From peripheral finger-derived pulse waveforms to aortic pressure waveform features: an application of a generalized transfer function.

OBJECTIVE: Aortic (central) pressure features are associated with cardiovascular complications and can be algorithmically derived from non-invasive peripheral arterial waveforms. This has conventionally been performed with a pressure waveform (i.e., tonometry or oscillometry) rather than with the optical-based sensor (photoplethysmography (PPG)) that is predominantly used in wearable health devices. Extraction of aortic features from a peripheral PPG waveform has yet to be investigated. This study aims to compare aortic features extracted from peripheral arterial waveforms acquired with different sensor modalities using the same transfer function. DESIGN AND METHOD: Radial tonometry (reference), finger volume-clamped PPG (Penáz) and fingertip PPG waveforms were measured in participants (n=29, 36±16 years, 15 female) under baseline conditions. Waveforms were converted into an aortic pressure waveform using the transfer function. Waveform features were extracted from the converted waveform. Extracted features were compared with correlation plots and a Bland-Altman analysis. RESULTS: Aortic pressure features extracted from a finger using the Penáz technique were comparable to radial tonometry derived features. Aortic features extracted from a fingertip waveform were more variable in comparison to radial tonometry-derived features. CONCLUSIONS: Aortic (central) pressure waveform features contain valuable haemodynamic information and have the capacity to be easily and conveniently implemented in wearable health devices. Future use of these features in wearable health devices incorporating PPG requires the development, and/or, optimization of a unique transfer function to more accurately represent the aortic pressure waveform for cardiovascular assessment.Clinical Relevance- Aortic pressure features might be used in wearable health devices following the development of a unique transfer function for optical-transduced peripheral vascular signals.

Bilateral cuff-induced lower limb post-ischemia hyperemia as a method for acute reduction in blood pressure for cuffless blood pressure device testing.

OBJECTIVE: Development and testing of cuffless blood pressure (BP) devices requires methods to increase and decrease BP. This is also required by cuffless BP validation standards. Pharmacological interventions, whilst successful, are not always feasible for all subpopulations or research settings. Non-pharmacological approaches for increasing BP are available, however, methods for decreasing BP are not well described. This study investigates the hyperemic response following bilateral leg-cuff ischemia as a method for acute BP lowering. DESIGN AND METHOD: Participants (n=8, 24±8 years, 6 female) had their BP measured by continuous (finger, Penáz technique) and intermittent (brachial cuff, oscillometric) methods before, during and following 3-minute leg-ischemia with the participant in an upright position. Total peripheral resistance (TPR) and cardiac output (CO) were calculated from finger BP waveforms. Maxima and minima responses in the variables were extracted and compared to resting conditions by repeated measures analysis of covariance. RESULTS: During the hyperemic period, systolic BP decreased by -22±3 mmHg (finger) and -6±1 mmHg (brachial). Diastolic BP decreased by -14±5 mmHg (finger) and -4 ±1 mmHg (brachial). Calculated TPR and CO varied, with both decreasing by half and almost doubling during the hyperemic response period. CONCLUSIONS: Leg-cuff ischemia provides a controlled, non-pharmacological intervention for decreasing systemic arterial BP. This removes some of the limitations in testing, development and validation of cuffless BP techniques and devices.

Combining content and elements of communication into an upper-level biochemistry course.

This report describes how a science communication module was incorporated into an advanced biochemistry course. Elements of communication were taught synergistically with biochemistry content in this course in an effort to expose students to a variety of effective oral communication strategies. Students were trained to use these established techniques and incorporated them into various presentations throughout the course. Three students describe their use of specific resources and how the skills learned relate to their future career. The importance and relevance of science communication are receiving unprecedented national attention. The academic scientific community must respond by incorporating more communication-centered instruction and opportunities in the classroom and laboratory.

Examination of tyrosine/adenine stacking interactions in protein complexes.

The π-stacking interactions between tyrosine amino acid side chains and adenine-bearing ligands are examined. Crystalline protein structures from the protein data bank (PDB) exhibiting face-to-face tyrosine/adenine arrangements were used to construct 20 unique 4-methylphenol/N9-methyladenine (p-cresol/9MeA) model systems. Full geometry optimization of the 20 crystal structures with the M06-2X density functional theory method identified 11 unique low-energy conformations. CCSD(T) complete basis set (CBS) limit interaction energies were estimated for all of the structures to determine the magnitude of the interaction between the two ring systems. CCSD(T) computations with double-ζ basis sets (e.g., 6-31G*(0.25) and aug-cc-pVDZ) indicate that the MP2 method overbinds by as much as 3.07 kcal mol(-1) for the crystal structures and 3.90 kcal mol(-1) for the optimized structures. In the 20 crystal structures, the estimated CCSD(T) CBS limit interaction energy ranges from -4.00 to -6.83 kcal mol(-1), with an average interaction energy of -5.47 kcal mol(-1), values remarkably similar to the corresponding data for phenylalanine/adenine stacking interactions. Geometry optimization significantly increases the interaction energies of the p-cresol/9MeA model systems. The average estimated CCSD(T) CBS limit interaction energy of the 11 optimized structures is 3.23 kcal mol(-1) larger than that for the 20 crystal structures.

Enhancing student interactions with the instructor and content using pen-based technology, YouTube videos, and virtual conferencing.

This report describes the incorporation of digital learning elements in organic chemistry and biochemistry courses. The first example is the use of pen-based technology and a large-format PowerPoint slide to construct a map that integrates various metabolic pathways and control points. Students can use this map to visualize the integrated nature of metabolism and how various hormones impact metabolic regulation. The second example is the embedding of health-related YouTube videos directly into PowerPoint presentations. These videos become a part of the course notes and can be viewed within PowerPoint as long as students are online. The third example is the use of a webcam to show physical models during online sessions using web-conferencing software. Various molecular conformations can be shown through the webcam, and snapshots of important conformations can be incorporated into the notes for further discussion and annotation. Each of the digital learning elements discussed in this report is an attempt to use technology to improve the quality of educational resources available outside of the classroom to foster student engagement with ideas and concepts. Biochemistry and Molecular Biology Education Vol. 39, No. 1, pp. 4-9, 2011.

Probing phenylalanine/adenine pi-stacking interactions in protein complexes with explicitly correlated and CCSD(T) computations.

To examine the effects of pi-stacking interactions between aromatic amino acid side chains and adenine bearing ligands in crystalline protein structures, 26 toluene/(N9-methyl)adenine model configurations have been constructed from protein/ligand crystal structures. Full geometry optimizations with the MP2 method cause the 26 crystal structures to collapse to six unique structures. The complete basis set (CBS) limit of the CCSD(T) interaction energies has been determined for all 32 structures by combining explicitly correlated MP2-R12 computations with a correction for higher-order correlation effects from CCSD(T) calculations. The CCSD(T) CBS limit interaction energies of the 26 crystal structures range from -3.19 to -6.77 kcal mol (-1) and average -5.01 kcal mol (-1). The CCSD(T) CBS limit interaction energies of the optimized complexes increase by roughly 1.5 kcal mol (-1) on average to -6.54 kcal mol (-1) (ranging from -5.93 to -7.05 kcal mol (-1)). Corrections for higher-order correlation effects are extremely important for both sets of structures and are responsible for the modest increase in the interaction energy after optimization. The MP2 method overbinds the crystal structures by 2.31 kcal mol (-1) on average compared to 4.50 kcal mol (-1) for the optimized structures.

Virtual office hours using a tablet PC: E-lluminating biochemistry in an online environment.

The availability of online collaboration software has provided new opportunities for instructors to interact with students outside the classroom. This report describes how Elluminate Live!®, a particular conferencing software package, can be used with a tablet PC to conduct virtual office hours in a biochemistry course. The educational value of engaging students in an online environment, with text messaging, voice-over-internet protocol (VoIP), and application sharing is also discussed. A student perspective is provided to illustrate the advantages of conducting virtual office hours and how the combination of online collaboration software and tablet PC technology can provide an enhanced learning experience.

Audio podcasting in a tablet PC-enhanced biochemistry course.

This report describes the effects of making audio podcasts of all lectures in a large, basic biochemistry course promptly available to students. The audio podcasts complement a previously described approach in which a tablet PC is used to annotate PowerPoint slides with digital ink to produce electronic notes that can be archived. The fundamentals of this approach are described, and data from student attitudinal and informational surveys are presented. The survey data suggest that the students have a positive attitude toward the combination of tablet-based instruction and audio podcasting. In addition, three students provide testimonials on how these technological tools allowed them to utilize their preferred learning styles to succeed in the course. Possible negative consequences of this approach, in terms of class attendance and note taking, are also analyzed and discussed.

Screen capture on the fly: Combining molecular visualization and a tablet PC in the biochemistry lecture*.

The biochemistry lecture is often the place where students receive the greatest exposure to the structural nature of biomolecules. The use of molecular visualization software and web-based animated tutorials has enhanced the way instructors teach this important area of structural biology. Using the software and tutorials in class is an excellent way to teach the diverse structural motifs found in biomolecules; however, integrating the computer-based molecular renderings shown in class into lecture notes is challenging. This report describes how incorporating a tablet PC into the biochemistry lecture can be used in conjunction with molecular visualization software to create a rich set of lecture notes. The pedagogical tools associated with a tablet PC make it an attractive addition to the biochemistry lecture, which usually has significant audio and visual learning components.

Establishing the principles of recognition in the adenine-binding region of an aminoglycoside antibiotic kinase [APH(3')-IIIa].

The protein-based molecular recognition of the adenine ring has implications throughout biological systems. In this paper, we discuss the adenine-binding region of an aminoglycoside antibiotic kinase [APH(3')-IIIa], which serves as an excellent model system for proteins that bind the adenine ring. This enzyme employs a hydrogen-bonding network involving water molecules along with enzyme backbone/side-chain atoms and a pi-pi stacking interaction to recognize the adenine ring. Our approach utilized site-directed mutagenesis, adenosine analogues and a variety of biophysical methods to probe the contacts in the adenine-binding region of APH(3')-IIIa. The results point to the polar nature of an adenine-Met90 contact in this binding pocket and the important role that Met90, the "gatekeeper" residue in structurally similar Ser/Thr protein kinases, plays in adenine binding. The results also suggest that small changes in the structure of the adenine ring can lead to significant changes in the ability of these analogues to occupy the adenine-binding region of the enzyme. Additional computational experiments indicate that both size and electronic factors are important in the binding of aromatic systems in this interaction-rich pocket. The principles governing adenine recognition established in this study may be applied to other protein-ligand complexes and used to navigate future studies directed at discovering potent and selective inhibitors of APH-type enzymes.

Modeling of benzocaine analog interactions with the D4S6 segment of NaV4.1 voltage-gated sodium channels.

Local anesthetics (LAs) are compounds that inhibit the propagation of action potentials in excitable tissues by blocking voltage-gated Na+ channels. Mutagenesis studies have demonstrated that several amino acid residues are important sites of LA interaction with the channel, but these studies provide little information regarding the molecular forces that govern drug-binding interactions, including the binding orientation of drugs. We used computational methods to construct a simple model of benzocaine analog binding with the D4S6 segment of rat skeletal muscle (NaV4.1) sodium channels. The model revealed that four hydrophobic residues form a binding cavity for neutral LAs, and docking studies indicated that increasing hydrophobicity among the benzocaine analogs allowed a better fit within the binding cavity. The similarities between our simple model and published experimental data suggested that modeling of LA interactions with sodium channels, along with experimental approaches, could further enhance our understanding of LA interactions with sodium channels.

Voltage-dependent inhibition of rat skeletal muscle sodium channels by aminoglycoside antibiotics.

Aminoglycoside (AG) antibiotics interact with numerous biological molecules, including some voltage-gated ion channels. The present study demonstrates that 4,5-disubstituted (neomycin class) and 4,6-disubstituted (kanamycin class) AGs inhibit whole-cell currents through cloned rat skeletal muscle sodium channels (mu1, Na(V)4.1). Increases in the amplitude of the step command reduced inhibition by extracellular AGs but increased inhibition by intracellularly applied AGs, indicating that the block was voltage dependent. Furthermore, intracellular neamine or sisomycin hastened the rate of macroscopic current decay at positive voltages. Extracellular solution containing sodium ions slowed the rate of current decay in the presence of intracellular sisomycin and decreased the apparent affinity of sisomycin from the intracellular side twofold. Current inhibition by extracellularly or intracellularly applied AGs was well fitted by the Woodhull model of pore block. The model indicated that most extracellularly applied AGs interact at a site that is an electrical distance of approximately 10-15% from the outside, whereas intracellularly applied neamine or sisomycin bind to sites that are approximately 49% and approximately 24%, respectively, into the electric field from the inside. Our data suggested that AG antibiotics induce a low-affinity, voltage-dependent block of mu1 channels.

A quenched molecular dynamics-rotating frame Overhauser spectroscopy study of a series of semibiosynthetically monoacylated anthocyanins.

Quenched molecular dynamics (QMD), in conjunction with NMR (ROESY) studies, was used to investigate the conformational behavior of some semibiosynthetic anthocyanins of the type 6-O-acyl-beta-D-Glcp-(166)-beta-D-Galp-(1-->O(3))-cyanidin, with and without a beta-D-Xylp branch at the 2-O-Gal position. These compounds, which are produced by the addition of selected carboxylic acids to growing tissue cultures of Daucus carota (wild carrot), are of interest as color-stabilized anthocyanins, some of which have potential as useful colorants in the nutraceutical and pharmaceutical industries. The QMD-ROESY studies, performed for the first time on anthocyanins, have led to the identification of families of conformers of these flexible molecules that are of interest in work toward determining the mechanism for stabilization of color among these compounds in solution.

Analysis of the pi-pi stacking interactions between the aminoglycoside antibiotic kinase APH(3')-IIIa and its nucleotide ligands.

A key contact in the active site of an aminoglycoside phosphotransferase enzyme (APH(3')-IIIa) is a pi-pi stacking interaction between Tyr42 and the adenine ring of bound nucleotides. We investigated the prevalence of similar Tyr-adenine contacts and found that many different protein systems employ Tyr residues in the recognition of the adenine ring. The geometry of these stacking interactions suggests that electrostatics play a role in the attraction between these aromatic systems. Kinetic and calorimetric experiments on wild-type and mutant forms of APH(3')-IIIa yielded further experimental evidence of the importance of electrostatics in the adenine binding region and suggested that the stacking interaction contributes approximately 2 kcal/mol of binding energy. This type of information concerning the forces that govern nucleotide binding in APH(3')-IIIa will facilitate inhibitor design strategies that target the nucleotide binding site of APH-type enzymes.