeat promoting FGF9 mRNA translation.

Transcription factors for the modulation of pluripotency and reprogramming.

Pluripotency and self-renewal are the defining traits of embryonic stem cells (ESCs) and this status quo is maintained by the core transcription factors Oct4, Sox2, and Nanog. Genome-wide mapping of the binding sites of these pivotal factors and other ESC transcriptional regulators has unraveled the transcriptional network governing pluripotency. Strikingly, a sizeable fraction of the binding sites of Oct4 and Nanog are not conserved in mouse and human ESCs. Binding site turnover and the presence of species-specific transposable elements are some of the factors contributing to this disp arity. Hence, comparing human and mouse ESCs will shed new light on the design of transcriptional regulatory networks for pluripotency. Despite the significant differences among pluripotent mammalian stem cells, the same set of transcription factors (Oct4, Sox2, Klf4, and c-Myc) can be used to reprogram human and mouse somatic cells into induced pluripotent stem cells. Recent works also demonstrate that there are multiple ways of imparting pluripotency. For instance, the nuclear receptors Nr5a2 and Esrrb can, respectively, substitute for Oct4 and Klf4 in reprogramming. This chapter summarizes the different roles of transcription factors in the modulation of pluripotent states and in the induction of pluripotent phenotypes.

Dedicated cytogenetics factor is critical for improving karyotyping results for childhood leukaemias - experience in the National University Hospital, Singapore 1989-2006.

INTRODUCTION: Childhood leukaemia accounts for more than 40% of new childhood cancer cases. Karyotyping of cytogenetic abnormalities in such cases continues to provide critical prognostic information which allows the delivery of an appropriate intensity of treatment. Unfortunately, karyotyping of childhood leukaemia is difficult, laborious and often unsuccessful. Banding resolution tends to be poor unlike routine antenatal cytogenetics. The aim of the study is to highlight the benefit of dedicated cytogenetics in improving karyotyping results. MATERIALS AND METHODS: We analysed the impact of setting up a team of cytogeneticists in the National University Hospital (NUH) on the success of karyotyping, evaluating cytogenetic data collected from 1989 to 2006. From 1989 to 2006, 4789 cases have been processed. Among them, 369 newly diagnosed and relapsed childhood acute leukaemia cases [281 acute lymphoblastic leukaemia (ALL) and 88 acute myeloid leukaemia (AML)] have been diagnosed at NUH. A dedicated cytogenetics laboratory with clearly defined standard operating procedures and quality control was set up in 2002. It used the established recommendation of a complete analysis of at least 20 metaphases per analysis. RESULTS: Overall, the frequency of successful karyotyping was significantly higher (P = 0.002) at 90.7% (185/204) from 2002-2006 compared to 79.4% (131/165) from 1989-2001. For ALL cases, the success rate improved from 77.6% (97/125) in 1989 to 2001 to 89.1% (139/156) in the 2002 to 2006 cohort. For AML, the success rate also was significantly improved (P = 0.04) from 85% (34/40) to 95.8% (46/48). Significantly, this high rate of success is still maintained despite a yearly increase in volume. CONCLUSION: The establishment of a dedicated cytogenetics service leads to an improvement in results.

Small-Signal Performance and Modeling of sub-50nm nMOSFETs with f above 460-GHz.

We have fabricated and tested the performance of sub-50nm gate nMOSFETs to assess their suitability for mixed signal applications in the super high frequency (SHF) band, i.e. 3-30GHz. For a 30nm×40 µm×2 device, we found f(T) =465GHz at V(ds)=2V, V(g)=0.67V, which is the highest cut-off frequency reported for a MOSFET produced on bulk silicon substrate so far. However, our measurements of f(max) and noise figure indicate that parasitics impose limitations on SHF operation. We also present a high-frequency ac model appropriate to sub-50nm gate length nanotransistors, which incorporates the effects of the parasitics. The model accurately accounts for measurements of the S and Y parameters in the frequency range from 1 to 50GHz.

[p27Kip1 independently promotes neuronal differentiation and migration in the cerebral cortex]. / p27Kip1 independently promotes neuronal differentiation and migration in the cerebral cortex.

The generation of glutamatergic neurons by stem and progenitor cells is a complex process involving the tight coordination of multiple cellular activities, including cell cycle exit, initiation of neuronal differentiation and cell migration. The mechanisms that integrate these different events into a coherent program are not well understood. Here we show that the cyclin-dependent kinase inhibitor p27Kip1 plays an important role in neurogenesis in the mouse cerebral cortex, by promoting the differentiation and radial migration of cortical projection neurons. Importantly, p27Kip1 promotes neuronal differentiation and neuronal migration via two distinct mechanisms, which are themselves independent of the cell cycle regulatory function of p27Kip1. p27Kip1 inactivation by gene targeting or RNA interference results in neuronal differentiation and radial migration defects, demonstrating that p27Kip1 regulates cell migration in vivo. The differentiation defect, but not the migration defect, is rescued by overexpression of the proneural gene Neurogenin 2. p27Kip1 acts by stabilizing Neurogenin 2 protein, an activity carried by the N-terminal half of the protein. The migration defect resulting from p27Kp1 inactivation is rescued by blocking RhoA signalling, an activity that resides in the c-terminal half of p27Kip1. Thus, p27Kip1 plays a key role in cortical development, acting as a modular protein that independently regulates and couples multiple cellular pathways contributing to neurogenesis.

The electromechanics of DNA in a synthetic nanopore.

We have explored the electromechanical properties of DNA on a nanometer-length scale using an electric field to force single molecules through synthetic nanopores in ultrathin silicon nitride membranes. At low electric fields, E < 200 mV/10 nm, we observed that single-stranded DNA can permeate pores with a diameter >/=1.0 nm, whereas double-stranded DNA only permeates pores with a diameter >/=3 nm. For pores <3.0 nm diameter, we find a threshold for permeation of double-stranded DNA that depends on the electric field and pH. For a 2 nm diameter pore, the electric field threshold is approximately 3.1 V/10 nm at pH = 8.5; the threshold decreases as pH becomes more acidic or the diameter increases. Molecular dynamics indicates that the field threshold originates from a stretching transition in DNA that occurs under the force gradient in a nanopore. Lowering pH destabilizes the double helix, facilitating DNA translocation at lower fields.

Bleeding in cardiac surgery: its prevention and treatment--an evidence-based review.

Expected and unexpected bleeding occur frequently in patients undergoing cardiac surgery. Bleeding after cardiac surgery can be broadly divided into two groups: surgical (unrecognized bleeding vessel, anastomosis, or other suture line) or nonsurgical bleeding (caused by coagulopathy). Factors influencing both surgical and nonsurgical bleeding can be further broken down into those occurring preoperatively and those that occur intraoperatively and postoperatively. A thorough understanding of these factors is necessary to reduce bleeding. This is a desirable clinical goal, because excessive bleeding is associated with adverse outcomes.

Complementary and alternative medicine use in multiracial Singapore.

OBJECTIVE: To determine the prevalence of complementary and alternative medicine (CAM) use in Singapore, the factors influencing CAM use, and the attitudes, beliefs and perceptions of the general population towards CAM. DESIGN: An interviewer-administered questionnaire survey in a housing estate with demographic and socioeconomic characteristics closely matching that of Singapore. RESULTS: 76% (95% C.I. 73.9-77.9%) used CAM over a 12-month period. Females were 2.1 times (95% C.I. 1.3-3.4) more likely than males to use CAM. Chinese (84%) were the most frequent users, followed by Malays (69%) and Indians (69%), with adjusted odds ratios of 0.4 (95% C.I. 0.2-0.7) for Malays and 0.4 (95% C.I. 0.2-0.8) for Indians. Traditional Chinese Medicine (88%) was the most widely used form of CAM, followed by Traditional Malay (Jamu) Medicine (8%) and Traditional Indian (Ayuverdic) Medicine (3%). Similar to western studies, CAM was more likely to be used for maintenance of health than for treatment of illness. Different from western studies, CAM use was not independently associated with household income, marital status, age and education. Seventy-four percent did not discuss their use of CAM with their western-trained doctors. CONCLUSIONS: The high prevalence of CAM use in multi-racial Singapore suggests the same may be true in other Asian countries. Western-trained doctors need to understand CAM better and communicate more with their patients regarding CAM use. The lack of a scientific evidence base for most forms of CAM notwithstanding, its ubiquitous use worldwide is something that governments and the medical profession cannot afford to ignore.

Beyond the Gene Chip.

We describe a prospective strategy for reading the encyclopedic information encoded in the genome: using a nanopore in a membrane formed from an MOS-capacitor to sense the charge in DNA. In principle, as DNA permeates the capacitor-membrane through the pore, the electrostatic charge distribution characteristic of the molecule should polarize the capacitor and induce a voltage on the electrodes that can be measured. Silicon nanofabrication and molecular dynamic simulations with atomic detail are technological linchpins in the development of this detector. The sub-nanometer precision available through silicon nanotechnology facilitates the fabrication of the detector, and molecular dynamics provides us with a means to design it and analyze the experimental outcomes.

Usefulness of Blalock-Taussig shunt Doppler flow velocity profiles in the assessment of pulmonary artery pressure and flow.

AIM: To assess the utility of continuous wave Doppler evaluation of velocity profiles across a Blalock-Taussig (BT) shunt in the evaluation of pulmonary artery pressure and pulmonary blood flow. METHODS AND RESULTS: Eleven children with complex congenital heart disease with a BT shunt as the sole source of pulmonary blood supply were studied prospectively (median age 5 (0.3-21) months). Doppler evaluations of shunt flow velocity profile and cardiac catheterization were carried out simultaneously. Pulmonary artery pressure and flow were estimated using the modified Bernoulli equation and velocity time integral of shunt flow. There was a positive correlation between (1) the Doppler estimates for mean pulmonary artery pressure, using the diastolic flow velocity, and the mean pulmonary venous wedge pressure ( r = 0.93, SEE = 1.0 mmHG; P<0.001 ) and (2) the Doppler derived and calculated pulmonary blood flow ( r = 0.9, SEE = 0.19 l/min; P<0.001). In contrast, the Doppler estimates for mean pulmonary artery pressure using the peak or mean Doppler gradients were poor. CONCLUSION: The diastolic BT shunt flow velocity can be used reliably to predict mean pulmonary artery pressure when a BT shunt is the sole source of pulmonary artery flow. There was agreement between Doppler predicted pulmonary blood flow and catheter based calculations. These findings may prove a useful tool for perioperative management.