Diversity of phage-displayed libraries of peptides during panning and amplification

The amplification of phage-displayed libraries is an essential step in the selection of ligands from these libraries. The amplification of libraries, however, decreases their diversity and limits the number of binding clones that a screen can identify. While this decrease might not be a problem for screens against targets with a single binding site (e.g., proteins), it can severely hinder the identification of useful ligands for targets with multiple binding sites (e.g., cells). This review aims to characterize the loss in the diversity of libraries during amplification. Analysis of the peptide sequences obtained in several hundred screens of peptide libraries shows explicitly that there is a significant decrease in library diversity that occurs during the amplification of phage in bacteria. This loss during amplification is not unique to specific libraries: it is observed in many of the phage display systems we have surveyed. The loss in library diversity originates from competition among phage clones in a common pool of bacteria. Based on growth data from the literature and models of phage growth, we show that this competition originates from growth rate differences of only a few percent for different phage clones. We summarize the findings using a simple two-dimensional "phage phase diagram", which describes how the collapse of libraries, due to panning and amplification, leads to the identification of only a subset of the available ligands. This review also highlights techniques that allow elimination of amplification-induced losses of diversity, and how these techniques can be used to improve phage-display selection and enable the identification of novel ligands.     

Application of optimal control to CPMG refocusing pulse design

We apply optimal control theory (OCT) to the design of refocusing pulses suitable for the CPMG sequence that are robust over a wide range of B(0) and B(1) offsets. We also introduce a model, based on recent progress in the analysis of unitary dynamics in the field of quantum information processing (QIP), that describes the multiple refocusing dynamics of the CPMG sequence as a dephasing Pauli channel. This model provides a compact characterization of the consequences and severity of residual pulse errors. We illustrate the methods by considering a specific example of designing and analyzing broadband OCT refocusing pulses of length 10t(180) that are constrained by the maximum instantaneous pulse power. We show that with this refocusing pulse, the CPMG sequence can refocus over 98% of magnetization for resonance offsets up to 3.2 times the maximum RF amplitude, even in the presence of ±10% RF inhomogeneity.     

Identifying defective sets using queries of small size

We examine the following version of a classic combinatorial search problem introduced by Rényi: Given a finite set $X$ of $n$ elements we want to identify an unknown subset $Y$ of $X$, which is known to have exactly $d$ elements, by means of testing, for as few as possible subsets $A$ of $X$, whether $A$ intersects $Y$ or not. We are primarily concerned with the non-adaptive model, where the family of test sets is specified in advance, in the case where each test set is of size at most some given natural number $k$. Our main results are nearly tight bounds on the minimum number of tests necessary when $d$ and $k$ are fixed and $n$ is large enough.     

Saturating Sperner Families

A family ${\mathcal{F} \subseteq 2^{[n]}}$ saturates the monotone decreasing property ${\mathcal{P}}$ if ${\mathcal{F}}$ satisfies ${\mathcal{P}}$ and one cannot add any set to ${\mathcal{F}}$ such that property ${\mathcal{P}}$ is still satisfied by the resulting family. We address the problem of finding the minimum size of a family saturating the k-Sperner property and the minimum size of a family that saturates the Sperner property and that consists only of l-sets and (l + 1)-sets.     

High‐Frequency Fe–H Vibrations in a Bridging Hydride Complex Characterized by NRVS and DFT

High‐spin iron species with bridging hydrides have been detected in species trapped during nitrogenase catalysis, but there are few general methods of evaluating Fe?H bonds in high‐spin multinuclear iron systems. An ⁵⁷Fe nuclear resonance vibrational spectroscopy (NRVS) study on an Fe(μ‐H)₂Fe model complex reveals Fe?H stretching vibrations for bridging hydrides at frequencies greater than 1200 cm^?1. These isotope‐sensitive vibrational bands are not evident in infrared (IR) spectra, showing the power of NRVS for identifying hydrides in this high‐spin iron system. Complementary density functional theory (DFT) calculations elucidate the normal modes of the rhomboidal iron hydride core.     

Electrochemical sensing of heavy metals in biological media: A review

Trace metals are required in the body as they play a significant role in several biochemical processes. Moreover, certain heavy metals are beneficial at appropriate levels. Copper (Cu), for example, is essential for red blood cell formation, bone strength, and infant growth. Despite these fundamental roles, Cu can become toxic at high levels. Other heavy metals such as lead (Pb), cadmium (Cd), manganese (Mn), and mercury (Hg), have been identified to cause acute and chronic health complications. For these reasons, rapid, real-time quantification of such metals in biological media is of interest to improving human health outcomes. Electrochemical methods offer numerous advantages, such as portability, capability to be miniaturized, low cost, and ease-of-use. In this review, we examine recent developments in electrochemical sensing for the detection of heavy metals in biological media. To meet the requirements for inclusion in this review, the electrochemical sensor must have been evaluated in biological media (blood, serum, sweat, saliva, urine, brain tissue/cells). Several applications are explored to examine recent advancements in electrochemical sensing within these matrices. Addressing the challenges through materials, device, and system innovations, it is expected that electrochemical sensing of heavy metals in biological media will facilitate future diagnoses and treatments in healthcare.     

Rapid postcolumn methodology for determination of paralytic shellfish toxins in shellfish tissue

A rapid liquid chromatographic (LC) method with postcolumn oxidation and fluorescence detection (excitation 330 nm, emission 390 nm) for the determination of paralytic shellfish toxins (PSTs) in shellfish tissue has been developed. Extracts prepared for mouse bioassay (MBA) were treated with trichloroacetic acid to precipitate protein, centrifuged, and pH-adjusted for LC analysis. Saxitoxin (STX), neoSTX (NEO), decarbamoylSTX (dcSTX), and the gonyautoxins, GTX1, GTX2, GTX3, GTX4, GTX5, dcGTX2, and dcGTX3, were separated on a polar-linked alkyl reversed-phase column using a step gradient elution; the N-sulfocarbamoyl GTXs, C1, C2, C3, and C4, were determined on a C-8 reversed-phase column in the isocratic mode. Relative toxicities were used to determine STX-dihydrochloride salt (diHCl) equivalents (STXeq). Calibration graphs were linear for all toxins studied with STX showing a correlation coefficient of 0.999 and linearity between 0.18 and 5.9 ng STX-diHCI injected (equivalent to 3.9-128 microg STXeq/100 g in tissue). Detection limits for individual toxins ranged from 0.07 microg STXeq/100 g for C1 and C3 to 4.1 microg STXeq/100 g for GTX1. Spike recoveries ranged from 76 to 112% in mussel tissue. The relative standard deviation (RSD) of repeated injections of GTX and STX working standard solutions was < 4%. Uncertainty of measurement at a level of 195 microg STXeq/100 g was 9%, and within-laboratory reproducibility expressed as RSD was 4.6% using the same material. Repeatability of a 65 microg STXeq/100 g sample was 3.0% RSD. Seventy-three samples were analyzed by the new postcolumn method and both AOAC Official Methods for PST determination: the MBA (y = 1.22x + 13.99, r2 = 0.86) and the precolumn LC oxidation method of Lawrence (y = 2.06x + 12.21, r2 = 0.82).     

Pd-catalyzed aryl amination mediated by well defined, N-heterocyclic carbene (NHC)-Pd precatalysts, PEPPSI

Pd-N-heterocyclic carbene (NHC)-catalyzed Buchwald-Hartwig amination protocols mediated by Pd-PEPPSI precatalysts is described. These protocols provide access to a range of hindered and functionalized drug-like aryl amines in high yield with both electron-deficient and electron-rich aryl- and heteroaryl chlorides and bromides. Variations in solvent polarity, base and temperature are tolerated, enhancing the scope and utility of this protocol. A mechanistic rationalization for base strength (pKb) requirements is also provided.     

Polymer‐coated Boron Doped Diamond Optically Transparent Electrodes for Spectroelectrochemical Sensors

Spectroelectrochemical sensors combine electrochemistry, spectroscopy, and partitioning into a film to provide improved selectivity for the target analyte. The sensor usually consists of an optically transparent electrode (OTE) coated with a charge selective polymer film. The polymer film is chosen to pre‐concentrate analyte at the OTE surface to improve the sensitivity and provide selectivity against like charged interferences. OTEs such as Indium Tin Oxide (ITO) have been used extensively for spectroelectrochemical sensors, but little is known about the applicability of such sensors using other OTE materials, such as Boron Doped Diamond (BDD). One distinct advantage of BDD OTEs over ITO OTEs is their significant increase in sensitivity for organic compounds, such as 4‐aminophenol and hydroquinone. We have developed absorption and fluorescence‐based sensing methods with a BDD OTE coated with a sulfonated ionomer film, Nafion. This is demonstrated with tris(2,2′‐bipyridyl)ruthenium(II) ion [Ru(bpy)₃²⁺] using an attenuated total reflectance (ATR) flow cell setup for both absorption and fluorescence. With a Nafion coated BDD optically transparent thin layer electrode (OTTLE), we developed a fluorescence based sensor for a common polyaromatic hydrocarbon (PAH), 1‐hydroxypyrene (1‐pyOH), achieving a detection limit of 80 nM (17 ppb). This work manifests new sensing applications while broadening the use of spectroelectrochemistry, OTEs, and BDD as an electrode material.