Highly sensitive and label-free digital detection of whole cell E. coli with interferometric reflectance imaging

Bacterial infectious diseases are a major threat to human health. Timely and sensitive pathogenic bacteria detection is crucial in identifying the bacterial contaminations and preventing the spread of infectious diseases. Due to limitations of conventional bacteria detection techniques there have been concerted research efforts towards development of new biosensors. Biosensors offering label free, whole bacteria detection are highly desirable over those relying on label based or pathogenic molecular components detection. The major advantage is eliminating the additional time and cost required for labeling or extracting the desired bacterial components. Here, we demonstrate rapid, sensitive and label free E. coli detection utilizing interferometric reflectance imaging enhancement allowing for visualizing individual pathogens captured on the surface. Enabled by our ability to count individual bacteria on a large sensor surface, we demonstrate a limit of detection of 2.2 CFU/ml from a buffer solution with no sample preparation. To the best of our knowledge, this high level of sensitivity for whole E. coli detection is unprecedented in label free biosensing. The specificity of our biosensor is validated by comparing the response to target bacteria E. coli and non target bacteria S. aureus, K. pneumonia and P. aeruginosa. The biosensor performance in tap water also proves that its detection capability is unaffected by the sample complexity. Furthermore, our sensor platform provides high optical magnification imaging and thus validation of recorded detection events as the target bacteria based on morphological characterization. Therefore, our sensitive and label free detection method offers new perspectives for direct bacterial detection in real matrices and clinical samples.First author draf

Observation on the age, growth and somatic condition of Carasobarbus luteus (Heckel, 1843) and Capoeta trutta (Heckel, 1843) (Cyprinidae) in the Tigris River, Turkey

This study was carried out to determine some biological characteristics including age, growth and somatic condition of Carasobarbus luteus and Capoeta trutta in the Turkish part of the Tigris River. The examined samples of C. luteus were distributed between II-IX years of age. The length-weigth relations of females and males were calculated as Log W =-4.7314 +3.0113 Log FL and Log W = -4.7631 +3.0263 Log FL respectively. Von Bertalanffy growth equations were estimated as Lt=40.09 [1-e^-0.087036 (t+1.55004)] for females and Lt=38.14 [1-e^-0.080056 (t+2.34838)] for males. The somatic condition was 1.9667 ± 0.1751 for females and 1.9967 ± 0.4205 for males. The observed samples of C. trutta were distributed between I-VI years of age. The length-weigth relationship of females and males were calculated as Log W = -4.6845 + 2.9303 Log FL, Log W = -4.7784 + 2.9746 Log FL, respectively. Von Bertalanffy growth equations were estimated as Lt=35.36 [1-e^-0.082817 (t+4.82738)] for females and Lt=28.82 [1-e^-0.12380 (t+4.40235)] for males. The somatic condition in female and male individuals were determined as; 1.4434 ± 0.1682 and 1.4722 ± 0.1984 respectively. Both species are economic fish in the Tigris River. Biological characteristics of the species determined in the present study, may contribute to a better understanding of the life cycle, thus providing useful data for its conservation and management

On the Solution of the Vibration Equation by Means of the Homotopy Perturbation Method

In this paper, we present a reliable algorithm, the homotopy perturbation method, to solve the well-known vibration equation for very large membrane which is given initial conditions. By using initial value, the explicit solutions of the equation for different cases have been derived, which accelerate the rapid convergence of the series solution. Numerical results show that the homotopy perturbation method is easy to implement and accurate when applied to differential equations. Numerical results for different particular cases of the problem are presented graphically

Exact solitary-wave Special Solutions for the Nonlinear Dispersive K(m,n) Equations by Means of the Homotopy Analysis Method

In this paper, we study the nonlinear dispersive K(m,n) equations which exhibit solutions with solitary patterns. New exact solitary solutions are found. The two special cases, K(2, 2) and K(3, 3), are chosen to illustrate the concrete features of the homotopy analysis method in K(m,n) equations. The nonlinear equations K(m,n) are studied for two different cases, namely when m = n being odd and even integers. General formulas for the solutions of K(m,n) equations are established

GÖKPINAR BARAJI (DENİZLİ) DOLUSAVAK VE EŞİK YAPISI TEMEL ZEMİNİNDE YAPILAN JEOTEKNİK ÇALIŞMALAR

Dams, regulators, irrigation canals etc. have been built to use water resources for economic aims. These types of engineering structures, have to control enormous volume of water, are required to determine all the geological and geotechnical properties of the construction site. The main goal of the study is to mitigate the geological and geotechnical hazards by assessing the pressuremeter test and borehole data performed on the spillway and gate of Gökpınar Dam in Denizli. Geological and geotechnical characteristics of the spillway and gate were also given in the text. Pressuremeter and pull-out tests were carried out on spillway and gate foundations and the obtained results have been correlated to projects data. Some details have also been given about re-enforcement of the weak soil includes cement injection, and bolts.Su kaynaklarının ekonomiye kazandırılması amacıyla baraj, gölet, regülatör ve sulama ana kanalları gibi yapılar inşa edilmektedir. Büyük miktardaki suyun kontrol altında tutulmasını gerektiren bu tür mühendislik yapılarının uzun yıllar kullanılabilmesi; üzerine inşa edileceği jeolojik birimlerin jeoteknik özelliklerinin iyi belirlenerek buna uygun proje tasarımı ve zemin iyileştirmesi yapılmasına bağlıdır. Bu çalışmada, Gökpınar Barajı (Denizli) dolusavak ve eşik yapısı temel zemininde yapılan saha incelemeleri ile temel sondajı ve presiyometre deneylerinin sonuçlarına göre yapılan jeoteknik iyileştirme önlemlerin belirlenmesi amaçlanmaktadır. Baraj alanındaki jeolojik birimlerin jeolojisi ile dolusavak ve eşik yapısının altındaki birimlerin mühendislik özellikleri hakkında bilgiler verilmiştir. Dolusavak ve eşik yapısının oturacağı birimlerin taşıma gücü ve oturma hesaplarına yönelik olarak yerinde (in-situ) presiyometre ve çekme deneyleri yapılmış; bu deneylerin sonuçları yorumlanarak, inşa edilecek yapıdan gelecek yük ile zeminin emniyetli taşıma gücü karşılaştırılmıştır. Zayıf taşıma gücüne sahip birimlerin güçlendirilmesi için alınması gereken önlemler ve güçlendirme işlemleri (zemin sağlamlaştırma enjeksiyonu, ankraj çalışması vb) hakkında bilgiler verilmiştir

Instrument-free protein microarray fabrication for accurate affinity measurements

Protein microarrays have gained popularity as an attractive tool for various fields, including drug and biomarker development, and diagnostics. Thus, multiplexed binding affinity measurements in microarray format has become crucial. The preparation of microarray-based protein assays relies on precise dispensing of probe solutions to achieve efficient immobilization onto an active surface. The prohibitively high cost of equipment and the need for trained personnel to operate high complexity robotic spotters for microarray fabrication are significant detriments for researchers, especially for small laboratories with limited resources. Here, we present a low-cost, instrument-free dispensing technique by which users who are familiar with micropipetting can manually create multiplexed protein assays that show improved capture efficiency and noise level in comparison to that of the robotically spotted assays. In this study, we compare the efficiency of manually and robotically dispensed α-lactalbumin probe spots by analyzing the binding kinetics obtained from the interaction with anti-α-lactalbumin antibodies, using the interferometric reflectance imaging sensor platform. We show that the protein arrays prepared by micropipette manual spotting meet and exceed the performance of those prepared by state-of-the-art robotic spotters. These instrument-free protein assays have a higher binding signal (~4-fold improvement) and a ~3-fold better signal-to-noise ratio (SNR) in binding curves, when compared to the data acquired by averaging 75 robotic spots corresponding to the same effective sensor surface area. We demonstrate the potential of determining antigen-antibody binding coefficients in a 24-multiplexed chip format with less than 5% measurement error.Boston University Ignition Program - Boston University; NSF -CORPS Award No. 2027109 and NSF-TT PFI Award No. 1941195 - National Science FoundationPublished versio

The role of surface chemistry in the efficacy of protein and DNA microarrays for label-free detection: an overview

The importance of microarrays in diagnostics and medicine has drastically increased in the last few years. Nevertheless, the efficiency of a microarray-based assay intrinsically depends on the density and functionality of the biorecognition elements immobilized onto each sensor spot. Recently, researchers have put effort into developing new functionalization strategies and technologies which provide efficient immobilization and stability of any sort of molecule. Here, we present an overview of the most widely used methods of surface functionalization of microarray substrates, as well as the most recent advances in the field, and compare their performance in terms of optimal immobilization of the bioreceptor molecules. We focus on label-free microarrays and, in particular, we aim to describe the impact of surface chemistry on two types of microarray-based sensors: microarrays for single particle imaging and for label-free measurements of binding kinetics. Both protein and DNA microarrays are taken into consideration, and the effect of different polymeric coatings on the molecules' functionalities is critically analyzed.SO766466 (INDEX) - European Union Horizon 2020; NSF iCorps Award n°5242027109 - National Science Foundation; NSF-TT PFI Award n°1941195 - National Science FoundationPublished versio

Highly multiplexed label-free imaging sensor for accurate quantification of small-molecule binding kinetics

Investigating the binding interaction of small molecules to large ligands is a compelling task for the field of drug development, as well as agro-biotechnology, since a common trait of drugs and toxins is often a low molecular weight (MW). Here, we improve the limit of detection of the Interferometric Reflectance Imaging Sensor (IRIS), a label-free, highly multiplexed biosensor, to perform small-molecule screening. In this work, characterization of small molecules binding to immobilized probes in a microarray format is demonstrated, with a limit of detection of 1 pg/mm2 in mass density. First, as a proof of concept to show the impact of spatial and temporal averaging on the system noise, detection of biotin (MW = 244.3 Da) binding to a streptavidin-functionalized chip is performed and the parameters are tuned to achieve maximum signal-to-noise ratio (SNR ≈ 34). The optimized system is then applied to the screening of a 20-multiplexed antibody chip against fumonisin B1 (MW = 721.8 Da), a mycotoxin found in cereal grains. The simultaneously recorded binding curves yield an SNR ≈ 8. Five out of twenty antibodies are also screened against the toxin in a lateral flow assay, obtaining consistent results. With the demonstrated noise characteristics, further sensitivity improvements are expected with the advancement of camera sensor technology.Published versio