Model‐Based Quality Assessment and Base‐Calling for Second‐Generation Sequencing Data

Summary Second‐generation sequencing (sec‐gen) technology can sequence millions of short fragments of DNA in parallel, making it capable of assembling complex genomes for a small fraction of the price and time of previous technologies. In fact, a recently formed international consortium, the 1000 Genomes Project, plans to fully sequence the genomes of approximately 1200 people. The prospect of comparative analysis at the sequence level of a large number of samples across multiple populations may be achieved within the next five years. These data present unprecedented challenges in statistical analysis. For instance, analysis operates on millions of short nucleotide sequences, or reads—strings of A,C,G, or T's, between 30 and 100 characters long—which are the result of complex processing of noisy continuous fluorescence intensity measurements known as base‐calling. The complexity of the base‐calling discretization process results in reads of widely varying quality within and across sequence samples. This variation in processing quality results in infrequent but systematic errors that we have found to mislead downstream analysis of the discretized sequence read data. For instance, a central goal of the 1000 Genomes Project is to quantify across‐sample variation at the single nucleotide level. At this resolution, small error rates in sequencing prove significant, especially for rare variants. Sec‐gen sequencing is a relatively new technology for which potential biases and sources of obscuring variation are not yet fully understood. Therefore, modeling and quantifying the uncertainty inherent in the generation of sequence reads is of utmost importance. In this article, we present a simple model to capture uncertainty arising in the base‐calling procedure of the Illumina/Solexa GA platform. Model parameters have a straightforward interpretation in terms of the chemistry of base‐calling allowing for informative and easily interpretable metrics that capture the variability in sequencing quality. Our model provides these informative estimates readily usable in quality assessment tools while significantly improving base‐calling performance.     

High‐Quality Graphene Microflower Design for High‐Performance Li–S and Al‐Ion Batteries

Poor quality and insufficient productivity are two main obstacles for the practical application of graphene in electrochemical energy storage. Here, high‐quality crumpled graphene microflower (GmF) for high‐performance electrodes is designed. The GmF possesses four advantages simultaneously: highly crystallized defect‐free graphene layers, low stacking degree, sub‐millimeter continuous surface, and large productivity with low cost. When utilized as carbon host for sulfur cathode, the GmF‐sulfur hybrid delivers decent areal capacities of 5.2 mAh cm^?2 at 0.1 C and 3.8 mAh cm^?2 at 0.5 C. When utilized as cathode of Al‐ion battery, the GmF affords a high capacity of 100 mAh g^?1 with 100% capacity retention after 5000 cycles and excellent rate capability from 0.1 to 20 A g^?1. This facile and large‐scale producible GmF represents a meaningful high‐quality graphene powder for practical energy storage technology. Meanwhile, this unique high‐quality graphene design provides an effective route to improve electrochemical properties of graphene‐based electrodes.     

Application of NMR spectroscopy for assignment of the absolute configuration of 8‐tert‐butyl‐2‐hydroxy‐7‐methoxy‐8‐methyl‐9‐oxa‐6‐azaspiro[4.5]dec‐6‐en‐10‐one

In order to assign the absolute configurations of 8‐tert‐butyl‐2‐hydroxy‐7‐methoxy‐8‐methyl‐9‐oxa‐6‐azaspiro[4.5]dec‐6‐en‐10‐one ( 2a , 2b ), their esters ( 5a , 5b , 5c , 5d ) with (R)‐ or (S)‐2‐methoxyphenylacetic acid ( 4a , 4b ) have been synthesized. The absolute configurations of these compounds have been determined on the basis of NOESY correlations between the protons of the tert‐butyl group and the cyclopentane fragment of the molecules. The crucial part of this analysis was assignment of the absolute configuration at C‐5. Additionally, by calculation of the chemical shift anisotropy, δ^RS, for the relevant protons, it was also possible to confirm the absolute configurations at the C‐2 centres of compounds 2a , 2b and 5a , 5b , 5c , 5d . Chirality, 25:422–426, 2013.© 2013 Wiley Periodicals, Inc.     

Health‐Related Quality of Life Varies among Obese Subgroups

Objective: To compare the health‐related quality of life (HRQOL) of overweight/obese individuals from different subgroups that vary in treatment‐seeking status and treatment intensity. Research Methods and Procedures: Participants were from five distinct groups, representing a continuum of treatment intensity: overweight/obese community volunteers who were not enrolled in weight‐loss treatment, clinical trial participants, outpatient weight‐loss program/studies participants, participants in a day treatment program for obesity, and gastric bypass patients. The sample was large (n = 3353), geographically diverse (subjects were from 13 different states in the U.S.), and demographically diverse (age range, 18 to 90 years; at least 14% African Americans; 32.6% men). An obesity‐specific instrument, the Impact of Weight on Quality of Life‐Lite questionnaire, was used to assess health‐related quality of life (HRQOL). Results: Results indicated that obesity‐specific HRQOL was significantly more impaired in the treatment‐seeking groups than in the nontreatment‐seeking group across comparable gender and body mass index (BMI) categories. Within the treatment groups, HRQOL varied by treatment intensity. Gastric bypass patients had the most impairment, followed by day treatment patients, followed by participants in outpatient weight‐loss programs/studies, followed by participants in clinical trials. Obesity‐specific HRQOL was more impaired for those with higher BMIs, whites, and women in certain treatment groups. Discussion: There are differences in HRQOL across subgroups of overweight/obese individuals that vary by treatment‐seeking status, treatment modality, gender, race, and BMI.     

HS‐SPME‐GC‐FID method for detection and quantification of Bacillus cereus ATCC 10702 mediated 2‐acetyl‐1‐pyrroline

A rapid micro‐scale solid‐phase micro‐extraction (SPME) procedure coupled with gas‐chromatography with flame ionized detector (GC‐FID) was used to extract parts per billion levels of a principle basmati aroma compound “2‐acetyl‐1‐pyrroline” (2‐AP) from bacterial samples. In present investigation, optimization parameters of bacterial incubation period, sample weight, pre‐incubation time, adsorption time, and temperature, precursors and their concentrations has been studied. In the optimized conditions, detection of 2‐AP produced by Bacillus cereus ATCC10702 using only 0.5 g of sample volume was 85 μg/kg. Along with 2‐AP, 15 other compounds produced by B. cereus were also reported out of which 14 were reported for the first time consisting mainly of (E)?2‐hexenal, pentadecanal, 4‐hydroxy‐2‐butanone, n‐hexanal, 2–6‐nonadienal, 3‐methoxy‐2(5H) furanone and 2‐acetyl‐1‐pyridine and octanal. High recovery of 2‐AP (87 %) from very less amount of B. cereus samples was observed. The method is reproducible fast and can be used for detection of 2‐AP production by B. cereus. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:1356–1363, 2014     

Synthesis and Olfactory Characterization of Silicon‐Containing Derivatives of the Acyclic Lily‐of‐the‐Valley Odorant 5,7,7‐Trimethyl‐4‐methylideneoctanal

5‐Methyl‐4‐methylidene‐6‐(trimethylsilyl)hexanal ( 1b ), a sila analog of the acyclic lily‐of‐the‐valley odorant 5,7,7‐trimethyl‐4‐methylideneoctanal ( 1a ), and the Si‐containing derivatives 2 – 6 were prepared in multistep syntheses, starting from Cl₃SiH and Cl₂SiMe₂, respectively. Compounds 1b, 2 – 6 , and their new precursors were characterized by elemental analyses (C, H, N) and NMR spectroscopic studies (¹H, ¹³C, ¹⁵N, and ²⁹Si). To gain more information about the structure? odor correlation in the family of lily‐of‐the‐valley or ‘muguet’ odorants, C/Si analogs 1a / 1b and derivatives 2 – 6 were evaluated for their olfactory properties.     

Enantioselective resolution of 4‐chloromandelic acid by liquid–liquid extraction using 2‐chloro‐N‐carbobenzyloxy‐L‐amino acid

A liquid–liquid extraction resolution of 4‐chloro‐mandelic acid (4‐ClMA) was studied by using 2‐chloro‐N‐carbobenzyloxy‐L‐amino acid (2‐Cl‐Z‐AA) as a chiral extractant. Important factors affecting the extraction efficiency were investigated, including the type of chiral extractant, pH value of aqueous phase, initial concentration of chiral extractant in organic phase, initial concentration of 4‐ClMA in aqueous phase, and resolution temperature. It was observed that the concentration of (R)‐4‐ClMA was much higher than that of (S)‐4‐ClMA in organic phase due to a higher stability of the complex formed between (R)‐4‐ClMA and 2‐Cl‐Z‐AA. A separation factor (α) of 3.05 was obtained at 0.02 mol/L 2‐Cl‐Z‐Valine dissolved in dichloromethane, pH of 2.0, concentration of 4‐ClMA of 0.11 mmol/Land T of 296.7K.     

Validated spectrofluorimetric method for the determination of carbamazepine in pharmaceutical dosage forms after reaction with 4‐chloro‐7‐‐nitrobenzo‐2‐oxa‐1,3‐diazole (NBD‐Cl)

A sensitive and simple spectrofluorimetric method has been developed and validated for the determination of the anti‐epileptic drug carbamazepine (CBZ) in its dosage forms. The method was based on a nucleophilic substitution reaction of CBZ with 4‐chloro‐7‐nitrobenzo‐2‐ oxa‐1,3‐diazole (NBD‐Cl) in borate buffer (pH 9) to form a highly fluorescent derivative that was measured at 530 nm after excitation at 460 nm. Factors affecting the formation of the reaction product were studied and optimized, and the reaction mechanism was postulated. The fluorescence–concentration plot is rectilinear over the range of 0.6–8 µg/mL with limit of detection of 0.06 µg/mL and limit of quantitation of 0.19 µg/mL. The method was applied to the analysis of commercial tablets and the results were in good agreement with those obtained using the reference method. Validation of the analytical procedures was evaluated according to ICH guidelines. Copyright © 2015 John Wiley & Sons, Ltd.     

Homo‐C‐nucleoside analogs IV. Synthesis of 4‐(2,5‐anhydro‐D‐altro‐pentitol‐1‐yl)‐2‐phenyl‐2H‐1,2,3‐triazole homo‐C‐nucleoside. CD assignment of the absolute configuration of the carbon bridge

Dehydrative cyclization of 4‐(D‐altro ‐pentitol‐1‐yl)2‐phenyl‐2H ‐1,2,3‐triazole in basic medium with one moler equivalent of p‐toluene sulfonyl chloride in pyridine solution gave the homo‐C‐ nucleoside 4‐(2,5‐anhydro‐D‐altro ‐1‐yl)‐2‐phenyl‐2H ‐1,2,3‐triazole. The structure and anomeric configuration was determined by acylation, nuclear magnetic resonance (NMR), and mass spectroscopy. The stereochemistry at the carbon bridge of homo‐C‐ nucleoside 2‐phenyl‐2H ‐1,2,3‐triazoles was determined by circular dichroism (CD) spectroscopy.     

Asymmetrically simultaneous synthesis of L‐homophenylalanine and N6‐protected‐2‐oxo‐6‐amino‐hexanoic acid by engineered Escherichia coli aspartate aminotransferase

L ‐Homophenylalanine (L ‐HPA) and N⁶‐protected‐2‐oxo‐6‐amino‐hexanoic acid (N⁶‐protected‐OAHA) can be used as building blocks for the manufacture of angiotensin‐converting enzyme inhibitors. To synthesize L ‐HPA and N⁶‐protected‐OAHA simultaneously from 2‐oxo‐4‐phenylbutanoic acid (OPBA) and N⁶‐protected‐L ‐lysine, several variants of Escherichia coli aspartate aminotransferase (AAT) were developed by site‐directed mutagenesis and their catalytic activities were investigated. Three kinds of N⁶‐protected‐L ‐lysine were tested as potential amino donors for the bioconversion process. AAT variants of R292E/L18H and R292E/L18T exhibited specific activities of 0.70±0.01 U/mg protein and 0.67±0.02 U/mg protein to 2‐amino‐6‐tert‐butoxycarbonylamino‐hexanoic acid (BOC‐lysine) and 2‐amino‐6‐(2,2,2‐trifluoro‐acetylamino)‐hexanoic acid, respectively. E. coli cells expressing R292E/L18H variant were able to convert OPBA and BOC‐lysine to L ‐HPA and 2‐oxo‐6‐tert‐butoxycarbonylamino‐hexanoic acid (BOC‐OAHA) with 96.2% yield in 8 h. This is the first report demonstrating a process for the simultaneous production of two useful building blocks, L ‐HPA and BOC‐OAHA. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

High‐Performance Liquid Chromatographic Enantioseparation of Unusual Isoxazoline‐Fused 2‐Aminocyclopentanecarboxylic Acids on (+)‐(18‐Crown‐6)‐2,3,11,12‐Tetracarboxylic Acid‐Based Chiral Stationary Phases

The enantiomers of four unusual isoxazoline‐fused 2‐aminocyclopentanecarboxylic acids were directly separated on chiral stationary phases containing (+)‐(18‐crown‐6)‐2,3,11,12‐tetracarboxylic acid as chiral selector. The nature of the alcoholic modifier (MeOH, EtOH, IPA) exerted a great effect on the retention, whereas the selectivity and resolution did not change substantially. Two types of dependence of retention on alcohol content were detected: k₁ increased continuously with increasing alcohol content or a U‐shaped retention curve was observed. A comparison of the chromatographic data obtained with HCOOH, AcOH, TFA, HClO₄, H₂SO₄, or H₃PO₄ as acidic modifier at a constant concentration demonstrated that in most cases, larger k values were obtained on the application of AcOH or HCOOH, and an increase of the acid content resulted in a decrease of retention. Some mechanistic aspects of the chiral recognition process are discussed with respect to the structures of the analytes and selector. The sequence of elution of the enantiomers was determined in all cases. Chirality 24:817‐824, 2012. © 2012 Wiley Periodicals, Inc.     

The special optical properties and application of the heterocyclic compound diethyl 6‐anilino‐5H‐2,3‐dithia‐5,7‐diazacyclopenta(cd)indene‐1,4‐dicarboxylate

The heterocyclic compound diethyl 6‐anilino‐5H‐2,3‐dithia‐5,7‐diazacyclopenta(cd)indene‐1,4‐dicarboxylate (D1) was found to form highly emissive aggregates in polar solvents, and the aggregate emission can be tuned by the simple addition of water to a dimethylsulfoxide solution. A theoretical study based on Density functional theory (DFT) calculations, shows that intermolecular interactions of D1 with solvent may be potential factors in the fluorescence change. In addition, the phenyl ring in D1 plays an important role because of its response to solvent. In the non‐aggregated state, deprotonation of the N–H of D1 can proceed easily on the addition of base, and the deprotonated compound might interact with Ag⁺, resulting in a significant change in color and fluorescence quenching, which make it a potential chemosensor for the selective detection of trace amounts of Ag⁺. Copyright © 2013 John Wiley & Sons, Ltd.     

Resolution of 1‐n‐Butyl‐3‐Methyl‐3‐Phospholene 1‐Oxide With TADDOL Derivatives and Calcium Salts of O,O'‐Dibenzoyl‐(2R,3R)‐ or O,O'‐di‐p‐Toluoyl‐(2R,3R)‐tartaric Acid

The resolution methods applying (?)‐(4R,5R)‐4,5‐bis(diphenylhydroxymethyl)‐2,2‐dimethyldioxolane (“TADDOL”), (?)‐(2R,3R)‐α,α,α',α'‐tetraphenyl‐1,4‐dioxaspiro[4.5]decan‐2,3‐dimethanol (“spiro‐TADDOL”), as well as the acidic and neutral Ca²⁺ salts of (?)‐O,O'‐dibenzoyl‐ and (?)‐O,O'‐di‐p‐toluoyl‐(2R,3R)‐tartaric acid were extended for the preparation of 1‐n‐butyl‐3‐methyl‐3‐phospholene 1‐oxide in optically active form. In one case, the intermediate diastereomeric complex could be identified by single‐crystal X‐ray analysis. The absolute P‐configuration of the enantiomers of the phospholene oxide was also determined by comparing the experimentally obtained and calculated CD spectra. Chirality 26:174–182, 2014. © 2014 Wiley Periodicals, Inc.     

ER‐to‐lysosome‐associated degradation of proteasome‐resistant ATZ polymers occurs via receptor‐mediated vesicular transport

Maintenance of cellular proteostasis relies on efficient clearance of defective gene products. For misfolded secretory proteins, this involves dislocation from the endoplasmic reticulum (ER) into the cytosol followed by proteasomal degradation. However, polypeptide aggregation prevents cytosolic dislocation and instead activates ill‐defined lysosomal catabolic pathways. Here, we describe an ER‐to‐lysosome‐associated degradation pathway (ERLAD) for proteasome‐resistant polymers of alpha1‐antitrypsin Z (ATZ). ERLAD involves the ER‐chaperone calnexin (CNX) and the engagement of the LC3 lipidation machinery by the ER‐resident ER‐phagy receptor FAM134B, echoing the initiation of starvation‐induced, receptor‐mediated ER‐phagy. However, in striking contrast to ER‐phagy, ATZ polymer delivery from the ER lumen to LAMP1/RAB7‐positive endolysosomes for clearance does not require ER capture within autophagosomes. Rather, it relies on vesicular transport where single‐membrane, ER‐derived, ATZ‐containing vesicles release their luminal content within endolysosomes upon membrane:membrane fusion events mediated by the ER‐resident SNARE STX17 and the endolysosomal SNARE VAMP8. These results may help explain the lack of benefits of pharmacologic macroautophagy enhancement that has been reported for some luminal aggregopathies.     

All‐Manganese‐Based Binder‐Free Stretchable Lithium‐Ion Batteries

Advanced electrode materials with bendability and stretchability are critical for the rapid development of fully flexible/stretchable lithium‐ion batteries. However, the sufficiently stretchable lithium‐ion battery is still underdeveloped that is one of the biggest challenges preventing from realizing fully deformable power sources. Here, a low‐temperature hydrothermal synthesis of a cathode material for stretchable lithium‐ion battery is reported by the in situ growth of LiMn₂O₄ (LMO) nanocrystals inside 3D carbon nanotube (CNT) film networks. The LMO/CNT film composite has demonstrated the chemical bonding between the LMO active materials and CNT scaffolds, which is the most important characteristic of the stretchable electrodes. When coupled with a wrinkled MnO_x /CNT film anode, a binder‐free, all‐manganese‐based stretchable full battery cell is assembled which delivers a high average specific capacity of ≈97 mA h g^?1 and stabilizes after over 300 cycles with an enormous strain of 100%. Furthermore, combining with other merits such as low cost, natural abundance, and environmentally friendly, the all‐manganese design is expected to accelerate the practical applications of stretchable lithium‐ion batteries for fully flexible and biomedical electronics.     

Spectrofluorimetric determination of aluminium using 2‐hydroxy‐1‐naphthylidene‐(8‐aminoquinoline)

A sensitive and selective spectrofluorimetric method has been developed for the rapid determination of aluminium. This method is based on the complex formation between aluminium and 2‐hydroxy‐1‐naphthylidene‐(8‐aminoquinoline) (HNAQ). The optimum conditions for the complex formation were a metal‐to‐ligand (M : L) stoichiometric ratio of 1:1, a pH of 5.5 and a 0.20 m acetate buffer. The fluorescence of the complex was monitored at an emission wavelength of 502 nm with excitation at 438 nm. Under these conditions, linear calibration curves were obtained in the ranges 0.05–1 and 1–5 ppm. The detection limit was 3.4 ppb for the former and 13.5 ppb for the latter. The maximum relative standard deviation of the method for an aluminium standard of 200 ppb was 1.5% (n = 5). This method was successfully applied for the determination of aluminium in drinking water, pharmaceutical antacid tablets and suspension samples. Copyright © 2010 John Wiley & Sons, Ltd.