Sharif Digital Repository

In ecological systems, heterogeneous interactions between pathogens take place simultaneously. This occurs, for instance, when two pathogens cooperate, while at the same time, multiple strains of these pathogens co-circulate and compete. Notable examples include the cooperation of human immunodeficiency virus with antibiotic-resistant and susceptible strains of tuberculosis or some respiratory infections with Streptococcus pneumoniae strains. Models focusing on competition or cooperation separately fail to describe how these concurrent interactions shape the epidemiology of such diseases. We studied this problem considering two cooperating pathogens, where one pathogen is further structured... 

Cooperation and competition between pathogens can alter the amount of individuals affected by a coinfection. Nonetheless, the evolution of the pathogens' behavior has been overlooked. Here, we consider a coevolutionary model where the simultaneous spreading is described by a two-pathogen susceptible-infected-recovered model in an either synergistic or competitive manner. At the end of each epidemic season, the pathogens species reproduce according to their fitness that, in turn, depends on the payoff accumulated during the spreading season in a hawk-and-dove game. This coevolutionary model displays a rich set of features. Specifically, the evolution of the pathogens' strategy induces abrupt... 

Since Gram-negative bacteria have a predominant role in nosocomial infections, there are high demands to develop a fast and sensitive method for diagnosis of bacteria in clinical samples. To address this challenge, we designed a novel electrochemical biosensor based on aptamers immobilized in engineered zeolitic imidazolate Framework-8 (ZIFs-8) via EDC-NHS chemistry. Cyclic voltammetry and electrochemical impedance spectroscopy techniques were conducted to monitor the electrochemical characterization. With respect to unique π-πinteractions between aptamer and graphene oxide (GO), the differential pulse voltammetry technique was applied with ferrocene-graphene oxide (Fc-GO) as an... 

The simultaneous emergence of several abrupt disease outbreaks or the extinction of some serotypes of multistrain diseases are fingerprints of the interaction between pathogens spreading within the same population. Here, we propose a general and versatile benchmark to address the unfolding of both cooperative and competitive interacting diseases. We characterize the explosive transitions between the disease-free and the epidemic regimes arising from the cooperation between pathogens and show the critical degree of cooperation needed for the onset of such abrupt transitions. For the competing diseases, we characterize the mutually exclusive case and derive analytically the transition point... 

Removal or suppression of key proteins in an essential pathway of a pathogen is expected to disrupt the pathway and prohibit the pathogen from performing a vital function. Thus disconnecting multiple essential pathways should disrupt the survival of a pathogen even when it has multiple pathways to drug resistance. We consider a scenario where the drug-resistance pathways are unknown. To disrupt these pathways, we consider a cut set S of G, where G is a connected simple graph representing the protein interaction network of the pathogen, so that G-S splits to two partitions such that the endpoints of each pathway are in different partitions. If the difference between the sizes of the two... 

Finding fast and reliable ways to detect pathogenic bacteria is crucial for addressing serious public health issues in clinical, environmental, and food settings. Here, we present a novel assay based on the conversion of an electrochemical signal into a more convenient optical readout for the visual detection of Escherichia coli. Electropolymerizing polyaniline (PANI) on an indium tin oxide screen-printed electrode (ITO SPE), we achieved not only the desired electrochromic behavior but also a convenient way to modify the electrode surface with antibodies (taking advantage of the many amine groups of PANI). Applying a constant potential to the PANI-modified ITO SPE induces a change in their... 

Graphene oxide flakes are considered as potential inhibitors for different pathogenic bacteria. However, the efficacy of inhibition changes for different types and strains of bacteria. In this work, we examine Pseudomonas aeruginosa and Staphylococcus aureus, two common hospital-acquired infections, which react quite differently to graphene oxide flakes. The minimum inhibitory tests yield two distinct outcomes: stopped proliferation for S. aureus versus almost no effect for P. aeruginosa. Integrating our experimental evidence with molecular dynamics simulations, we elucidate the molecular machinery involved, explaining the behavior we see in scanning electron microscopy images. According to... 

Drug delivery is a rapidly growing area of research motivated by the nanotechnology revolution, the ideal of personalized medicine, and the desire to reduce the side effects of toxic anti-cancer drugs. Amongst a bewildering array of different nanostructures and nanocarriers, those examples that are fundamentally bio-inspired and derived from natural sources are particularly preferred. Delivery of vaccines is also an active area of research in this field. Bacterial cells and their components that have been used for drug delivery, include the crystalline cell-surface layer known as “S-layer” bacterial ghosts, bacterial outer membrane vesicles, and bacterial products or derivatives (e.g.... 

Nucleic acid amplification using polymerase chain reaction (PCR) method has been widely used in different fields such as agricultural science, medicine, pathogen identification, and forensics to name a few. Today, it seems inevitable to have a robust, simple PCR system for diagnostics at the point-of-care (POC) level. Many photonic PCR systems have been proposed in the literature that benefit from plasmonic photothermal heating to achieve the common PCR thermal cycling. However, non-homogeneous temperature distribution is a challenge in some of them. In the present work, to achieve more efficient gene amplification, the effect of adding TiO2 nanoparticles has been investigated in a photonic... 

The purpose of this study was to prepare and characterize an optimized system of tannic acid-loaded niosomes as a potential carrier for antibacterial and anti-biofilm delivery. The niosomal formulation was optimized using response surface methodology (RSM). The effects of the molar ratio of surfactant to cholesterol, drug concentration, and molar ratio of Span 60 to Tween 60 on particle size and drug entrapment efficiency of the niosomal nanocarrier were studied. The optimized nanoparticles were characterized in terms of the morphology, in vitro release profile, and antibacterial properties. Moreover, Fourier-transform infrared spectroscopy (FTIR) and differential scanning calorimetry (DSC)... 

Nucleic acid amplification using polymerase chain reaction (PCR) method has been widely used in different fields such as agricultural science, medicine, pathogen identification, and forensics to name a few. Today, it seems inevitable to have a robust, simple PCR system for diagnostics at the point-of-care (POC) level. Many photonic PCR systems have been proposed in the literature that benefit from plasmonic photothermal heating to achieve the common PCR thermal cycling. However, non-homogeneous temperature distribution is a challenge in some of them. In the present work, to achieve more efficient gene amplification, the effect of adding TiO2 nanoparticles has been investigated in a photonic... 

Higher than a standard level, the humidity provides a suitable environment for the pathogenic microorganisms to grow and increases energy consumption for cooling, increasing greenhouse gas emissions. Desiccant air-conditioning (DAC) is an effective method to reduce humidity and energy simultaneously. Conventional desiccants are not suitable for use as a desiccant in building air conditioners, mainly because of high regeneration temperature and other issues such as limited equilibrium capacity and hydrothermal and cyclic instability. Metal-organic frameworks (MOFs) are a novel class of porous crystalline materials without the disadvantages of traditional desiccants. They benefit from a huge... 

Human parvovirus B19 (B19) is a small, non-enveloped virus and belongs to Parvoviridae family. B19 persists in many tissues such as thyroid tissue and even thyroid cancer. The main aim of this study was to determine the presence of B19, its association with increased inflammation in thyroid tissue, and thus its possible role in thyroid cancer progression. Studies have shown that virus replication in non-permissive tissue leads to overexpression of non-structural protein and results in upregulation of proinflammatory cytokines such as interleukin 6 and tumor necrosis factor alpha. A total of 36 paraffin-embedded thyroid specimens and serum were collected from patients and 12 samples were used... 

Acute respiratory syndrome coronavirus 2 (SARS-CoV-2), also called COVID-19, is one of the most contagious viruses resulting in a progressive pandemic. Since specific antiviral treatments have not been developed yet and its fatal rate is almost high, early and fast detection is critical for controlling the outbreak. In this study, a piezoelectric microcantilever biosensor has been designed for detecting COVID-19 samples directly without requiring preparation steps. The biosensor acts as a transducer and is coated with the related antibody. When the SARS-CoV-2 antigens adsorbed on the microcantilever top surface through their spike proteins, a surface stress due to the mass change would be...