The Role of Rigid Residues in Modulating TEM-1 β-Lactamase Function and Thermostability

The relationship between protein motions (i.e., dynamics) and enzymatic function has begun to be explored in β-lactamases as a way to advance our understanding of these proteins. In a recent study, we analyzed the dynamic profiles of TEM-1 (a ubiquitous class A β-lactamase) and several ancestrally reconstructed homologues. A chief finding of this work was that rigid residues that were allosterically coupled to the active site appeared to have profound effects on enzyme function, even when separated from the active site by many angstroms. In the present work, our aim was to further explore the implications of protein dynamics on β-lactamase function by altering the dynamic profile of TEM-1 using computational protein design methods. The Rosetta software suite was used to mutate amino acids surrounding either rigid residues that are highly coupled to the active site or to flexible residues with no apparent communication with the active site. Experimental characterization of ten designed proteins indicated that alteration of residues surrounding rigid, highly coupled residues, substantially affected both enzymatic activity and stability; in contrast, native-like activities and stabilities were maintained when flexible, uncoupled residues, were targeted. Our results provide additional insight into the structure-function relationship present in the TEM family of β-lactamases. Furthermore, the integration of computational protein design methods with analyses of protein dynamics represents a general approach that could be used to extend our understanding of the relationship between dynamics and function in other enzyme classes.     

Change detection in desktop virtual environments: An eye-tracking study

It is common knowledge that attention is important for learning. We need to utilize attention in order to learn something efficiently and effectively. Similarly, we may also need to acquire familiarity with (i.e., learn) our surroundings in order to utilize our attention. In this study, learning is defined as a product of one’s exposure to natural visual stimuli. Using a virtual model of a natural scene, we investigate both attention and its relationship to learning, according to this definition. Specifically, our focus is the effect of environment familiarity on gaze direction. Our findings reveal that the factor of familiarity with one’s surroundings in virtual reality environments exerts a significant influence on peoples’ ability to detect a variety of specific changes that occur within scenes under their observation.     

Evaluation of an adaptive and intelligent educational hypermedia for enhanced individual learning of mathematics: A qualitative study

The purpose of this study is to design a personalized adaptive and intelligent web based tutoring system based on learning style and expert system named UZWEBMAT and to evaluate its effects on 10th grade students’ learning of the unit of probability. In the study, initially, learning objects were prepared in three different ways in relation to three sub-learning areas of Visual–Auditory–Kinesthetic (VAK) learning style for each subject of the probability unit. These were appropriate for secondary school mathematics curricula. Then, they were transferred into the digital environment. Each student’s dominant learning style determines the content to which s/he will be directed since s/he is directed to the content that is appropriate for his/her learning style. The course to be followed by the students within UZWEBMAT and their browsing around the pages are decided by expert system integrated into the system. This expert system sets the situations in which s/he will get solution supports and the course s/he will follow in accordance with the performance of the student. Hereby, each student may follow a different course, and the solution supports s/he will get may also differ highlighting the individual learning. The sample of the study consists of 81 10th grade students and 3 mathematics teachers from two high schools in Trabzon, Turkey. Qualitative data were obtained both from the teachers and students participating in the study in order to answer the research questions about the implementation and evaluation of UZWEBMAT for mathematics teaching in a high school classroom. Obtained data were analyzed using qualitative data analysis methods. According to the results of the present study, positive opinions of students and teachers such as taking into account the individual learning differences and deriving mathematical relations and formulas through exploration became prominent. In addition, there were also other positive opinions of students and teachers such as providing permanent learning and introducing learning responsibility to the students. In this sense, it was concluded that UZWEBMAT is a beneficial instrument for both students and teachers.     

Synthesis and Characterization of Ferromagnetic Nickel Nanoparticles

Nickel nanoparticles on mass production scale have been prepared using a modified polyol process with Ni(CH₃COO)₂?4H₂O, NaOH, 1,2 propandiol and hydrazinium hydroxide (N₂H₄?H₂O). A?mixture of face centered cubic (fcc) metallic nickel nanoparticles with 12 nm diameter were obtained. We have experimentally studied the structure of nanoparticle by X-ray and Scanning Electron Microscopy (SEM, EDS). The magnetic properties of the prepared Ni film have been studied by Ferromagnetic Resonance (FMR) technique, Vibrating Sample Magnetometer (VSM) and Vector Network Analyzer (VNA). The effective g-factor and magnetic anisotropy constant were determined as g _eff=2.25 and K _eff=85?Oe, respectively.     

Design and development of an innovative individualized adaptive and intelligent e-learning system for teaching–learning of probability unit: Details of UZWEBMAT

In this study, an innovative adaptive and intelligent web based e-learning system, UZWEBMAT (Turkish abbreviation of Adaptive and INtelligent WEB based MAThematics teaching–learning system) was designed, developed and implemented. This e-learning system was intended for learning and teaching secondary school level permutation-combination-binomial expansion and probability subjects. Content which was prepared according to Turkish curriculum for secondary school mathematics course was transformed into learning objects in three different ways in accordance with VAK (Visual–Auditory–Kinesthetic) learning styles. Primary/secondary/tertiary learning styles of learners registering the system are determined and each learner receives the content appropriate for his/her dominant learning style. Also, they can be directed to contents of other styles according to their performances thanks to an expert system. Learning objects constituting the content were prepared according to constructivist approach. An active role for the learner was the purpose. Tips and intelligent solution supports within the learning objects were presented with expert system support to the learners. With this structure, UZWEBMAT bears the characteristics of intelligent tutoring system as well as an adaptive e-learning environment. All the movements of learners studying with UZWEBMAT are recorded and the necessary information is reported to both learners and teachers in a visualized way.     

UV curable lens production using molecular weight controlled PEEK based acrylic oligomer (Ac-PEEK)

We produced UV curable lenses with properties blocking short wave UV light. In the UV-curable formulations, we used an oligomer (Ac-PEEK) with another urethan oligomer (Mw = 2000). Radically active, molecular weight controlled Ac-PEEK was obtained by reacting 2-hydroxyl ethyl methacrylate with molecular- weight- controlled and isocyanate terminated PEEK (Mn = 4500). We characterized all synthesized monomer, oligomer and optical materials with UV/Vis spectrophotometer with interferogram, elemental analyser, mass spectrophotometer, proton nuclear magnetic resonance, Fourier transform infrared spectroscopy, thermal gravimetric analyzer, differential scanning calorimeter, scanning electron microscopy and gas chromatography. Results suggested that newly synthesized oligomer with the structure of PEEK absorbs short wave UV-light. Ageing tests [ISO 11979-5, Ophthalmic implants—intraocular lenses (IOL)—Part 5: Biocompatibility] performed on the IOL materials were successful. High contact angle of the obtained lenses suggests that all lenses were hydrophobic and SEM results revealed that lenses are morphologically homogeneous. Based on all positive properties just mentioned, we safely conclude that the lenses produced in this study are very promising for IOL production.     

Synthesis and spectroelectrochemistry of dithieno(3,2‐b:2′,3′‐d)pyrrole derivatives

New π‐conjugated polymers containing dithieno(3,2‐b:2′,3′‐d)pyrrole (DTP) were successfully synthesized via electropolymerization. The effect of structural differences on the electrochemical and optoelectronic properties of the 4‐[4H‐dithieno(3,2‐b:2′,3′‐d)pyrrol‐4‐yl]aniline (DTP–aryl–NH₂), 10‐[4H‐dithiyeno(3,2‐b:2′,3′‐d)pirol‐4‐il]dekan‐1‐amine (DTP–alkyl–NH₂), and 1,10‐bis[4H‐dithieno(3,2‐b:2′,3′‐d)pyrrol‐4‐yl] decane (DTP–alkyl–DTP) were investigated. The corresponding polymers were characterized by cyclic voltammetry, NMR (¹H‐NMR and ¹³C‐NMR), and ultraviolet–visible spectroscopy. Changes in the electronic nature of the functional groups led to variations in the electrochemical properties of the π‐conjugated systems. The electroactive polymer films revealed redox couples and exhibited electrochromic behavior. The replacement of the DTP–alkyl–DTP unit with DTP–aryl–NH₂ and DTP–alkyl–NH₂ resulted in a lower oxidation potential. Both the poly(10‐(4H‐Dithiyeno[3,2‐b:2′,3′‐d]pirol‐4‐il)dekan‐1‐amin) (poly(DTP–alkyl–NH₂)) and poly(1,10‐bis(4H‐dithieno[3,2‐b:2′,3′‐d]pyrrol‐4‐yl) decane) (poly(DTP–alkyl–DTP)) films showed multicolor electrochromism and also fast switching times (<1 s) in the visible and near infrared regions. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014 , 131, 40701.