Marzhan Sypabekova

Tuberculosis diagnosis using immunodominant, secreted antigens of Mycobacterium tuberculosis

Tuberculosis (TB) remains a major public health concern in most low-income countries. Hence, rapid and sensitive TB diagnostics play an important role in detecting and preventing the disease. In addition to established diagnostic methods, several new approaches have been reported. Some techniques are simple but time-consuming, while others require complex instrumentation. One prominent and readily available approach is to detect proteins that Mycobacterium tuberculosis secretes, such as Mpt64, the 6-kDa early secreted antigenic target (Esat6), the 10-kDa culture filtrate protein (Cfp10), and the antigen 85 (Ag85) complex. Although their functions are not fully understood, a growing body of molecular evidence implicates them in M. tuberculosis virulence. Currently these biomarkers are either being used or investigated for use in skin patch tests, biosensor analyses, and immunochromatographic, immunohistochemical, polymerase chain reaction-based, and enzyme-linked immunosorbent assays. This review provides a comprehensive discussion of the roles these immunodominant antigens play in M. tuberculosis pathogenesis and compares diagnostic methods based on the detection of these proteins with more established tests for TB.

Role of viruses in the development of breast cancer.

The most common cancer worldwide among women is breast cancer. The initiation, promotion, and progression of this cancer result from both internal and external factors. The International Agency for Research on Cancer stated that 18-20% of cancers are linked to infection, and the list of definite, probable, and possible carcinogenic agents is growing each year. Among them, biological carcinogens play a significant role. In this review, data covering infection-associated breast and lung cancers are discussed and presented as possible involvements as pathogens in cancer. Because carcinogenesis is a multistep process with several contributing factors, we evaluated to what extent infection is significant, and concluded that members of the herpesvirus, polyomavirus, papillomavirus, and retrovirus families definitely associate with breast cancer. Detailed studies of viral mechanisms support this conclusion, but have presented problems with experimental settings. It is apparent that more effort needs to be devoted to assessing the role of these viruses in carcinogenesis, by characterizing additional confounding and synergistic effects of carcinogenic factors. We propose that preventing and treating infections may possibly stop or even eliminate certain types of cancers.

CFD Modeling of Chamber Filling in a Micro-Biosensor for Protein Detection

Tuberculosis (TB) remains one of the main causes of human death around the globe. The mortality rate for patients infected with active TB goes beyond 50% when not diagnosed. Rapid and accurate diagnostics coupled with further prompt treatment of the disease is the cornerstone for controlling TB outbreaks. To reduce this burden, the existing gap between detection and treatment must be addressed, and dedicated diagnostic tools such as biosensors should be developed. A biosensor is a sensing micro-device that consists of a biological sensing element and a transducer part to produce signals in proportion to quantitative information about the binding event. The micro-biosensor cell considered in this investigation is designed to operate based on aptamers as recognition elements against Mycobacterium tuberculosis secreted protein MPT64, combined in a microfluidic-chamber with inlet and outlet connections. The microfluidic cell is a miniaturized platform with valuable advantages such as low cost of analysis with low reagent consumption, reduced sample volume, and shortened processing time with enhanced analytical capability. The main purpose of this study is to assess the flooding characteristics of the encapsulated microfluidic cell of an existing micro-biosensor using Computational Fluid Dynamics (CFD) techniques. The main challenge in the design of the microfluidic cell lies in the extraction of entrained air bubbles, which may remain after the filling process is completed, dramatically affecting the performance of the sensing element. In this work, a CFD model was developed on the platform ANSYS-CFX using the finite volume method to discretize the domain and solving the Navier–Stokes equations for both air and water in a Eulerian framework. Second-order space discretization scheme and second-order Euler Backward time discretization were used in the numerical treatment of the equations. For a given inlet–outlet diameter and dimensions of an in-house built cell chamber, different inlet liquid flow rates were explored to determine an appropriate flow condition to guarantee an effective venting of the air while filling the chamber. The numerical model depicted free surface waves as promoters of air entrainment that ultimately may explain the significant amount of air content in the chamber observed in preliminary tests after the filling process is completed. Results demonstrated that for the present design, against the intuition, the chamber must be filled with liquid at a modest flow rate to minimize free surface waviness during the flooding stage of the chamber.

Electrochemical aptasensor using optimized surface chemistry for the detection of Mycobacterium tuberculosis secreted protein MPT64 in human serum

Tuberculosis (TB) remains one of the leading causes of mortality worldwide. There is a great need for the development of diagnostic tests, which are reliable, sensitive, stable, and low cost to enable early diagnosis of TB in communities with scarce resources. This study reports the optimization and evaluation of a synthetic receptor, an aptamer, for the detection of the secreted protein MPT64, which is a highly immunogenic polypeptide of Mycobacterium tuberculosis, a causative agent of TB. The study investigates combinatorial effects of an aptamer linker and a co-adsorbent onto a gold electrode for optimal binding efficiency and reduced non-specific interactions for label-free detection of MPT64 using electrochemical impedance spectroscopy. Two types of co-adsorbents and two types of aptamer linkers were studied and high specificity and sensitivity to MPT64 was observed for a surface prepared with a thiol PEGylated aptamer HS-(CH2)6-OP(O)2O-(CH2CH2O)6-TTTTT-aptamer and 6-mercaptohexanol in a ratio of 1:100. The developed aptamer-based sensor was successfully used with spiked human serum sample with a limit of detection of 81 pM This work demonstrates the use of the MPT64 aptamer as a lower cost, more sustainable and stable alternative of antibodies for the development of point-of-care TB biosensors decreasing the detection time from several days or hours to thirty minutes.

Detection of tilted fiber Bragg grating fiber-optic sensors with short-term KLT: towards low-cost biosensors

Tilted Fiber Bragg Grating (TFBG) optical fiber sensors can be employed as refractive index sensors, and functionalized as biosensors. The TFBG cladding modes exhibit a small yet detectable sensitivity to the refractive index in the surrounding of the sensing region. One of the weaknesses of TFBG is that classical interrogation methods require narrow wavelength resolution to analyze these spectral features which can be achieved only through a bulky setup. In this work, we propose a demodulation method, namely the short term Karhunen-Loeve Transform (ST-KLT) that can be applied to a low-cost spectrometer that detects the TFBG reflection spectrum. The method is capable of detecting refractive index variations in the order of 10-3 - 10-4 refractive index units (RIU), and is a potential pillar towards low-cost TFBG biosensors.

Detection of various Thrombin concentrations using etched fiber Bragg gratings functionalized with DNA aptamer

The response of etched fiber Bragg grating (EFBG) functionalized with 29-mer DNA aptamer to the different concentrations of Thrombin protein has been investigated. Etched FBGs are an efficient technology for detection of refractive index, and have been demonstrated also for biosensors applications. EFBGs have a simpler manufacturing approach comparing to other methodologies and are based on a low-cost device; their fabrication can be achieved by simple chemical etching, without requiring fusion splicing. During the test we assessed its feasibility for small variations of thrombin concentrations (10μg/ml, 20μg/ml, 40μg/ml and 80μg/ml). In particular, we performed experiments of chemical etching with hydrofluoric acid, which progressively depletes the fiber cladding exposing the core to the outer medium. Additionally, unstriped not etched FBGs were also used as a control for temperature pattern compensation. Before functionalization, EFBG was calibrated with different sucrose and ethanol solutions that validated the sensitivity to refractive index change. EFBG was further silanized with 3-Aminopropyl-triethoxysilane (APTES) in order to immobilize Thrombin binding aptamer on the silica surface of the fiber. The change of Bragg wavelength when functionalized EFBG is exposed to different concentrations of Thrombin using Micron Optics Hyperion si255-x55 sensing system was demonstrated. A small yet detectable sensitivity (several tens of nanomolars) even between small protein variations allows hypothesizing a future use of this kind of functionalized fiber for biosensor development.

An etched chirped fiber Bragg grating for measurement of refractive index and temperature pattern

In this work, partially etched chirped fiber Bragg grating (pECFBG) for the real-time multi-parameter measurement of temperature and refractive index is proposed. The sensor is fabricated by wet-etching a portion of a linearly chirped FBG with linear chirp profile. Obtained CFBG has two active areas: the unetched part of the grating that can be used either as a uniform temperature sensor, or to detect thermal gradients experienced through the grating length; the etched part, besides having a similar thermal sensitivity, is exposed to refractive index sensing through the variations of external refractive index. Overall, the pECFBG structure behaves as a compact sensor with multi-parameter capability, that can both measure temperature and refractive index on the same grating, but also spatially resolve temperature detection through the grating section. The results have been validated through both a model and experimental setup, showing that the mutual correlation algorithm applied to different spectral parts of the grating is able to discriminate between uniform and gradient-shaped temperature profiles, and refractive index changes. The reflected spectra showed a clear correlation between the RI change of the surrounding media and spectral shift with temperature variations.

Partially etched chirped fiber Bragg grating (pECFBG) for joint temperature, thermal profile, and refractive index detection

In this work, a partially etched chirped fiber Bragg grating (pECFBG) is introduced, as a compact sensor for multi-parametric measurement of temperature, thermal gradients over the active length, and refractive index. The sensor is fabricated by wet-etching a portion of a 14-mm linearly chirped FBG with linear chirp profile. The resulting device has two active areas: the unetched part of the grating (2 mm) can be used either as a uniform temperature sensor, or to detect thermal gradients experienced through the grating length by means of a spectral reconstruction technique; the etched part (12 mm), besides having a similar thermal sensitivity, is exposed to refractive index sensing through the introduction of a sensitivity to external refractive index. Overall, the pECFBG structure behaves as a compact sensor with multi-parameter capability, that can both measure temperature and refractive index on the same grating, but also spatially resolve temperature detection through the grating section. The results have been validated through both a model and experimental setup, showing that the mutual correlation algorithm applied to different spectral parts of the grating is able to discriminate between uniform and gradient-shaped temperature profiles, and refractive index changes.

Wavelet analysis of multi-mode behavior of an etched Fiber Bragg Grating Sensor operating in sucrose solutions

Fiber optic sensors represent an attractive alternative in chemical, bio-chemical and medical applications. Their success can be retrieved in their peculiar properties such as: electromagnetic interference immunity, fast response, high sensitivity, and small size. In this context, Fiber Bragg Gratings (FBGs) play a key role in applications like measurements of temperature and strain. The mechanism of FBGs is related to the dependence between the characteristic wavelength reflected by the FBG and the effective index of the modes propagating inside the fibers. This property can be exploited to engineer a new and inexpensive class of FBG devices for measuring refractive index of solutions. By reducing the cladding thickness of the single mode fiber, where the FBG is inscribed, the structure becomes three layers and the modes guidance properties become more and more dependent on the external environment, including the refractive index of the solution to measure. In this work, an FBG has been etched by a solution of HF acid and immersed in different solutions of water and sucrose. Results show a strong multi-modal behavior induced by the guidance properties of the three-layer system. The reflected spectra, characterized by a large band whose width, are strictly dependent on the sucrose concentration in solution. As the sucrose increases, the refractive index of the solution increases. The bandwidth reduces, showing a wavelength shift toward longer wavelength. While the wavelength shift is not so relevant the variation of the bandwidth is significant, suggesting an effective interrogation method based on wavelet signal processing.

Interrogation of coarsely sampled Tilted Fiber Bragg Grating (TFBG) sensors with KLT

Tilted fiber Bragg gratings (TFBG) can be used as refractive index sensors, as their cladding modes, amplitude, and wavelength changes with the outer refractive index. However, as cladding modes have bandwidths that are narrower than the resolution of most infrared spectrometers, they can be detected only with an optical spectrum or vector analyzers. In this work, we demonstrate that through ad hoc implementation, the Karhunen-Loeve transform (KLT) algorithm can be used to demodulate a TFBG even using a coarse interrogator (156 pm), whereas cladding modes cannot be discriminated in the TFBG spectrum. We observe that the KLT output results are a reliable indicator to detect refractive index changes up to 1.85 ⋅ 10−3 refractive index units (RIU), down to a resolution of ~10−5 RIU. The KLT can be used to demodulate TFBG sensors and biosensors operating in small refractive index change conditions.