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.

Study and comparison of four forest structures on Mt. Chortiatis (northern Greece)

EL proyecto estudia y analiza la estructura de cuatro bosques en el monte Chortiatis, Grecia.

Petroleum hydrocarbons in fresh waters: a preliminary desk study and bibliography

A literature survey was carried out into the effects of petroleum hydrocarbons in freshwater, from the toxicity, biodegradability and concentration aspects. It was supplemented by a selective search on hydrocarbons in the marine environment for comparison. The aim was to determine the major inputs of these hydrocarbons, their accumulation, effects and fate in freshwaters. The search was confined to the period 1965-1978. The bibliography contains 390 references, divided by subject.

Distribution of Healthcare resources II.Study and Comparison of a Linear Programming Problem and its Dual. Resolution and Evaluation of a Practical Case and its Programming using Excel and Win QSB.

[EN]This research had as primary objective to model different types of problems using linear programming and apply different methods so as to find an adequate solution to them. To achieve this objective, a linear programming problem and its dual were studied and compared. For that, linear programming techniques were provided and an introduction of the duality theory was given, analyzing the dual problem and the duality theorems. Then, a general economic interpretation was given and different optimal dual variables like shadow prices were studied through the next practical case: An aesthetic surgery hospital wanted to organize its monthly waiting list of four types of surgeries to maximize its daily income. To solve this practical case, we modelled the linear programming problem following the relationships between the primal problem and its dual. Additionally, we solved the dual problem graphically, and then we found the optimal solution of the practical case posed through its dual, following the different theorems of the duality theory. Moreover, how Complementary Slackness can help to solve linear programming problems was studied. To facilitate the solution Solver application of Excel and Win QSB programme were used.

Dispersion of gamma-Alumina Nano-Sized Spherical Particles in a Calamitic Liquid Crystal. Study and Optimization of the Confinement Effects

We report an experimental study on confined systems formed by butyloxybenzylidene octylaniline liquid crystal (4O.8) + gamma-alumina nanoparticles. The effects of the confinement in the thermal and dielectric properties of the liquid crystal under different densities of nanoparticles is analyzed by means of high resolution Modulated Differential Scanning Calorimetry (MDSC) and broadband dielectric spectroscopy. First, a drastic depression of the N-I and SmA-N transition temperatures is observed with confinement, the more concentration of nanoparticles the deeper this depression is, driving the nematic range closer to the room temperature. An interesting experimental law is found for both transition temperatures. Second, the change in shape of the heat capacity peaks is quantified by means of the full width half maximum (FWHM). Third, the confinement does not noticeably affect the molecular dynamics. Finally, the combination of nanoparticles and the external applied electric field tends to favor the alignment of the molecules in metallic cells. All these results indicate that the confinement of liquid crystals by means of gamma-alumina nanoparticles could be optimum for liquid crystal-based electrooptic devices.

Fish tracking technology development. Phases 1 and 2, project definition desk study and equipment

The document reports on the major findings from a definition study to appraise the options to develop fish tracking equipment, in particular tags and data logging systems, in order to improve the effeciency of the Agency tracking studies and to obtain a greater understanding of fish biology. The definition study was in two parts. The first, Phase 1, collated and evaluated all the known tracking systems that may be suitable for studies of fish which are either produced commercially or have been constructed for specific in-house studies. Phase 2 was an evaluation of all the tracking equipment considered to merit further investigation in Phase 1. The deficiencies between existing and required technologies to improve the efficiency of Agency's tracking studies and to obtain a greater understanding of fish biology are also identified.

Morphometric study and length-weight relationship of Therapon jarbua, Forsskal

The different morphometric characters of Therapon jarbua showed a linear relationship and uniformity in the various biometric measurements whereas the length-weight relationship showed a curvilinear graph. The studies also indicate that there is no significant difference, in the morphometric characters and length-weight relationship between the males and females. Ponderal index values for males and females was found to fluctuate between 1.3 to 1.5 for most of their life times with the peaks and crests appearing at different lengths for males and females.

The study and production of fish sauce from Caspian Sea lam fish with traditional fermentation method and microbe and enzyme adding method and identification of important bacteria

Fish sauce is a popular fermented product used in south Asian countries which is made from different small fishes in this research work it was attempted to produce fish sauce from kilka of the Caspian sea, the fish sauce was made from three models of kilka ,such as whole kilka , cooked whole kilka and dressed kilka , each of these models treated it four different fashions of fermentation such as:1- Traditional method, 2- Enzymatic method 3- Microbial method, 4- Mixture of enzyme and microb The results of this investigation showed that time of fermentation for the traditional method was six month, enzymatic method one month, microbial method 3 month and the mixture of enzyme and microb 1 month. The rate of fermentation was least for dressed Kilka, microbial and biochemical changes of Kilka fish sauce were evaluated, total bacterial count was 2.1-6.15 log cfu/ml total volatile nitrogen (TVN) in samples recorded was 250 mg /100g, the amount of protein varied between 10-13 percent, the name of commercial enzymes added was Protamex and Flavourzyme, the bacteria added was L act ob acillus and Pediococous, fish sauce containers fish and 20% salt, temperature of keeping for fermentation was 37 degree c for 6 month.

Comparative study and expression analysis of the interferon gamma gene locus cytokines in Xenopus tropicalis

Using bioinformatics approach, the genome locus containing interleukin (IL)-22, IL-26, and interferon gamma (IFN-gamma) genes has been identified in the amphibian, Xenopus tropicalis. Like that in other vertebrates such as fish, birds, and mammals, the Xenopus IL-22, IL-26, and IFN-gamma are clustered in the same chromosome and the adjacent genes are conserved. The genomic structures of the Xenopus IL-22, IL-26, and IFN-gamma gene were identical to that of their mammalian counterparts. The Xenopus IL-22 and IL-26 genes contained five exons and four introns while the Xenopus IFN-gamma gene consisted of four exons and three introns. The Xenopus IL-22, IL-26, and IFN-gamma share 14.1-41.6%, 14.6-31.2%, and 23.7-36.5% identity to their counterparts in other species, respectively. Reverse-transcription polymerase chain reaction (PCR) and real-time quantitative PCR analyses revealed that the expression of IL-22, IL-26, and IFN-gamma genes was significantly upregulated after simulation with bacterial polyliposaccharide and/or synthetic double-stranded poly(I:C), suggesting these cytokines like those in other vertebrates play an important role in regulating immune response in Xenopus.

RBS/channeling study and photoluminscence properties of Er-implanted GaN

The Raman back scattering/channeling technique was used to analyze the damage recovery at different annealing temperatures and to determine the lattice location of the Er-implanted GaN samples. A better damage recovery was observed with increasing annealing temperature below 1000degreesC, but a complete recovery of the implantation damage cannot be achieved. For a sample annealed for at 900degreesC 30 min the Er and Ga angular scans across the <0001> axis was measured indicating that about 76% of Er ions occupies substitutional sites. Moreover, the photoluminscence (PL) properties of Er-implanted GaN thin films have been also studied. The experimental results indicate that those samples annealed at a higher temperature below 1000degreesC had a stronger 1539nm PL intensity. The thermal quenching of PL intensity for samples annealed at 900degreesC measured at temperatures from 15K to 300K is 30%.

Calorimetric study and thermal analysis of crystalline nicotinic acid

As one primary component of Vitamin B-3, nicotinic acid [pyridine 3-carboxylic acid] was synthesized, and calorimetric study and thermal analysis for this compound were performed. The low-temperature heat capacity of nicotinic acid was measured with a precise automated adiabatic calorimeter over the temperature rang from 79 to 368 K. No thermal anomaly or phase transition was observed in this temperature range. A solid-to-solid transition at T-trs = 451.4 K, a solid-to-liquid transition at T-fus = 509.1 K and a thermal decomposition at T-d = 538.8 K were found through the DSC and TG-DTG techniques. The molar enthalpies of these transitions were determined to be Delta(trs)H(m =) 0.81 kJ mol(-1), Delta(fus)H(m) 27.57 kJ mol(-1) and Delta(d)H(m) = 62.38 kJ mol(-1), respectively, by the integrals of the peak areas of the DSC curves.