Microstructure Bio-Material for Behavioral Analysis

Biological applications have a limitation of creating tissue like structures in order to mimic the advanced real like structures, such as human tissues in a small scale. Conventional methods of using lab mice for cancer behavior have limitations due to observation complications. Fabricating an artificial human tissue which can behave similar to a human body tissue consists of components, such as Laminin and Collagen. Collagen in human tissue has elements, such as integrin and serum. Creating serum based proteins are somewhat challenging due to the conditional requirements. This particular approach will address the primary state of the art technique of observing the interaction with cells by mimicking the organs on a chip with blood circulation using a micro-fluidic pump. Bio-material hydrogel structures implanted on a silicon polymer based chip described in this thesis will overcome the limitations of in-vitro analysis. Water purification has become a vital issue in developing countries of the world. Water pollution due to Ammonia has been one of the major concerns with industrial revolution. Purifications were mainly done by chemical methods that can cause human health concerns. The analytically demonstrated method in this thesis using bio-compatible hydrogel will address a new dimension to the water conservation method without causing health issues and eliminating the environmental pollution due to complicated degradable structures. Filtration and efficiency are among the main concerns of using bacteria types such as AOB/NOB directly without encapsulating. Application of using bio-compatible hydrogel based dual encapsulated single pallet structure described in this thesis will address the issue of filtering capability. Pallets can be removed once nitrified, without letting it grow inside the water contaminating aqua based living breads and plants. The process will improve the efficiency of Ammonia removal due to encapsulation. Drug delivery using micro locomotives in neuro-surgery has become one of the future concerns with the development of science. Conventional delivery systems such as vaccines and open surgeries take longer response time once surgeries become more complex. Moreover there is a risk factor of injuring healthy nerves in the organ. Drug delivery approaches of drug encapsulated microspheres and drug embedded nematodes described in this thesis become more applicable to complex scenarios. Nematodes become useful in the future of microsurgeries, as many biologists are focusing on using their healthy nerves to implant in humans. Therefore, such applications like magnetizing nematodes help move locomotives to targeted locations and capture scan images for future medical approaches

Proteasomes generate spliced epitopes by two different mechanisms and as efficiently as non-spliced epitopes

Proteasome-catalyzed peptide splicing represents an additional catalytic activity of proteasomes contributing to the pool of MHC-class I-presented epitopes. We here biochemically and functionally characterized a new melanoma gp100 derived spliced epitope. We demonstrate that the gp100mel47–52/40–42 antigenic peptide is generated in vitro and in cellulo by a not yet described proteasomal condensation reaction. gp100mel47–52/40–42 generation is enhanced in the presence of the β5i/LMP7 proteasome-subunit and elicits a peptide- specific CD8+ T cell response. Importantly, we demonstrate that different gp100mel-derived spliced epitopes are generated and presented to CD8+ T cells with efficacies comparable to non-spliced canonical tumor epitopes and that gp100mel-derived spliced epitopes trigger activation of CD8+ T cells found in peripheral blood of half of the melanoma patients tested. Our data suggest that both transpeptidation and condensation reactions contribute to the frequent generation of spliced epitopes also in vivo and that their immune relevance may be comparable to non-spliced epitopes

C19orf48 encodes a minor histocompatibility antigen recognized by CD8+ cytotoxic T cells from renal cell carcinoma patients.

PURPOSE: Tumor regression has been observed in some patients with metastatic renal cell carcinoma (RCC) after nonmyeloablative allogeneic hematopoietic cell transplantation (HCT). Cellular and molecular characterization of antigens recognized by tumor-reactive T cells isolated from responding patients could potentially provide insight into the mechanisms of tumor regression. EXPERIMENTAL DESIGN: CD8+ CTL clones that recognized a novel RCC-associated minor histocompatibility (H) antigen presented by HLA-A*0201 were isolated from two patients with metastatic RCC who experienced tumor regression or stable disease following nonmyeloablative allogeneic HCT. These clones were used to screen a cDNA library and isolate the unique cDNA encoding the antigen. RESULTS: An alternative open reading frame in the C19orf48 gene located on chromosome 19q13 encodes the HLA-A*0201-restricted minor H antigen recognized by the RCC-reactive T cells. The differential T-cell recognition of donor- and recipient-derived target cells is attributable to a nonsynonymous single-nucleotide polymorphism within the nucleotide interval that encodes the antigenic peptide. Assays for gene expression and CTL recognition showed that the C19orf48-encoded peptide is widely expressed in renal tumors and solid tumors of other histologies. The antigenic peptide can be processed for CTL recognition via both TAP-dependent and TAP-independent pathways. CONCLUSIONS: Donor T-cell responses against the HLA-A*0201-restricted minor H antigen encoded by C19orf48 may contribute to RCC regression after MHC-matched allogeneic HCT

Prioritization of fish communities with a view to conservation and restoration on a large scale European basin, the Loire (France)

The hierarchical organization of important sites for the conservation or the restoration of fish communities is a great challenge for managers, especially because of financial or time constraints. In this perspective, we developed a methodology, which is easy to implement in different locations. Based on the fish assemblage characteristics of the Loire basin (France), we created a synthetic conservation value index including the rarity, the conservation status and the species origin. The relationship between this new synthetic index and the Fish-Based Index allowed us to establish a classification protocol of the sites along the Loire including fish assemblages to be restored or conserved. Sites presenting disturbed fish assemblages, a low rarity index, few threatened species, and a high proportion of non-native species were considered as important for the restoration of fish biodiversity. These sites were found mainly in areas where the assemblages are typical of the bream zone, e.g. with a higher number of eurytopic and limnophilic species. On the contrary, important sites for conservation were defined as having an important conservation potential (high RI, a lot of threatened species, and few nonnatives fish species) and an undisturbed fish assemblage similar to the expected community if habitats are undisturbed. Important sites for conservation were found in the Loire basin’s medium reaches which host assemblages typical for the grayling and the barbell zones, e.g. with a higher number of rheophilic species. The synthetic conservation value index could be adapted and completed with other criteria according to management priorities and capacities

Computer simulation of diffusion processes in tilt spatio-periodic potentials

Нещодавно було показано, що в істотно нерівноважних системах коефіцієнт дифузії може вести себе немонотонно з температурою. Одним із прикладів таких систем з аномальною температурної залежністю є рух броунівських часток в просторово-періодичних структурах. Метою статті було дослідження зміни температурної залежності дифузії в недодемпфованих системах з низьким коефіцієнтом тертя. В роботі методами комп'ютерного моделювання вивчено зміна коефіцієнта дифузії частинок в широкому діапазоні температур в нахилених просторово-періодичних потенціалах для різних значень коефіцієнта тертя. Показано, що дифузія досягає максимуму при певній величині зовнішньої сили. Її значення залежить від величини коефіцієнта тертя. Показано, що на відміну від звичайної залежності Аррениуса, в разі нахиленого періодичного потенціалу, максимальний коефіцієнт дифузії зростає, а не зменшується з пониженням температури експоненціальним чином. Встановлено, що така залежність характерна для всіх недодемпфованих систем. Показано, що для просторово-періодичних структур існує обмежена ділянка сил, в якому спостерігається зростання коефіцієнта дифузії зі зменшенням температури. Це область так званої температурно-аномальної дифузії (ТАД). Визначено ширина і положення області ТАД в залежності від коефіцієнта тертя γ і параметрів системи. Показано, що зі зменшенням γ, ширина області ТАД зменшується пропорційно γ. При цьому коефіцієнт дифузії в області ТАД, навпаки зростає ~γ. Отримані дані про температурно-аномальної дифузії мають важливе значення для різних областей фізики і техніки та відкривають перспективи створення новітніх технологій управління процесами дифузії.It was recently shown that in essentially nonequilibrium systems, the diffusion coefficient can behave nonmonotonically with temperature. One example of such systems with anomalous temperature dependence is the motion of Brownian particles in spatially periodic structures. The aim of the article was to study the change in the temperature dependence of diffusion in underdamped systems with a low coefficient of friction. In this paper, computer simulation methods are used to study the change in the diffusion coefficient of particles in a wide range of temperatures in oblique spatially periodic potentials for different values of the friction coefficient. It is shown that diffusion reaches a maximum at a certain external force. Its value depends on the coefficient of friction. It is shown that, in contrast to the usual Arrhenius dependence, in the case of an inclined periodic potential, the maximum diffusion coefficient increases while temperature is decreasing exponentially. It is established that such a dependence is common to all underdamped systems. It is shown that for spatially periodic structures there is a limited portion of forces in which an increase in the diffusion coefficient while decreasing temperature is observed. This is the area of the so-called temperature-anomalous diffusion (TAD). The width and position of the TAD region are determined depending on the friction coefficient γ and the system parameters. It has been shown that a decrease in γ, width TAD region decreases proportionally γ. In this case, the diffusion coefficient in the TAD region, on the contrary, increases ~γ. The data obtained on the temperature and the anomalous diffusion are important for various fields of physics and engineering, and opens new prospects for a diffusion process control technology

Search for the best indicators for the presence of a VPS13B gene mutation and confirmation of diagnostic criteria in a series of 34 patients genotyped for suspected Cohen syndrome

BACKGROUND: Cohen syndrome is a rare autosomal recessive inherited disorder that results from mutations of the VPS13B gene. Clinical features consist of a combination of mental retardation, facial dysmorphism, postnatal microcephaly, truncal obesity, slender extremities, joint hyperextensibility, myopia, progressive chorioretinal dystrophy, and intermittent neutropenia.PATIENTS AND METHODS: The aim of the study was to determine which of the above clinical features were the best indicators for the presence of VPS13B gene mutations in a series of 34 patients with suspected Cohen syndrome referred for molecular analysis of VPS13B. RESULTS: 14 VPS13B gene mutations were identified in 12 patients, and no mutation was found in 22 patients. The presence of chorioretinal dystrophy (92% vs 32%, p=0.0023), intermittent neutropenia (92% vs 5%, p<0.001), and postnatal microcephaly (100% vs 48%, p=0.0045) was significantly higher in the group of patients with a VPS13B gene mutation compared to the group of patients without a mutation. All patients with VPS13B mutations had chorioretinal dystrophy and/or intermittent neutropenia. The Kolehmainen diagnostic criteria provided 100% sensibility and 77% specificity when applied to this series. CONCLUSION: From this study and a review of more than 160 genotyped cases from the literature, it is concluded that, given the large size of the gene, VPS13B screening is not indicated in the absence of chorioretinal dystrophy or neutropenia in patients aged over 5 years. The follow-up of young patients could be a satisfactory alternative unless there are some reproductive issues

The 20S Proteasome Splicing Activity Discovered by SpliceMet

The identification of proteasome-generated spliced peptides (PSP) revealed a new unpredicted activity of the major cellular protease. However, so far characterization of PSP was entirely dependent on the availability of patient-derived cytotoxic CD8+ T lymphocytes (CTL) thus preventing a systematic investigation of proteasome-catalyzed peptide splicing (PCPS). For an unrestricted PSP identification we here developed SpliceMet, combining the computer-based algorithm ProteaJ with in vitro proteasomal degradation assays and mass spectrometry. By applying SpliceMet for the analysis of proteasomal processing products of four different substrate polypeptides, derived from human tumor as well as viral antigens, we identified fifteen new spliced peptides generated by PCPS either by cis or from two separate substrate molecules, i.e., by trans splicing. Our data suggest that 20S proteasomes represent a molecular machine that, due to its catalytic and structural properties, facilitates the generation of spliced peptides, thereby providing a pool of qualitatively new peptides from which functionally relevant products may be selected