A device for extraction, manipulation and stretching of DNA from single human chromosomes

We describe the structure and operation of a micro/nanofluidic device in which individual metaphase chromosomes can be isolated and processed without being displaced during exchange of reagents. The change in chromosome morphology as a result of introducing protease into the device was observed by time-lapse imaging; pressure-driven flow was then used to shunt the chromosomal DNA package into a nanoslit. A long linear DNA strand (>1.3 Mbp) was seen to stretch out from the DNA package and along the length of the nanoslit. Delivery of DNA in its native metaphase chromosome package as well as the microfluidic environment prevented DNA from shearing and will be important for preparing ultra-long lengths of DNA for nanofluidic analysis.     

On ideal classes of number fields containing integral ideals of equal norms

In this paper we study various groups of ideal classes of number fields containing integral ideals of equal norms and the distribution of integral ideals in such groups.     

Experimental evaluation of a hyperbolic ion trap for fourier transform ion cyclotron resonance mass spectrometry

The Penning ion trap, consisting of hyperbolically curved electrodes arranged as an unbroken ring electrode capped by two end electrodes whose interelectrode axis lies along the direction of an applied static magnetic field, has long been used for single-ion trapping. More recently, it has been used in “parametric” mode for ion cyclotron resonance (lCR) detection of off-axis ions. In this article, we describe and test a Penning trap whose ring electrode has been cut into four equal quadrants for conventional dipolar ICR excitation (on one pair of opposed ring quadrants) and dipolar ICR detection (on the other pair). In direct comparisons to a cubic trap, the present hyperbolic trap offers somewhat improved ICR mass spectral peak shape, higher mass resolving power, and comparable frequency shift as a function of trapping voltage. Mass measurement accuracy over a wide mass range is improved twofold and mass discrimination is somewhat worse than for a cubic trap. The relative advantages of parametric, dipolar, and quadrupole modes are briefly discussed in comparison to screened and unscreened cubic traps.     

Partition polytopes over 1-dimensional points

Received March 1996 / Revised version received April 5, 1998 Published online January 20, 1999     

Monomer-scale design of functional protein polymers using consensus repeat sequences

Protein-based polymers possess chemically defined sequences that can encode diverse properties and functions into a new class of biopolymeric materials. However, sequence variation that emerges from evolution can obscure the sequence–function relationships of naturally derived polymers. One strategy to clarify these relationships is to identify common sequences between proteins with similar functions. These conserved sequences often emerge from repeat proteins, and “consensus repeat sequences” provide a convenient platform for systematic investigations of biopolymer sequence–property relationships. In this review, we highlight recent approaches to engineer tunable polymeric materials using monomer-scale design of consensus repeat proteins. We explore established and emerging protein-based materials with mechanical resilience, thermodynamic phase behavior, chemical responsiveness, biomolecular transport, and hierarchical structure. Overall, recent advances in the monomer-scale design of repetitive protein polymers present exciting fundamental and translational opportunities for polymer scientists and engineers.     

Engineering Multifunctional RNAi Nanomedicine To Concurrently Target Cancer Hallmarks for Combinatorial Therapy

Cancer hallmarks allow the complexity and heterogeneity of tumor biology to be better understood, leading to the discovery of various promising targets for cancer therapy. An amorphous iron oxide nanoparticle (NP)‐based RNAi strategy is developed to co‐target two cancer hallmarks. The NP technology can modulate the glycolysis pathway by silencing MCT4 to induce tumor cell acidosis, and concurrently exacerbate oxidative stress in tumor cells via the Fenton‐like reaction. This strategy has the following features for systemic siRNA delivery: 1) siRNA encapsulation within NPs for improving systemic stability; 2) effective endosomal escape through osmotic pressure and/or endosomal membrane oxidation; 3) small size for enhancing tumor tissue penetration; and 4) triple functions (RNAi, Fenton‐like reaction, and MRI) for combinatorial therapy and in vivo tracking.     

The zeta functions of complexes from PGL(3): A representation-theoretic approach

The zeta function attached to a finite complex X _Γ arising from the Bruhat-Tits building for PGL₃(F) was studied in [KL], where a closed form expression was obtained by a combinatorial argument. This identity can be rephrased using operators on vertices, edges, and directed chambers of X _Γ. In this paper we re-establish the zeta identity from a different aspect by analyzing the eigenvalues of these operators using representation theory. As a byproduct, we obtain equivalent criteria for a Ramanujan complex in terms of the eigenvalues of the operators on vertices, edges, and directed chambers, respectively.     

Microanalysis of the antiretroviral nevirapine in human hair from HIV-infected patients by liquid chromatography-tandem mass spectrometry

Sufficient drug exposure is crucial for maintaining durable responses to HIV treatments. However, monitoring drug exposure using single blood samples only provides short-term information and is highly subject to intra-individual pharmacokinetic variation. Drugs can accumulate in hair over a long period of time, so hair drug levels can provide drug exposure information over prolonged periods. We now report on a specific, sensitive, and reproducible liquid chromatography-tandem mass spectrometry method for measuring nevirapine (NVP), a widely used antiretroviral drug, levels in human hair using even a single short strand of hair. Hair samples are cut into small segments, and the drug is extracted in methanol/trifluoroacetic acid (v/v, 9:1) shaken at 37 °C in a water bath overnight, followed by liquid–liquid extraction under alkaline conditions. The extracted samples are then separated on a BDS-C₁₈ column with a mobile phase composed of 50% acetonitrile containing 0.15% acetic acid and 4 mM ammonium acetate with an isocratic elution for a total run time of 3 min and detected by triple quadrupole electrospray multiple reaction mode at precursor/product ion at 267.0 > 225.9 m/z. Deuterated nevirapine-d5 was used as an internal standard. This method was validated from 0.25 to 100 ng/mg using 2 mg hair samples. The accuracies for spiked NVP hair control samples were 98–106% with coefficients of variation (CV) less than 10%. The CV for incurred hair control samples was less than 7%. The extraction efficiency for incurred control hair samples was estimated at more than 95% by repeated extractions. This method has been successfully applied to analyze more than 1,000 hair samples from participants in a large ongoing cohort study of HIV-infected participants. We also showed that NVP in human hair can easily be detected in a single short strand of hair. This method will allow us to identify drug non-adherence using even a single strand of hair.