Experimental studies on the flow through soft tubes and channels

Experiments conducted in channels/tubes with height/diameter less than 1 mm with soft walls made of polymer gels show that the transition Reynolds number could be significantly lower than the corresponding value of 1200 for a rigid channel or 2100 for a rigid tube. Experiments conducted with very viscous fluids show that there could be an instability even at zero Reynolds number provided the surface is sufficiently soft. Linear stability studies show that the transition Reynolds number is linearly proportional to the wall shear modulus in the low Reynolds number limit, and it increases as the 1/2 and 3/4 power of the shear modulus for the `inviscid' and `wall mode' instabilities at high Reynolds number. While the inviscid instability is similar to that in the flow in a rigid channel, the mechanisms of the viscous and wall mode instabilities are qualitatively different. These involve the transfer of energy from the mean flow to the fluctuations due to the shear work done at the interface. The experimental results for the viscous instability mechanism are in quantitative agreement with theoretical predictions. At high Reynolds number, the instability mechanism has characteristics similar to the wall mode instability. The experimental transition Reynolds number is smaller, by a factor of about 10, than the theoretical prediction for the parabolic flow through rigid tubes and channels. However, if the modification in the tube shape due to the pressure gradient, and the consequent modification in the velocity profile and pressure gradient, are incorporated, there is quantitative agreement between theoretical predictions and experimental results. The transition has important practical consequences, since there is a significant enhancement of mixing after transition.

After transition in a soft-walled microchannel

In comparison to the flow in a rigid channel, there is a multifold reduction in the transition Reynolds number for the flow in a microchannel when one of the walls is made sufficiently soft, due to a dynamical instability induced by the fluid-wall coupling, as shown by Verma & Kumaran (J. Fluid Mech., vol. 727, 2013, pp. 407-455). The flow after transition is characterised using particle image velocimetry in the x-y plane, where x is the streamwise direction and y is the cross-stream coordinate along the small dimension of the channel of height 0.2-0.3 mm. The flow after transition is characterised by a mean velocity profile that is flatter at the centre and steeper at the walls in comparison to that for a laminar flow. The root mean square of the streamwise fluctuating velocity shows a characteristic sharp increase away from the wall and a maximum close to the wall, as observed in turbulent flows in rigid-walled channels. However, the profile is asymmetric, with a significantly higher maximum close to the soft wall in comparison to that close to the hard wall, and the Reynolds stress is found to be non-zero at the soft wall, indicating that there is a stress exerted by fluid velocity fluctuations on the wall. The maximum of the root mean square of the velocity fluctuations and the Reynolds stress (divided by the fluid density) in the soft-walled microchannel for Reynolds numbers in the range 250-400, when scaled by suitable powers of the maximum velocity, are comparable to those in a rigid channel at Reynolds numbers in the range 5000-20 000. The near-wall velocity profile shows no evidence of a viscous sublayer for (y upsilon(*)/nu) as low as two, but there is a logarithmic layer for (y upsilon(*)/nu) up to approximately 30, where the von Karman constants are very different from those for a rigid-walled channel. Here, upsilon(*) is the friction velocity, nu is the kinematic viscosity and y is the distance from the soft surface. The surface of the soft wall in contact with the fluid is marked with dye spots to monitor the deformation and motion along the fluid-wall interface. Low-frequency oscillations in the displacement of the surface are observed after transition in both the streamwise and spanwise directions, indicating that the velocity fluctuations are dynamically coupled to motion in the solid.

Combined Effect of Cryogel Matrix and Temperature-Reversible Soluble-Insoluble Polymer for the Development of in Vitro Human Liver Tissue

Hepatic cell culture on a three-dimensional (3D) matrix or as a hepatosphere appears to be a promising in vitro biomimetic system for liver tissue engineering applications. In this study, we have combined the concept of a 3D scaffold and a spheroid culture to develop an in vitro model to engineer liver tissue for drug screening. We have evaluated the potential of poly(ethylene glycol)-alginate-gelatin (PAG) cryogel matrix for in vitro culture of human liver cell lines. The synthesized cryogel matrix has a flow rate of 7 mL/min and water uptake capacity of 94% that enables easy nutrient transportation in the in vitro cell culture. Youngs modulus of 2.4 kPa and viscoelastic property determine the soft and elastic nature of synthesized cryogel. Biocompatibility of PAG cryogel was evaluated through MTT assay of HepG2 and Huh-7 cells on matrices. The proliferation and functionality of the liver cells were enhanced by culturing hepatic cells as spheroids (hepatospheres) on the PAG cryogel using temperature-reversible soluble-insoluble polymer, poly(N-isopropylacrylamide) (PNIPAAm). Pore size of the cryogel above 100 mu m modulated spheroid size that can prevent hypoxia condition within the spheroid culture. Both the hepatic cells have shown a significant difference (P < 0.05) in terms of cell number and functionality when cultured with PNIPAAm. After 10 days of culture using 0.05% PNIPAAm, the cell number increased by 11- and 7-fold in case of HepG2 and Huh-7 cells, respectively. Similarly, after 10 days of hepatic spheroids culture on PAG cryogel, the albumin production, urea secretion, and CYP450 activity were significantly higher in case of culture with PNIPAAm. The developed tissue mass on the PAG cryogel in the presence of PNIPAAm possess polarity, which was confirmed using F-actin staining and by presence of intercellular bile canalicular lumen. The developed cryogel matrix supports liver cells proliferation and functionality and therefore can be used for in vitro and in vivo drug testing.

Single cell proteomics microchip to profile immune function, with applications in stem cell biology, translational disease mechanism study and clinical therapeutics monitoring

In response to infection or tissue dysfunction, immune cells develop into highly heterogeneous repertoires with diverse functions. Capturing the full spectrum of these functions requires analysis of large numbers of effector molecules from single cells. However, currently only 3-5 functional proteins can be measured from single cells. We developed a single cell functional proteomics approach that integrates a microchip platform with multiplex cell purification. This approach can quantitate 20 proteins from >5,000 phenotypically pure single cells simultaneously. With a 1-million fold miniaturization, the system can detect down to ~100 molecules and requires only ~104 cells. Single cell functional proteomic analysis finds broad applications in basic, translational and clinical studies. In the three studies conducted, it yielded critical insights for understanding clinical cancer immunotherapy, inflammatory bowel disease (IBD) mechanism and hematopoietic stem cell (HSC) biology.

To study phenotypically defined cell populations, single cell barcode microchips were coupled with upstream multiplex cell purification based on up to 11 parameters. Statistical algorithms were developed to process and model the high dimensional readouts. This analysis evaluates rare cells and is versatile for various cells and proteins. (1) We conducted an immune monitoring study of a phase 2 cancer cellular immunotherapy clinical trial that used T-cell receptor (TCR) transgenic T cells as major therapeutics to treat metastatic melanoma. We evaluated the functional proteome of 4 antigen-specific, phenotypically defined T cell populations from peripheral blood of 3 patients across 8 time points. (2) Natural killer (NK) cells can play a protective role in chronic inflammation and their surface receptor – killer immunoglobulin-like receptor (KIR) – has been identified as a risk factor of IBD. We compared the functional behavior of NK cells that had differential KIR expressions. These NK cells were retrieved from the blood of 12 patients with different genetic backgrounds. (3) HSCs are the progenitors of immune cells and are thought to have no immediate functional capacity against pathogen. However, recent studies identified expression of Toll-like receptors (TLRs) on HSCs. We studied the functional capacity of HSCs upon TLR activation. The comparison of HSCs from wild-type mice against those from genetics knock-out mouse models elucidates the responding signaling pathway.

In all three cases, we observed profound functional heterogeneity within phenotypically defined cells. Polyfunctional cells that conduct multiple functions also produce those proteins in large amounts. They dominate the immune response. In the cancer immunotherapy, the strong cytotoxic and antitumor functions from transgenic TCR T cells contributed to a ~30% tumor reduction immediately after the therapy. However, this infused immune response disappeared within 2-3 weeks. Later on, some patients gained a second antitumor response, consisted of the emergence of endogenous antitumor cytotoxic T cells and their production of multiple antitumor functions. These patients showed more effective long-term tumor control. In the IBD mechanism study, we noticed that, compared with others, NK cells expressing KIR2DL3 receptor secreted a large array of effector proteins, such as TNF-α, CCLs and CXCLs. The functions from these cells regulated disease-contributing cells and protected host tissues. Their existence correlated with IBD disease susceptibility. In the HSC study, the HSCs exhibited functional capacity by producing TNF-α, IL-6 and GM-CSF. TLR stimulation activated the NF-κB signaling in HSCs. Single cell functional proteome contains rich information that is independent from the genome and transcriptome. In all three cases, functional proteomic evaluation uncovered critical biological insights that would not be resolved otherwise. The integrated single cell functional proteomic analysis constructed a detail kinetic picture of the immune response that took place during the clinical cancer immunotherapy. It revealed concrete functional evidence that connected genetics to IBD disease susceptibility. Further, it provided predictors that correlated with clinical responses and pathogenic outcomes.

Deep tissue fluorescence imaging with time-reversed light

Advances in optical techniques have enabled many breakthroughs in biology and medicine. However, light scattering by biological tissues remains a great obstacle, restricting the use of optical methods to thin ex vivo sections or superficial layers in vivo. In this thesis, we present two related methods that overcome the optical depth limit—digital time reversal of ultrasound encoded light (digital TRUE) and time reversal of variance-encoded light (TROVE). These two techniques share the same principle of using acousto-optic beacons for time reversal optical focusing within highly scattering media, like biological tissues. Ultrasound, unlike light, is not significantly scattered in soft biological tissues, allowing for ultrasound focusing. In addition, a fraction of the scattered optical wavefront that passes through the ultrasound focus gets frequency-shifted via the acousto-optic effect, essentially creating a virtual source of frequency-shifted light within the tissue. The scattered ultrasound-tagged wavefront can be selectively measured outside the tissue and time-reversed to converge at the location of the ultrasound focus, enabling optical focusing within deep tissues. In digital TRUE, we time reverse ultrasound-tagged light with an optoelectronic time reversal device (the digital optical phase conjugate mirror, DOPC). The use of the DOPC enables high optical gain, allowing for high intensity optical focusing and focal fluorescence imaging in thick tissues at a lateral resolution of 36 µm by 52 µm. The resolution of the TRUE approach is fundamentally limited to that of the wavelength of ultrasound. The ultrasound focus (~ tens of microns wide) usually contains hundreds to thousands of optical modes, such that the scattered wavefront measured is a linear combination of the contributions of all these optical modes. In TROVE, we make use of our ability to digitally record, analyze and manipulate the scattered wavefront to demix the contributions of these spatial modes using variance encoding. In essence, we encode each spatial mode inside the scattering sample with a unique variance, allowing us to computationally derive the time reversal wavefront that corresponds to a single optical mode. In doing so, we uncouple the system resolution from the size of the ultrasound focus, demonstrating optical focusing and imaging between highly diffusing samples at an unprecedented, speckle-scale lateral resolution of ~ 5 µm. Our methods open up the possibility of fully exploiting the prowess and versatility of biomedical optics in deep tissues.

High-fidelity replication of Dammann gratings using soft lithography

We report the experimental results of using the soft lithography method for replication of Dammann gratings. By using an elastomeric stamp, uniform grating structures were transferred to the LTV-curable polymer. To evaluate the quality of the replication, diffraction images and light intensity were measured. Compared with the master devices, the replicas of Dammann gratings show a slight deviation in both surface relief profile and optical performance. Experimental results demonstrated that high-fidelity replication of Dammann gratings is realized by using soft lithography with low cost and high throughput. (C) 2008 Optical Society of America.

Complexity and Uniqueness of the Aromatic Profile of Smoked and Unsmoked Herreno Cheese

In this work, the volatile fraction of unsmoked and smoked Herreno cheese, a type of soft cheese from the Canary Islands, has been characterized for the first time. In order to evaluate if the position in the smokehouse could influence the volatile profile of the smoked variety, cheeses smoked at two different heights were studied. The volatile components were extracted by Solid Phase Microextraction using a divinylbenzene/carboxen/polydimethylsiloxane fiber, followed by Gas Chromatography/Mass Spectrometry. In total, 228 components were detected. The most numerous groups of components in the unsmoked Herreno cheese were hydrocarbons, followed by terpenes and sesquiterpenes, whereas acids and ketones were the most abundant. It is worth noticing the high number of aldehydes and ketones, and the low number of alcohols and esters in this cheese in relation to others, as well as the presence of some specific unsaturated hydrocarbons, terpenes, sesquiterpenes and nitrogenated derivatives. The smoking process enriches the volatile profile of Herreno cheese with ketones and diketones, methyl esters, aliphatic and aromatic aldehydes, hydrocarbons, terpenes, nitrogenated compounds, and especially with ethers and phenolic derivatives. Among these, methylindanones or certain terpenes like a-terpinolene, have not been detected previously in other types of smoked cheese. Lastly, the results obtained suggest a slightly higher smoking degree in the cheeses smoked at a greater height.

Changes in body composition and fatty acid profile during embryogenesis of quillback rockfish (Sebastes maliger)

We investigated developmental changes in the body compositions and fatty acid (FA) profiles of embryos and preparturition larvae of the quillback rockfish (Sebastes maliger). Comparisons of proximate composition data from early-stage embryos with data from hatched preparturition larvae taken from wild-caught gravid females indicated that embryos gain over one-third their weight in moisture while consuming 20% of their dry tissue mass for energy as they develop into larvae. Lipid contributed 60% of the energy consumed and was depleted more rapidly than protein, indicating a protein-sparing effect. Oil globule volume was strongly correlated with lipid levels, affirming its utility as an indicator of energetic status. FA profiles of early embryos differed significantly from those of hatched larvae. Differences in the relative abundances of FAs between early embryos and hatched larvae indicated different FA depletion rates during embryonic development. We conclude that some metabolically important FAs may prove useful in assessing the condition of embryos and preparturition larvae, particularly 20:4n-6, which cannot be synthesized by many marine fish and which is conserved during embryogenesis. Variability in body composition and energy use among rockfish species should be considered when interpreting any measures of condition.

Associação de componentes dietéticos com desordens alimentares e seus agravos em adolescentes atletas tenistas e não atletas

Adolescentes apresentam rápido crescimento e intensas mudanças corporais que os tornam vulneráveis em termos nutricionais. A prática de restrições alimentares, bastante comum entre adolescentes, pode levar a inadequações nutricionais que parecem ser o primeiro sinal para o início de uma desordem alimentar (DA). A participação feminina no esporte e o número de casos de DA em adolescentes atletas de modalidades que exigem exposição do corpo, agilidade e leveza dos movimentos, como o tênis, têm aumentado nos últimos anos. As DA podem levar a complicações de saúde como irregularidades menstruais (IM) e baixa densidade mineral óssea (DMO), caracterizando a Tríade da Mulher Atleta (TMA). Desta forma, acredita-se que alguns componentes dietéticos podem ter associação com DA e seus agravos. O objetivo do presente estudo foi avaliar a associação de componentes dietéticos com desordens alimentares, irregularidades menstruais e composição corporal em adolescentes atletas tenistas e não atletas do sexo feminino. Trata-se de estudo do tipo transversal. Foram realizadas avaliações do desenvolvimento puberal pela auto-aplicação dos critérios de Tanner; da composição corporal pela absortometria radiológica de dupla energia (DXA); dos parâmetros dietéticos por registro alimentar de três dias alternados; das DA pela aplicação de três questionários validados (Eating Attitudes Test - EAT-26, Bulimic Investigatory Test, Edinburgh- BITE e o Body Shape Questionnaire - BSQ); do ciclo menstrual por questionário validado e da DMO também pelo DXA. A Tríade da Mulher Atleta (TMA) foi estabelecida pela presença concomitante de DA e/ou baixa disponibilidade de energia (BDE), IM e baixa DMO. Foram realizadas associações por meio de correlações de Spearman entre as variáveis numéricas de componentes dietéticos com DA e composição corporal. Também foram realizadas associações por meio do teste qui-quadrado, teste exato de Fisher ou prova binomial para as variáveis categóricas de adequação dos componentes dietéticos com DA e seus agravos. Participaram do estudo 75 adolescentes (25 tenistas, 50 não atletas) apresentando desenvolvimento puberal similar. Atletas obtiveram melhor perfil da composição corporal quanto ao tecido adiposo. Quanto à ingestão de macronutrientes, os carboidratos merecem destaque. Em ambos os grupos, a maioria das participantes apresentaram baixa ingestão de carboidratos, sendo este percentual de inadequação significativamente maior para as atletas. Os micronutrientes que obtiveram maior percentual de inadequação foram folato e cálcio em ambos os grupos. Verificou-se que 92%, 32% e 24% das atletas e 72%, 8% e 30% das não atletas preencheram critérios para DA e/ou BDE, IM e baixa massa óssea, respectivamente. Apesar de adolescentes atletas tenistas e não atletas apresentarem prevalência de DA similares, as não atletas apresentaram maior insatisfação com a imagem corporal pelo teste BSQ. No entanto, as atletas parecem estar em situação mais grave uma vez que apresentaram maior prevalência de BDE e de IM. A DMO e a prevalência de TMA foram similares entre os grupos. Foi verificada associação inversa e significativa entre alguns componentes dietéticos (principalmente energia e carboidratos) e os escores do teste BSQ. Foi possível concluir que a baixa ingestão de alguns componentes dietéticos, principalmente energia e carboidratos, podem funcionar como marcadores para desordens alimentares em ambos os grupos a fim de previnir posteriores consequências à saúde

Seismic triggering of submarine slides in soft cohesive soil deposits

The geological profile of many submerged slopes on the continental shelf consists of normally to lightly overconsolidated clays with depths ranging from a few meters to hundreds of meters. For these soils, earthquake loading can generate significant excess pore water pressures at depth, which can bring the slope to a state of instability during the event or at a later time as a result of pore pressure redistribution within the soil profile. Seismic triggering mechanisms of landslide initiation for these soils are analyzed with the use of a new simplified model for clays which predicts realistic variations of the stress-strain-strength relationships as well as pore pressure generation during dynamic loading in simple shear. The proposed model is implemented in a finite element program to analyze the seismic response of submarine slopes. These analyses provide an assessment of the critical depth and estimated displacements of the mobilized materials and thus are important components for the estimation of submarine landslide-induced tsunamis. © 2003 Elsevier B.V. All rights reserved.

Mechanics of biological networks: from the cell cytoskeleton to connective tissue.

From the cell cytoskeleton to connective tissues, fibrous networks are ubiquitous in metazoan life as the key promoters of mechanical strength, support and integrity. In recent decades, the application of physics to biological systems has made substantial strides in elucidating the striking mechanical phenomena observed in such networks, explaining strain stiffening, power law rheology and cytoskeletal fluidisation - all key to the biological function of individual cells and tissues. In this review we focus on the current progress in the field, with a primer into the basic physics of individual filaments and the networks they form. This is followed by a discussion of biological networks in the context of a broad spread of recent in vitro and in vivo experiments.

Molecular cloning and expression profile of putative antilipopolysaccharide factor in Chinese shrimp (Fenneropenaeus chinensis)

A new antimicrobial protein gene of the anti-lipopolysaccharide factor family (tentatively named as ALFFc) has been cloned from hemocytes of the Chinese shrimp Fenneropenaeus chinensis by rapid amplification of 3' and 5' complementary DNA ends with polymerase chain reaction. The full-length complementary DNA of ALFFc consists of 600 bp with a 369-bp open reading frame, encoding 123 amino acids. The deduced peptide contains a putative signal peptide of 25 amino acids and mature peptide of 98 amino acids. The molecular mass of the deduced mature peptide is 13799.16 Da. It is highly cationic, with a theoretical pI of 10.3. The deduced amino acid sequence of ALFFc showed 56% homology with sequences of Tachypleus tridentatus and L. polyhemus. The tissue expression profile of this gene was studied by Northern blot, and ALFFc transcripts were mainly detected in hemocytes, gill, and intestine. RNA in situ hybridization showed that ALFFc was constitutively expressed in hemocytes. Capillary electrophoresis reverse transcriptase PCR was used to quantify the variation of messenger RNA transcription level during the artificial infection process with Vibrio anguillarum. Significant enhancement of ALFFc transcription appeared during the first 24 hours in response to Vibrio infection. These results provide useful information for understanding the function of ALFFc in shrimp.

Ex vivo culture of patient tissue and examination of gene delivery

Gene therapy has emerged as a realistic prospect for the treatment of cancer due to its potential for selective tumour cell targeting. The greatest challenge gene delivery vectors face is the ability to safely and efficiently deliver genes into target cells. The overall objectives of this thesis are to evaluate the efficacy of various gene delivery methods in a clinically relevant tumour model and to also investigate potential strategies for tumour selective delivery. We began with the development of a tumour slice model system using patient waste tissue. This model involves the use of fresh human tumour tissue, cut into thin slices and maintained ex vivo and is universally applicable to gene delivery methods, using a real-time luminescence detection method to assess gene delivery. The nature of the ex vivo culture system permitted examination of specific physiological variables, the influence of intratumoural factors and tissue specific effects on vector expression. Adenoviral vectors under the control of the human CXCR4 promoter demonstrated a 'tumour on' and 'normal off' expression profile when compared with the ubiquitously active CMV promoter when tested in patient tumour tissue. In addition, we developed an ex vivo system of changing oxygenation using the hypoxia inducer, cobalt, to mimic the transient hypoxic conditions found in solid tumours. We found that Adenoviral transgene expression was robust in the cycling hypoxic conditions relevant to solid tumours and re-oxygenation of chronically hypoxic tissue enhanced transgene expression. Finally, we demonstrated an AAV-based tumour targeting strategy using a tumour-selective promoter allowing for the efficient targeting of AAV vectors to cancer cells and the sparing of normal tissue in both murine metastatic liver tumours models and patient tissue. The thesis highlights the importance of indepth preclinical assessment of novel therapeutics and may serve as a platform for further testing of novel gene delivery approaches.

Bioluminescence imaging of glucose in tissue surrounding polyurethane and glucose sensor implants.

BACKGROUND: The bioluminescence technique was used to quantify the local glucose concentration in the tissue surrounding subcutaneously implanted polyurethane material and surrounding glucose sensors. In addition, some implants were coated with a single layer of adipose-derived stromal cells (ASCs) because these cells improve the wound-healing response around biomaterials. METHODS: Control and ASC-coated implants were implanted subcutaneously in rats for 1 or 8 weeks (polyurethane) or for 1 week only (glucose sensors). Tissue biopsies adjacent to the implant were immediately frozen at the time of explant. Cryosections were assayed for glucose concentration profile using the bioluminescence technique. RESULTS: For the polyurethane samples, no significant differences in glucose concentration within 100 μm of the implant surface were found between bare and ASC-coated implants at 1 or 8 weeks. A glucose concentration gradient was demonstrated around the glucose sensors. For all sensors, the minimum glucose concentration of approximately 4 mM was found at the implant surface and increased with distance from the sensor surface until the glucose concentration peaked at approximately 7 mM at 100 μm. Then the glucose concentration decreased to 5.5-6.5 mM more than 100 μmm from the surface. CONCLUSIONS: The ASC attachment to polyurethane and to glucose sensors did not change the glucose profiles in the tissue surrounding the implants. Although most glucose sensors incorporate a diffusion barrier to reduce the gradient of glucose and oxygen in the tissue, it is typically assumed that there is no steep glucose gradient around the sensors. However, a glucose gradient was observed around the sensors. A more complete understanding of glucose transport and concentration gradients around sensors is critical.

Radiation-induced bystander and adaptive responses in cell and tissue models.

The use of microbeam approaches has been a major advance in probing the relevance of bystander and adaptive responses in cell and tissue models. Our own studies at the Gray Cancer Institute have used both a charged particle microbeam, producing protons and helium ions and a soft X-ray microprobe, delivering focused carbon-K, aluminium-K and titanium-K soft X-rays. Using these techniques we have been able to build up a comprehensive picture of the underlying differences between bystander responses and direct effects in cell and tissue-like models. What is now clear is that bystander dose-response relationships, the underlying mechanisms of action and the targets involved are not the same as those observed for direct irradiation of DNA in the nucleus. Our recent studies have shown bystander responses even when radiation is deposited away from the nucleus in cytoplasmic targets. Also the interaction between bystander and adaptive responses may be a complex one related to dose, number of cells targeted and time interval.