A New Variant of Emissive RNA Alphabets

A new fluorescent ribonucleoside alphabet (^mthN) consisting of pyrimidine and purine analogues, all derived from methylthieno[3,4-d]pyrimidine as the heterocyclic core, is described. Large bathochromic shifts and high microenvironmental susceptibility of their emission relative to previous alphabets derived from thieno[3,4-d]pyrimidine (^thN) and isothiazole[4,3-d]pyrimidine (^tzN) scaffolds are observed. Subjecting the purine analogues to adenosine deaminase, guanine deaminase and T7 RNA polymerase indicate that, while varying, all but one enzyme tolerate the corresponding ^mthN/^mthNTP substrates. The robust emission quantum yields, high photophysical responsiveness and enzymatic accommodation suggest that the ^mthN alphabet is a biophysically viable tool and can be used to probe the tolerance of nucleoside/tide-processing enzymes to structural perturbations of their substrates.     

Selection of phage-displayed antibodies with high affinity and specificity by electrophoresis in microfluidic devices

A method development aimed for high-throughput and automated antibody screening holds great potential for areas ranging from fundamental molecular interactions to the discovery of novel disease markers, therapeutic targets, and monoclonal antibody engineering. Surface display techniques enable efficient manipulation of large molecular libraries in small volumes. Specifically, phage display appeared as a powerful technology for selecting peptides and proteins with enhanced, target-specific binding affinities. Here, we present a phage-selection microfluidic device wherein electrophoresis was performed under two orthogonal electric fields through an agarose gel functionalized with the respective antigen. This microdevice was capable of screening and sorting in a single round high-affinity phage-displayed antibodies against virus glycoproteins, including human immunodeficiency virus-1 glycoprotein 120 or the Ebola virus glycoprotein (EBOV-GP). Phages were differentially and laterally swept depending on their antigen affinity; the high-affinity phages were recovered at channels proximal to the application site, whereas low-affinity phages migrated distal after electrophoresis. These experiments proved that the microfluidic device specifically designed for phage-selection is rapid, sensitive, and effective. Therefore, this is an efficient and cost-effective method that allowed highly controlled assay conditions for isolating and sorting high-affinity ligands displayed in phages.     

Small molecule antagonists of cell-surface heparan sulfate and heparin–protein interactions

Surfen, bis-2-methyl-4-amino-quinolyl-6-carbamide, was previously reported as a small molecule antagonist of heparan sulfate (HS), a key cell-surface glycosaminoglycan found on all mammalian cells. To generate structure–activity relationships, a series of rationally designed surfen analogs was synthesized, where its dimeric structure, exocyclic amines, and urea linker region were modified to probe the role of each moiety in recognizing HS. An in vitro assay monitoring inhibition of fibroblast growth factor 2 binding to wild-type CHO cells was utilized to quantify interactions with cell surface HS. The dimeric molecular structure of surfen and its aminoquinoline ring systems was essential for its interaction with HS, and certain dimeric analogs displayed higher inhibitory potency than surfen and were also shown to block downstream FGF signaling in mouse embryonic fibroblast cells. These molecules were also able to antagonize other HS–protein interactions including the binding of soluble RAGE to HS. Importantly, selected molecules were shown to neutralize heparin and other heparinoids, including the synthetic pentasaccharide fondaparinux, in a factor Xa chromogenic assay and in vivo in mice. These results suggest that small molecule antagonists of heparan sulfate and heparin can be of therapeutic potential for the treatment of disorders involving glycosaminoglycan–protein interactions.     

Preconcentrative separation of chromium(III) species from chromium(VI) by cloud point extraction and determination by flame atomic absorption spectrometry

Microchimica Acta - We describe a high-throughput technique for the determination of chromium species in water samples by flame atomic absorption spectrometry (FAAS) after preconcentrative...     

Split Weight Enumerators for the Preparata Codes with Applications to Designs

For quaternary Preparata and Kerdock codes of length N=2 ^m ,m odd, we prove that the split complete weight enumerator for a coordinate partition into 3 and N-3 coordinates is independent of the chosen partition. The result implies that the words of a given complete weight in either a Preparata code or Kerdock code define a 3-design.     

Determination of selected polychlorinated biphenyls in water samples by ultrasound-assisted emulsification-microextraction and gas chromatography-mass-selective detection

Ultrasound-assisted emulsification-microextraction (USAEME) procedure was developed for the determination of selected polychlorinated biphenyls (PCBs) in 10 mL of water samples by gas chromatography-mass-selective detection. After determination of the most suitable solvent and extraction time, several other parameters including solvent volume, centrifugation time and ionic strength of the sample were optimized using a 2³ factorial experimental design. The optimized USAEME procedure used 200 μL of chloroform as extraction solvent, 10 min of extraction with no ionic strength adjustment at 25 °C and 5 min of centrifugation at 4000 rpm. The limits of detection ranged from 14 ng L⁻¹ (for PCB153) to 30 ng L⁻¹ (for PCB101). Recoveries of PCBs from fortified distilled water are over 80% for three different fortification levels between 0.1 and 5 μg L⁻¹ and relative standard deviations of the recoveries are below 10%. The performance of the proposed method was compared with those involving traditional liquid-liquid extraction (LLE) and solid phase extraction (SPE) on the real water samples (i.e., tap and well water as well as domestic and industrial wastewaters, etc.) and comparable efficiencies were obtained. The proposed USAEME procedure has been demonstrated to be viable, simple, rapid and easy to use for residue analysis of PCBs in water samples.     

Dimensional variation in production of high-aspect-ratio micro-pillars array by micro powder injection molding

Micro powder injection molding (μPIM) is one of the potential processes for the mass production of metallic microstructures and micro components. Here, μPIM is the miniaturization of conventional PIM, which involves four processing steps: mixing, injection molding, debinding and sintering. This paper looks into the feasibility and effectiveness of μPIM as a key mass production process for the fabrication of metallic micro components. For it to be an effective re-production process, it is imperative to examine how well parts can be duplicated/fabricated from a master mold. In this work, the dimensional variation of high-aspect-ratio micro-pillars arrays, in particular the dimensional shrinkage, global warpage, and surface roughness at each stage of the μPIM process for a range of molding pressures, are quantified and compared in detail. The sensitivity of the dimensional variation of the microstructures to the packing pressure is reported. The mechanism behind the dimensional variation is analyzed. PACS 81.20.Ev; 81.20.Hy; 81.70.Fy; 07.60.Ly; 81.05.-t     

FFT-based algorithms for the string matching with mismatches problem

The string matching with mismatches problem requires finding the Hamming distance between a pattern P of length m and every length m substring of text T with length n. Fischer and Paterson's FFT-based algorithm solves the problem without error in O(σnlogm), where σ is the size of the alphabet Σ [SIAM–AMS Proc. 7 (1973) 113–125]. However, this in the worst case reduces to O(nmlogm). Atallah, Chyzak and Dumas used the idea of randomly mapping the letters of the alphabet to complex roots of unity to estimate the score vector in time O(nlogm) [Algorithmica 29 (2001) 468–486]. We show that the algorithm's score variance can be substantially lowered by using a bijective mapping, and specifically to zero in the case of binary and ternary alphabets. This result is extended via alphabet remappings to deterministically solve the string matching with mismatches problem with a constant factor of 2 improvement over Fischer–Paterson's method.