A family of novel DNA sequencing instruments based on single-photon detection

We have developed a family of high-performance capillary DNA sequencing instruments based on a novel multicolor fluorescent detection technology. This technology is based on two technical innovations: the multilaser excitation of fluorescence of labeled DNA fragments and the "color-blind" single-photon detection of modulated fluorescence. Our machines employ modern digital and broadband techniques that are essential for achieving superior instrument performance. We discuss the design and testing results for several versions of the automated single lane DNA sequencers, as well as our approach to scaling up to multilane instruments.     

Zum Diskussionsbeitrag von W. Brauer

Ohne Zusammenfassung

---

c B.

     

Two derivatives of 5‐amino­tetrazole: 5‐amino‐1‐phenyl­tetrazole and 5‐amino‐1‐(1‐naphthyl)­tetrazole

In the mol­ecules of 5‐amino‐1‐phenyl­tetrazole, C₇H₇N₅, (I), and 5‐amino‐1‐(1‐naphthyl)­tetrazole, C₁₁H₉N₅, (II), the tetrazole rings and aryl fragments are not coplanar; corresponding dihedral angles are 50.58 (5) and 45.19 (7)° for the two independent mol­ecules of (I), and 64.14 (5)° for (II). Intermolecular N—H⋯N hydrogen bonds between the amino groups and tetrazole N atoms are primarily responsible for formation of two‐dimensional networks extending parallel to the bc plane in both compounds. The presence of the amino group has a distinct effect on the geometry of the tetrazole rings in each case.     

Analysis of 5-methyltetrahydrofolate in human blood, serum and urine by on-line coupling of capillary isotachophoresis and zone electrophoresis

The predominant circulating folate coenzyme in plasma/serum, 5‐methyltetrahydrofolate (5‐MTHF) was determined in human blood, serum and urine using a method based on the hyphenation of capillary ITP and zone electrophoresis. Measurements were done with a commercially available instrument for capillary isotachophoresis equipped with a column‐switching system. The choice of electrolytes was limited by the instability of 5‐MTHF and volatility of electrolytes for the potential coupling of the instrumentation with MS detector. To get an insight into the separability of individual sample components in an isotachophoretic analysis, we constructed zone existence diagrams for isotachophoretic electrolyte systems having a leading electrolyte composed of acetate and ammonium of pH 4.5 and 7.0, hydrocarbonate and ammonium, pH 7.8, chloride and ammonium, pH 5.6, and chloride and creatinine, pH 5.0, with hydroxide ion as the terminator. For isotachophoretic preseparation, the non‐volatile leading electrolyte with good buffering capacity composed of 1×10⁻² M HCl and 2.5×10⁻² M creatinine, pH 5.0, and terminating electrolyte composed of 1×10⁻² M MES was selected as the most suitable. The optimum BGE for CZE analysis from the standpoint of analyte stability, separability and volatility for MS coupling was 1×10⁻² M acetate with 3.5×10⁻² M ammonium, pH 4.5. Using this combination of electrolytes, LODs reached with optical detection at 220 nm were 1.6×10⁻⁷ M in human blood, 1.1×10⁻⁷ M in human serum and 4.7×10⁻⁶ M in human urine. Estimated content of 5‐MTHF in blood and serum samples of women following oral daily administration of 0.8 mg of folic acid was 1.2×10⁻⁵ and 5.8×10⁻⁶ M, respectively.     

Synthesis of the new adducts of imines and enamines with PH acids and their derivatives

Nucleophilic or radical addition of esters of trivalent organophosphorus acids with PH fragments to various imines and enamines is proposed as convenient methods for the synthesis of new substituted aminomethyl organophosphorus compounds with three‐, four‐, and five‐coordinated phosphorus. Also the new functionalized derivatives of these compounds with acyl and methanesulfonyl moieties are synthesized, and some properties of the obtained compounds are presented. © 2009 Wiley Periodicals, Inc. Heteroatom Chem 20:70–80, 2009; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20513     

Comparison of extraction techniques for the isolation of explosives and their degradation products from soil

A comparison of four extraction techniques used for the isolation of 14 explosive compounds (Method 8330-Explosives) from spiked soil samples is described. Soxhlet warm extraction (SWE), pressurized solvent extraction (PSE), microwave assisted extraction (MAE) and supercritical fluid extraction (SFE) were included. The effects of basic extraction conditions – i.e. type of extraction solvent, temperature, pressure, and extraction time – were investigated. The best extraction recovery of the monitored compounds from spiked soil was obtained using pressurized solvent extraction. Recoveries of explosives using the PSE technique were in the range from 65 to 112%. Extraction recoveries by Soxhlet warm extraction and supercritical fluid extraction reached 65–99% and 52–75%, respectively. The lowest extraction recoveries (28–65%) were obtained using microwave assisted extraction. A very low extraction recovery for tetryl was observed in all cases but the best results were achieved by pressurized solvent extraction (58%).     

Preparative production and separation of 2-acetamido-2-deoxymannopyranoside-containing saccharides using borate-saturated polyolic exclusion gels

A new separation method based on the combination of exclusion and ion exchange chromatography in borate buffer was developed. It allows semi-preparatory and preparatory separation of isobaric N-acylhexosamines (C-2 epimers) and corresponding methyl glycosides (anomers and tautomers). Three types of polyolic gels were tested for these separations. Ion-exchange HPLC was used as a rapid and reliable method for the quantification of the respective analytes. NMR studies of the interactions of N-acetylhexosamines with borate confirmed the importance of a proper stereochemical arrangement of acetamido sugars for their interactions with borate anions.     

Diastereoselective Synthesis of (Z)‐6‐(2‐Oxo‐1,2‐dihydro‐3H‐indol‐3‐ylidene)‐3,3a,9,9a‐tetrahydroimidazo[4,5‐e]thiazolo[3,2‐b]‐1,2,4‐triazin‐2,7(1H,6H)‐diones

Two efficient and diastereoselective procedures for the synthesis of (Z)‐6‐(2‐oxo‐1,2‐dihydro‐3H‐indol‐3‐ylidene)‐3,3a,9,9a‐tetrahydroimidazo[4,5‐e]thiazolo[3,2‐b]‐1,2,4‐triazin‐2,7(1H,6H)‐diones by aldol‐crotonic condensation of 1,3‐dimethyl‐3a,9a‐diphenyl‐3,3a,9,9a‐tetrahydroimidazo[4,5‐e]thiazolo[3,2‐b]‐1,2,4‐triazin‐2,7(1H,6H)‐dione with isatins under acidic or basic catalysis are reported. Isomerization in (Z)‐7‐(1‐allyl‐2‐oxo‐1,2‐dihydro‐3H‐indol‐3‐ylidene)‐1,3‐dimethyl‐3a,9a‐diphenyl‐1,3a,4,9a‐tetrahydroimidazo[4,5‐e]thiazolo[2,3‐c]‐1,2,4‐triazin‐2,8(3H,7H)‐dione was observed under basic conditions.     

Volatile profiling reveals intracellular metabolic changes in <Emphasis Type="Italic">Aspergillus parasiticus</Emphasis>: <Emphasis Type="Italic">veA</Emphasis> regulates branched chain amino acid and ethanol metabolism

Background  

Filamentous fungi in the genus Aspergillus produce a variety of natural products, including aflatoxin, the most potent naturally occurring carcinogen known. Aflatoxin biosynthesis, one of the most highly characterized secondary metabolic pathways, offers a model system to study secondary metabolism in eukaryotes. To control or customize biosynthesis of natural products we must understand how secondary metabolism integrates into the overall cellular metabolic network. By applying a metabolomics approach we analyzed volatile compounds synthesized by Aspergillus parasiticus in an attempt to define the association of secondary metabolism with other metabolic and cellular processes.     

Determination of butoxyacetic acid (biomarker of ethylene glycol monobutyl ether exposure) in human urine candidate reference material

Ethylene glycol monobutyl ether (EGBE), an industrial solvent, is absorbed by the body not only by inhalation but also by dermal absorption (liquid or vapour). EGBE is metabolized to butoxyacetic acid (BAA). Pooled freeze-dried urine candidate reference material (RM) was prepared from urine obtained from persons occupationally exposed to EGBE. This material has the advantage of containing butoxyacetic acid in both the free and conjugated (glutamine and glycine) forms, as found in native urine. In all GC method modifications used, acid hydrolysis was used to release BAA from its conjugated form. The amount of butoxyacetic acid in homogeneity and stability testing was measured by GC after derivatisation with N-tert-butyldimethylsilyl-N-methyltrifluoroacetamide. Detection was by MS in EI mode, in the authors’ laboratory. For interlaboratory comparison of the reference material GC methods with MS, FID, and ECD were used. Different extraction solvents (dichloromethane–isopropanol 2:1, ethyl acetate, or dichloromethane) and derivatisation reagents (trimethylsilyldiazomethane, N-tert-butyldimethylsilyl-N-methyltrifluoroacetamide) were used. Using ANOVA (at the statistical level α = 0.05) no changes were found in the concentration of butoxyacetic acid during fifteen month isochronous stability testing, or in homogeneity testing. The uncertainty contributions were u _h = 8.8 mg L⁻¹ and u _s = 6.5 mg L⁻¹. The concentration of butoxyacetic acid in freeze-dried urine RM was evaluated from the results of eight laboratory data sets within an interlaboratory comparison by use of the interactive statistical software IPECA. The contribution to total uncertainty derived from interlaboratory comparison was u _i = 12.7 mg L⁻¹. The reference value (c = 273 ± 33 mg L⁻¹) is an unweighted arithmetic average of accepted results. The value is traceable to the pure butoxyacetic acid (98% w/w; Acros Organic #257760010) used as calibrant. The uncertainty given is combined expanded uncertainty derived from the results from interlaboratory comparison, and from homogeneity and stability tests (k = 2). The reference material will be used to verify method performance in the biological monitoring of occupational exposure to EGBE.