Yekbun Adiguzel

Breath sensors for lung cancer diagnosis

The scope of the applications of breath sensors is abundant in disease diagnosis. Lung cancer diagnosis is a well-fitting health-related application of this technology, which is of utmost importance in the health sector, because lung cancer has the highest death rate among all cancer types, and it brings a high yearly global burden. The aim of this review is first to provide a rational basis for the development of breath sensors for lung cancer diagnostics from a historical perspective, which will facilitate the transfer of the idea into the rapidly evolving sensors field. Following examples with diagnostic applications include colorimetric, composite, carbon nanotube, gold nanoparticle-based, and surface acoustic wave sensor arrays. These select sensor applications are widened by the state-of-the-art developments in the sensors field. Coping with sampling sourced artifacts and cancer staging are among the debated topics, along with the other concerns like proteomics approaches and biomimetic media utilization, feature selection for data classification, and commercialization.

Secondary structure of lipidated Ras bound to a lipid bilayer

Ras proteins are small guanine nucleotide binding proteins that regulate many cellular processes, including growth control. They undergo distinct post‐translational lipid modifications that are required for appropriate targeting to membranes. This, in turn, is critical for Ras biological function. However, most in vitro studies have been conducted on nonlipidated truncated forms of Ras proteins. Here, for the first time, attenuated total reflectance‐FTIR studies of lipid‐modified membrane‐bound N‐Ras are performed, and compared with nonlipidated truncated Ras in solution. For these studies, lipidated N‐Ras was prepared by linking a farnesylated and hexadecylated N‐Ras lipopeptide to a truncated N‐Ras protein (residues 1–181). It was then bound to a 1‐palmitoyl‐2‐oleoyl‐sn‐glycero‐3‐phosphocholine bilayer tethered on an attenuated total reflectance crystal. The structurally sensitive amide I absorbance band in the IR was detected and analysed to determine the secondary structure of the protein. The NMR three‐dimensional structure of truncated Ras was used to calibrate the contributions of the different secondary structural elements to the amide I absorbance band of truncated Ras. Using this novel approach, the correct decomposition was selected from several possible solutions. The same parameter set was then used for the membrane‐bound lipidated Ras, and provided a reliable decomposition for the membrane‐bound form in comparison with truncated Ras. This comparison indicates that the secondary structure of membrane‐bound Ras is similar to that determined for the nonlipidated truncated Ras protein for the highly conserved G‐domain. This result validates the multitude of investigations of truncated Ras without anchor in vitro. The novel attenuated total reflectance approach opens the way for detailed studies of the interaction network of the membrane‐bound Ras protein.

Glucose determination based on a two component self-assembled monolayer functionalized surface-enhanced Raman spectroscopy (SERS) probe

In this report, we present a new detection method for blood glucose, using gold nanorod SERS, a surface enhanced Raman scattering probe embedded in two component self-assembled monolayers (SAMs). Gold nanorod particles and a gold coated slide surface were modified with the two component SAMs consisting of 3-mercaptophenylboronic acid (3-MBA) and 1-decanethiol (1–DT). The immobilization of 3-MBA/1-DT surface-functionalized gold nanoparticles onto 3-MBA/1-DT modified gold-coated slide surfaces was achieved by the cooperation of hydrophobic forces. Two component SAM functionalized substrates were used as SERS probes, by means of the boronic acid and the alkyl spacer functional groups that serve as the molecular recognition and penetration agents, respectively. The SERS platform surface was characterized by cyclic voltammetry, contact angle measurements, AFM (atomic force microscopy) and Raman spectroscopy. Optimum values of the parameters such as pH, time and (3-MBA/1-DT) molar ratio were also examined for the glucose determination. The analytical performance was evaluated and linear calibration graphs were obtained in the glucose concentration range of 2–16 mM, which is also in the range of the blood glucose levels, and the detection limit was found to be 0.5 mM. As a result, the SERS platform was also used for the determination of glucose in plasma samples.

CMOS Cell Sensors for Point-of-Care Diagnostics

The burden of health-care related services in a global era with continuously increasing population and inefficient dissipation of the resources requires effective solutions. From this perspective, point-of-care diagnostics is a demanded field in clinics. It is also necessary both for prompt diagnosis and for providing health services evenly throughout the population, including the rural districts. The requirements can only be fulfilled by technologies whose productivity has already been proven, such as complementary metal-oxide-semiconductors (CMOS). CMOS-based products can enable clinical tests in a fast, simple, safe, and reliable manner, with improved sensitivities. Portability due to diminished sensor dimensions and compactness of the test set-ups, along with low sample and power consumption, is another vital feature. CMOS-based sensors for cell studies have the potential to become essential counterparts of point-of-care diagnostics technologies. Hence, this review attempts to inform on the sensors fabricated with CMOS technology for point-of-care diagnostic studies, with a focus on CMOS image sensors and capacitance sensors for cell studies.

Relationship between functional promoter polymorphism in the XBP1 gene (−116C/G) and atherosclerosis, ischemic stroke and hyperhomocysteinemia

ER stress is associated with a range of pathological conditions, among which, the ischemia/reperfusion injury is also found. The mechanistic array of links among the ER stress and thrombovascular diseases is poorly understood. The XBP1 gene is a transcription factor which modulates the ER stress response; and the XBP1 (−116 C/G) gene polymorphism causes an impairment of its positive feedback system. In the present study we investigated the prevalence of XBP1 gene (−116 C/G) polymorphism, separately among the patients with atherosclerosis, ischemic stroke and hyperhomocysteinemia. The G allele and the (−116 G/G) genotype of the XBP1 (−116 C/G) gene polymorphism were found to be a significant risk factor for the patients with Ischemic Stroke. Yet, this allele was seemingly less significant in case of patients with atherosclerosis and hyperhomocysteinemia. Hence, the XBP1 (−116 C/G) gene polymorphism and especially its involvement in a homozygous state are suggested to take active role in the ER stress related ischemia/reperfusion injury.

Effect of eNOS and ET-1 Polymorphisms in Thromboangiitis Obliterans

Thromboangiitis obliterans (TAO), or Buerger disease, is a segmental occlusive inflammatory disorder of the arteries and veins, and etiopathogenesis is still obscure. It is strongly connected to the use of tobacco products, especially smoking. Smoking cessation is obligatory for success of the medical treatment. In the current study, we investigated the prevalence of endothelial nitric oxide synthase (eNOS) 894 G→T and endothelin-1 (ET-1) 8000 T→C polymorphisms in association with TAO to reveal any possible involvement in the TAO pathophysiology. The T allele of the eNOS 894 G→T polymorphism was found to be associated with the prevention of TAO.

From the Physiocrats to Fairness in Nations

In this review, work from three centuries of biophysical economics is presented, starting from the physiocrats’ early work in biophysical economics in 1755, to the most recent modeling of modern societies with approaches from biophysics and physics, to explain the wealth distribution, opinions and power structures in societies and nations. At the same time, we are also dealing with generalizations, in particular, how to define and create fairness in nations. The general conclusions emphasize the strength of socio-econo-physics in explaining nations, also in comparison to the other approaches, due to the unbiased starting points and diversity in methods. The results emphasize that fairness is increased with citizens’ activities that create smoother income distributions and improving the flow of opportunities in the nation. Fairness also fights unjust socio-economic biases and suggests advancing citizens-managed organizations.

Commentary on “Biophysical Economics” and Evolving Areas

In this Issue, papers in the area of socio-econo-physics and biophysical economics are presented. We have recently introduced socio-econo-physics and biophysical economics in Biophysical Reviews and Letters (BRL), yet saw 3 to 4 relevant papers just in these most recent three quarters. In this commentary, we therefore would like to elaborate on the topics of socio-econo-physics and biophysical economics and to introduce these concepts to the readers of BRL and the biophysical community of science, with the purpose of supporting many more publications here in BRL, in this evolving area.

Historical and Critical Review on Biophysical Economics

Biophysical economics is initiated with the long history of the relation of economics with ecological basis and biophysical perspectives of the physiocrats. It inherently has social, economic, biological, environmental, natural, physical, and scientific grounds. Biological entities in economy like the resources, consumers, populations, and parts of production systems, etc. could all be dealt by biophysical economics. Considering this wide scope, current work is a “biophysical economics at a glance” rather than a comprehensive review of the full range of topics that may just be adequately covered in a book-length work. However, the sense of its wide range of applications is aimed to be provided to the reader in this work. Here, modern approaches and biophysical growth theory are presented after the long history and an overview of the concepts in biophysical economics. Examples of the recent studies are provided at the end with discussions. This review is also related to the work by Cleveland, “Biophysical Economics: From Physiocracy to Ecological Economics and Industrial Ecology” [C. J. Cleveland, in Advances in Bioeconomics and Sustainability: Essay in Honor of Nicholas Gerogescu-Roegen, eds. J. Gowdy and K. Mayumi (Edward Elgar Publishing, Cheltenham, England, 1999), pp. 125–154.]. Relevant parts include critics and comments on the presented concepts in a parallelized fashion with the Cleveland’s work.

Studies on visual detection and surface modification testing of glass microfiber filter paper based biosensor

Glass microfibers are commonly used as biomolecule adsorption media, as structural or disposable components of the optical biosensors. While any improvement in these components are appreciated, utilizing basic tools of traditional approaches may lead to original sensor opportunities as simple, functional designs that can be easily disseminated. Following this pursuit, surface modification of glass microfiber paper surface was performed by 3-aminopropyltriethoxysilane (APTES) and resulting improvement in the cell entrapment capacity could be observed visually, only after Gram staining. Gram staining offered rapid validation of enhanced binding on the glass surface. The same APTES-modified samples were also tested for binding of complementary DNA sequences and the results were less straightforward due to the necessity of DNA visualization by using a fluorescent stain, YOYO-1. Accordingly, when there were no surface modification, DNA and YOYO-1 adsorbed readily on the glass microfiber filter paper, and prolonged the interaction between DNA and YOYO-1. YOYO-1 adsorption on glass could be recognized from the color profile of YOYO-1 emission. This phenomenon can be used to examine suitability of APTES coverage on glass surfaces since YOYO-1 emission can be distinguished by its glass adsorbed versus DNA-bound forms. Aptness of surface coverage is vital to biosensor studies in the sense that it is preceding the forthcoming surface modifications and its precision is imperative for attaining the anticipated interaction kinetics of the surface-immobilized species. The proposed testing scheme offered in this study secures the work, which is aimed to be carried out utilizing such sensing systems and device components.