Yekbun Adiguzel

We investigated the short sequences involving Omicron 21K and Omicron 21L variants to reveal any possible molecular mimicry-associated autoimmunity risks and changes in those. We first identified common 6mers of the viral and human protein sequences present for both the mutant (Omicron) and nonmutant (SARS-CoV-2) versions of the same viral sequence and then predicted the binding affinities of those sequences to the HLA supertype representatives. We evaluated change in the potential autoimmunity risk, through comparative assessment of the nonmutant and mutant viral sequences and their similar human peptides with common 6mers and affinities to the same HLA allele. This change is the lost and the new, or de novo, autoimmunity risk, associated with the mutations in the Omicron 21K and Omicron 21L variants. Accordingly, e.g., the affinity of virus-similar sequences of the Ig heavy chain junction regions shifted from the HLA-B*15:01 to the HLA-A*01:01 allele at the mutant sequences. Addit...

This dataset contains files that are generated for and after blastp searches and HLA-affinity prediction results regarding the work entitled "In silico study of molecular mimicry between SARS-CoV-2 and Neutrophil Extracellular Traps composition in supernatants of patients with Systemic Lupus Erythematosus and Lupus Nephritis." File names are self-descriptive, therefore there is not a separate description file.

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.

Abstract Shannon’s information communication theory tells much about the reliable message transmission and has a wide scope of application in communication technologies. The aim of this work is to present the implementation of the information communication theory in the cellular recognition or molecular interaction event models to quantify the message transmission capacities of molecular binding patterns and complexes. It has implications in molecular evolution such that the pattern formation by varied combinations of a possible number of binding events does not necessitate the presence of different types of receptor–ligand complexes. Signals through the same and different types of receptor–ligand complexes seem to have equal information amounts. This is suggesting the possible role of pattern formation in differentiation of distinct conditions, maybe even changing local concentration gradients or so, through sensing the patterns of relevance. Further, recognition of the patterns that are formed up of the same binding partners would be the step preceding the recognition of the patterns with discrete binding partners. All these considerations are valid for cellular networks, wherein the communicating cells are the sources of binding target molecules and are thus imposing diffusion dependent concentration gradients and variations in the probabilities of the binding events.

AimThis study aims to predict autoimmunity-related pathological mechanisms that posses risk for individuals with certain HLA serotypes and are common to the pathogenicity of certain coronaviruses including SARS-CoV-2, based on homology to a SARS-CoV-2 peptide.MethodsCoronavirus-associated sequences, which are homologous to the SARS-CoV-2 peptide CFLGYFCTCYFGLFC, are obtained. Human peptides that have at least 7 residue matches with those coronavirus sequences, and the SARS-CoV-2 peptide, are obtained. Then, epitope pairs, which are sourced by those coronavirus and human sequences’ alignments, are identified. There, epitope pairs that are predicted to bind strongly not only to the same HLA allele with each other but also to the same HLA allele with the respective alignment of the SARS-CoV-2 peptide are selected.ResultsFollowing is the list of proteins (or regions) with predicted HLA-A*02:01 or HLA-A*24:02 epitopes, which are not only common but also homologous to the epitopes that ar...

Sensor-based diagnostics are increasing rapidly and in clinics, they can transform the health care as they will be in use out of clinics as well, namely, by the non-clinicians and people without expertise. The trade-off between the advantages and disadvantages of their implementation into the clinical settings should be decisive in their use, at the current state. Yet, disadvantages must be carefully worked out and tried to be eliminated in any case, while keeping the inborn benefits. Therefore, we would like to draw attention to the reliability and security risks of personal health data and associated concerns. We further discuss the related issues of sensor-based diagnostics, mobile health (mHealth) and eHealth. The debate starts with the current states of the rules and regulations. It is argued that there is prompt need for internationally consolidated solutions for vast device types and uses onto which the local needs may have to be implemented without violating the basic assets...

Based on the Shannon's information communication theory, information amount of the entire length of a polymeric macromolecule can be calculated in bits through adding the entropies of each building block. Proteins, DNA and RNA are such macromolecules. When only the building blocks' variation is considered as the source of entropy, there is seemingly lower information in case of the protein if this approach is applied directly on a protein of specific size and the coding sequence size of the mRNA corresponding to the particular length of the protein. This decrease in the information amount seems contradictory but this apparent conflict is resolved by considering the conformational variations in proteins as a new variable in the calculation and balancing the approximated entropy of the coding part of the mRNA and the protein. Probabilities can change therefore we also assigned hypothetical probabilities to the conformational states, which represent the uneven distribution as the time spent in one conformation, providing the probability of the presence in either or one of the possible conformations. Results that are obtained by using hypothetical probabilities are in line with the experimental values of variations in the conformational-state of protein populations. This equalization approach has further biological relevance that it compensates for the degeneracy in the codon usage during protein translation and it leads to the conclusion that the alphabet size for the protein is rather optimal for the proper protein functioning within the thermodynamic milieu of the cell. The findings were also discussed in relation to the codon bias and have implications in relation to the codon evolution concept. Eventually, this work brings the fields of protein structural studies and molecular protein translation processes together with a novel approach.

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 C...

The cell and its basic constituents are introduced here through a biophysical and information communication theoretic approach in biology and biosemiotics. With this purpose, the requirements of primordial cellular structures, single binding events, and signalling cascades are first mentioned stepwise, in relation to the model of the cellular sensing mechanism. This is followed by the concepts of cross reactions in sensing and pattern recognitions, wherein an information theoretic approach is addressed and the features of multicellularity are discussed along. Multicellularity is introduced as the path that leads to the loss of the direct causal relations. The loss of true causal relation is considered as a form of translation that enables meaning-encoded communication over the informative processes. In this sense, semiosis may not be exclusive. Synthetic biology is exemplified as a form of artificial selection mechanisms for the generation of 'self-reproducing' systems with information coding and processing machineries. These discussions are summarised at the end.

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.

ABSTRACT 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.

ABSTRACT This paper presents a CMOS image sensor with a 32 × 32 pixel array suitable for cell capture, detection, and quantification. Pixels measuring 15 μm × 15 μm have a modified structure, suitable for post-CMOS electroless gold plating, which enables surface activation for cell capture without the need for any intermediate layer. This structure also increases the detection probability of captured cells as opposed to non-captured ones, owing to a special light mask (metal shield) implemented on pixels. The light mask enables detection of cells as small as 3 μm in diameter despite the larger pixel size. The proof of concept is demonstrated in this work by imaging yeast cells adsorbed on the sensor surface.

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.

ABSTRACT This paper presents a CMOS image sensor with a 32 × 32 pixel array for cell capture, detection, and quantification. Pixels measuring 15 μm × 15 μm have a modified structure, suitable for post-CMOS electroless gold plating, which enables surface activation for cell capture without the need for any intermediate layer. This structure also increases the detection probability of captured cells, even when cells are much smaller than the pixel, owing to a special light mask implemented on pixels. Cells as small as 3 μm in diameter can be detected with this pixel structure. The proof of concept for surface activation of the gold coated sensor pixels was demonstrated by capturing and imaging MCF-7 breast cancer cells on the modified sensor surface. Accordingly, electroless gold coating of the Al pixels was achieved and the gold coated surface of the CMOS image sensor was activated with thiol-modified antibodies that can capture MCF-7 cells. Cells were then optically detected under green LED illumination.

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.

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.