110 research outputs found
Physicochemical and antigenic properties correlation in Streptococcus gordonii vaccine vectors and development of a Streptococcus pneumoniae intra-tracheal mouse model of pneumonia
No full textIn the present thesis, the correlation between the physicochemical and antigenic properties of different recombinant Streptococcus gordonii vaccine vectors was studied. Evaluation of vaccine efficacy, antigenicity and immugenicity is a crucial step in developing vaccines, thus investigating a simple method to analyze vaccine efficacy besides other methods could be a major part of developing bacterial vaccine vectors. To approach this, isoelectric point measurements and zeta-potential titration as well as antigenicity and immunogenicity of S.gordonii vaccine vectors (with fbpA, RPS, gtfg genes mutations expressing H1 antigen) were used. These data showed that strains with more positive surface charge had higher heterologous antigen recognition and lower antibody responses in the serum of immunized mice. This correlation between surface charge and antigenicity and immunogenicity revealed the importance of using simple methods such as zeta potential titration and isoelectric point measurements to predict engineered vaccine vectors antigenicity and possible efficacy. In the second part of the thesis the immune recall in the days following Streptococcus pneumoniae lung infection by transcriptomic analysis was studied. S. pneumoniae is the most common bacterial cause of community-acquired pneumonia. Host-pathogen interaction is poorly understood, and factors that drive a more severe phenotype are unknown. One way to study host response to pathogen is using the stimulation of immune system cells with live or killed bacteria. We combined transcriptomic and cytokine level analysis on stimulated mouse splenocytes revealing the presence of a recall immune response involving both innate and adaptive immunity, stronger from the fourth day after infection. This model could analyze immune responses involved in pneumococcal infection as well as vaccine and experimental therapies efficacy in future studies. Finally, the development of a S. pneumoniae mouse model of pneumonia by intra-tracheal infection was set up. The nasopharynx of humans is the only natural reservoir for the pneumococci. To mimic human pneumonia, mice models are widely used. Bacteria can be administered to mice intranasally, intratracheally or as aerosols. Pneumococcal pneumonia was induced in mice by intra-tracheal inoculation with different doses of S. pneumoniae TIGR4. Data showed high colonization of bacteria in lung, liver and spleen starting 24 hours post-infection. Pneumonia mortalities were observed in all mice infected by 108 within 24 hours of infection. Further analysis should be done to investigate the host-pathogen interaction as well as vaccine and experimental therapies efficacy by using this model
Corrigendum to “Lunar Dust Induces Minimal Pulmonary Toxicity Compared to Earth Dust” [Life Sciences in Space Research, Volume 45, May 2025, Pages 72-80] (Life Sciences in Space Research (2025) 45 (72–80), (S2214552425000252), (10.1016/j.lssr.2025.02.005))
No full textThe author Samaneh Toukhanbeigli has been added. This author was added during the revisions process to the document, but this was not updated in the system and was missed during the proofs. The author contributed greatly to the experiments conducted during revisions
Simplifying Stochastic Mathematical Models of Biochemical Systems
No full textStochastic modeling of biochemical reactions taking place at the cellular level has become the subject of intense research in recent years. Molecular interactions in a single cell exhibit random fluctuations. These fluctuations may be significant when small populations of some reacting species are present and then a stochastic description of the cellular dynamics is required. Often, the biochemically reacting systems encountered in applications consist of many species interacting through many reaction channels. Also, the dynamics of such systems is typically non-linear and presents multiple time-scales. Consequently, the stochastic mathematical models of biochemical systems can be quite complex and their analysis challenging. In this paper, we present a method to reduce a stochastic continuous model of well-stirred biochemical systems, the Chemical Langevin Equation, while preserving the overall behavior of the system. Several tests of our method on models of practical interest gave excellent results
Sensitivity Analysis of Stochastic Discrete Biochemical Systems and Applications
No full textThe development and analysis of mathematical models of cellular processes are fundamental problems in Computational Biology. In many cases, these processes are represented as systems of biochemical reactions. This thesis studies a discrete stochastic model of homogeneous biochemically reacting systems, the Chemical Master Equation. Sensitivity analysis is a prominent tool for investigating the properties of a model, such as robustness with respect to variations in its parameters. We discuss a number of finite-difference sensitivity estimators for the Chemical Master Equation. In addition, we propose some new measures of practical parameter identifiability for this model, based on local sensitivity estimates. Also, we introduce a novel model reduction strategy of stochastic discrete biochemical networks, which utilizes sensitivity analysis and requires solving an optimization problem. The new methods are successfully tested on several critical models, arising in applications, including the epidermal growth factor receptor signalling pathway, the tumor suppressor protein and the Gemcitabine biochemical networks.</p
Quantifying Parameter Interdependence in Stochastic Discrete Models of Biochemical Systems
No full textStochastic modeling of biochemical processes at the cellular level has been the subject of intense research in recent years. The Chemical Master Equation is a broadly utilized stochastic discrete model of such processes. Numerous important biochemical systems consist of many species subject to many reactions. As a result, their mathematical models depend on many parameters. In applications, some of the model parameters may be unknown, so their values need to be estimated from the experimental data. However, the problem of parameter value inference can be quite challenging, especially in the stochastic setting. To estimate accurately the values of a subset of parameters, the system should be sensitive with respect to variations in each of these parameters and they should not be correlated. In this paper, we propose a technique for detecting collinearity among models’ parameters and we apply this method for selecting subsets of parameters that can be estimated from the available data. The analysis relies on finite-difference sensitivity estimations and the singular value decomposition of the sensitivity matrix. We illustrated the advantages of the proposed method by successfully testing it on several models of biochemical systems of practical interest
A research about the real author of Marzbanname Tabari
No full textMarzbanname is the name of a book which includes narrations and allegories and marzban wrote it in old tabari language. Mohammad Ibn Ghazi maltivi in 598 A.H. and sadoddin varavini in the first half of seventh century translated it to farsi. Onsorolma' ali keykavos, the writer of Ghaboosname and Ibn Esfandyar, the writer of tarikhe – Tabarestam believe that marzban ibne Rostam ibne shervin (the 13th king of Bavandiya kiyosiye chain) in the real writer of marzbanname. But sa'daddin varavini believes that marzban ibne shervin (shervin = 5th king of Bavandiye kiyosiye) is the writer of it. Reza Gholi khane – hedayat knows marzban- Ibn – e – rostam as the outher of marzban-e-Deylami in some other books. Among the contemporaries, shefer knows marzban-ibn –e-rostam-ibn –e- sorkhab – ibn – e- Gharan as the author of marzban name, but Allame Ghazvini rejects this hierarchical order. Allame Dehkhoda, Esmaeil mahjouri, Ardeshir Barzegar and Hossein Eslami believe that marzban- ibn- e- Rostam wrote maezban name. mohammad Roshan reject all and say that there is no book named marzban name tabari.This article believes that varavini's speech about the writer of marzbanname is correct but not of onsorolma' ali keykavoos and ibne Esfandyar's speech
Investigating the impact of using modified cool materials by titanium dioxide (TiO2)-based photocatalytic self-cleaning nanoparticles in urban facades on urban microclimate parameters
No full textPurpose: On the one hand, one of the most important global strategies to improve thermal comfort in urban spaces is using cool materials (high albedo materials) in urban facades. On the other hand, using cool materials in urban facades is a big challenge. Over time, the albedo of cool materials that modified by titanium dioxide (TiO2)-based photocatalytic self-cleaning materials (PSTiO2) does not decrease. In fact, its self-cleaning property prevents the loss of the initial albedo of the material. The self-cleaning performance of these materials was investigated in previous researches. However, their thermal performance in urban space has not been investigated yet. This paper studied the performance of these materials on the urban square facade. Design/methodology/approach: The thermal performance of PSTiO2 on the thermal comfort of the urban square was evaluated by ENVI-met(v4). The results simulated by ENVI-met software with field measurements in the urban Square were compared. Field measurements of air temperature were conducted on 22 July and 30 March. Findings: The results showed that these materials, despite their self-cleaning properties, have significant thermal impact in the urban environment. Using plaster modified by PSTiO2 (albedo 0.6) improved slightly by nearly 0.2 °C the thermal comfort of the urban square. Whereas, white paint modified by PSTiO2 (albedo 0.9) reduced the physiologically equivalent temperature (PET) by 0.5 °C, because reflection of solar radiation increased between the buildings facades. The simulation results showed that due to the space is more enclosed in the square entrance, the mean radiant temperature (Tmrt) increased. As a result, PET index rose too. Originality/value: This study shows that employing cool and self-cleaning materials in the urban facades of Jolfa Square, in addition to have self-cleaning property, is effective in the amount of thermal comfort of the square. In the parts of the square where the enclosure is less, an improvement in thermal comfort was observed. The performance of the cool and self-cleaning materials in the facade in terms of thermal comfort is completely dependent on the physical parameters of the urban space
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