Hobbes: optimized gram-based methods for efficient read alignment

Recent advances in sequencing technology have enabled the rapid generation of billions of bases at relatively low cost. A crucial first step in many sequencing applications is to map those reads to a reference genome. However, when the reference genome is large, finding accurate mappings poses a significant computational challenge due to the sheer amount of reads, and because many reads map to the reference sequence approximately but not exactly. We introduce Hobbes, a new gram-based program for aligning short reads, supporting Hamming and edit distance. Hobbes implements two novel techniques, which yield substantial performance improvements: an optimized gram-selection procedure for reads, and a cache-efficient filter for pruning candidate mappings. We systematically tested the performance of Hobbes on both real and simulated data with read lengths varying from 35 to 100 bp, and compared its performance with several state-of-the-art read-mapping programs, including Bowtie, BWA, mrsFast and RazerS. Hobbes is faster than all other read mapping programs we have tested while maintaining high mapping quality. Hobbes is about five times faster than Bowtie and about 2–10 times faster than BWA, depending on read length and error rate, when asked to find all mapping locations of a read in the human genome within a given Hamming or edit distance, respectively. Hobbes supports the SAM output format and is publicly available at http://hobbes.ics.uci.edu.     

Binding studies of pyriproxyfen to DNA by multispectroscopic atomic force microscopy and molecular modeling methods

In this work, multispectroscopic atomic force microscopy and molecular modeling [ONIOM 2(B3LYP/6-31++G(d,p): Universal Force Field (UFF)) level] techniques were used to study the interaction between Calf-Thymus-DNA (CT-DNA) and pyriproxyfen (PYR) insecticide. The binding constant of PYR with double-strand deoxyribonucleic acid (ds-DNA) was obtained by ultraviolet-visible absorbance spectroscopy as 2.8×10(4) at 20°C. Thermodynamic parameters, that is, ΔH, ΔS°, and ΔG, were -53.82?kJ mol(-1), 96.11?J mol(-1), and -82.46?KJ mol(-1), respectively. Thermal denaturation study of DNA with PYR revealed the ΔT(m) of 3.0 and 6.0°C at r(i)=0.5 and 1.0, respectively. The Fourier transform infrared study showed a major interaction of PYR with G-C and A-T base pairs and a minor perturbation of the backbone PO(2) group. Further, PYR induces detectable changes in the circular dichroism spectrum of CT-DNA. In fluorimetric studies, the dynamic enhancement constants (k(D)) and bimolecular enhancement constant (k(B)) were calculated, which showed that the fluorescence enhancement was initiated by a static process in the ground state. The hybrid of quantum mechanical/molecular mechanics theoretical calculations revealed that the interaction is base sequence dependent, and PYR interacts more with DNA via the AT base sequence. From the data we concluded that PYR may interact with ds-DNA via two modes: intercalating and outside groove binding.     

Electronic sensor for sulfide dioxide based on AlN nanotubes: a computational study

Single-walled aluminum nitride nanotubes (AlNNTs) are introduced as an electronic sensor for detection of sulfur dioxide (SO(2)) molecules based on density functional theory calculations. The proposed sensor benefits from several advantages including high sensitivity: HOMO-LUMO energy gap of the AlNNT is appreciably sensitive toward the presence of SO(2) so that it decreases from 4.11?eV in the pristine tube to 1.01?eV in the SO(2)-adsorbed form, pristine application: this nanotube can detect the SO(2) molecule in its pristine type without manipulating its structure through doping, chemical functionalization, making defect, etc., short recovery time: the adsorption energy of SO(2) molecule is not so large to hinder the recovery of AlNNTs and therefore the sensor will possess short recovery times, and good selectivity: the tube can selectively detect the SO(2) molecule in the presence of several molecules such as H(2)O, CO, NH(3), HCOH, CO(2), N(2), and H(2).     

In vitro study of DNA interaction with clodinafop-propargyl herbicide

The interaction of native calf thymus DNA with clodinafop-propargyl (CP), in 10 mM HEPES aqueous solutions at neutral pH 7.2, has been investigated by spectrophotometric, circular dichroism (CD), spectrofluorometric, melting temperature (Tm), and viscosimetric techniques. It was found that CP molecules could intercalate between base pairs of DNA as evidenced by hyperchromism in UV absorption band of DNA, an increase in melting temperature, a sharp increase in specific viscosity of DNA, induced CD spectral changes, and increase in the fluorescence of methylene blue (MB)-DNA solutions in the presence of increasing amounts of CP, which indicates that it is able to release the intercalated MB completely. All results suggest that the CP interacts with calf thymus DNA by an intercalative mode of binding.     

Graphene/Graphene Oxide-Based Ultrasensitive Surface Plasmon Resonance Biosensor

Plasmonics - Surface plasmon resonance (SPR)-based biosensing is an accurate and sensitive technique used to evaluate the biomolecular interactions in real time in a label-free environment. Several...     

Increased production of yersiniabactin and an anthranilate analog through media optimization

Yersiniabactin (Ybt) is a mixed nonribosomal peptide‐polyketide natural product that binds a wide range of metals with the potential to impact processes requiring metal retrieval and removal. In this work, we substantially improved upon the heterologous production of Ybt and an associated anthranilate analog through systematic screening and optimization of culture medium components. Specifically, a Plackett‐Burman design‐of‐experiments methodology was used to screen 22 components and to determine those contributing most to siderophore production. L‐cysteine, L‐serine, glucose, and casamino acids significantly contributed to the production of both compounds. Using this approach together with metabolic engineering of the base biosynthetic process, Ybt and the anthranilate analog titers were increased to 867 ± 121 mg/L and 16.6 ± 0.3 mg/L, respectively, an increase of ～38 and ～79‐fold relative to production in M9 medium. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1193–1200, 2017     

Triangular interplay between ROS,ABA and GA in dormancy alleviation of <Emphasis Type="Italic">Bunium persicum</Emphasis> seeds by cold stratification

Seeds of Bunium persicum (Boiss.) B. Fedtsch. have complex physiological dormancy that can be released by 15 weeks stratification. The present study revealed that cold stratification enhanced content of H₂O₂, O^{2 -·} and application of GA₃ and ROS donors (Fenton reagent, H₂O₂, methylviologen and menadione) did not affect or only slightly promoted the germination of non-stratified, fully dormant seeds. Dormancy was markedly decreased by ROS-generating reagents, GA₃ and fluridone (an inhibitor of ABA biosynthesis) and was enhanced by ROS-decreasing compounds (DMTU, Tiron, SB and DPI), diniconazole (Dinc, an inhibitor of ABA catabolism) and paclobutrazol (PAC, an inhibitor of GA biosynthesis) when dormancy was partially removed by cold stratification. The response to these compounds reduced with increasing time of stratification. ABA inhibited germination by repressing of NADPH oxidase activity and ROS accumulation and conversely, GA triggered germination by promoting an increase of NADPH oxidase activity and ROS levels. Data in this study, for the first time suggest releasing deep complex physiological dormancy by cold stratification is associated with interplay between ROS and ABA/GA.     

Effects of foliar application of BAP on source and sink strength in four six-rowed barley (Hordeum vulgare L.) cultivars

A field experiment was conducted to investigate the effects of foliar application of a synthetic cytokinin (BAP) on source and sink strength of four different six-rowed barley (Hordeum vulgare L.) cultivars. Different spraying treatments consisting of spraying on whole plant, spraying only on leaves and spraying only on ears started at anthesis and continued for 7 days. One additional spraying was carried out on late period of grain filling. Results showed that spraying only on leaves did not affect ear weight, grain yield and 1,000-grain weight, while the two other treatments increased all above mentioned traits. Neither of treatments affected stem weight, biological yield and contribution of stem reserves in grain filling. Exogenous cytokinin did not increase photosynthetic rate and chlorophyll content in treated leaves until late period of grain filling, although there was no significant increase in final grain weight due to late application of BAP. Our results suggested that effects of foliar application of BAP were mostly due to increased sink size soon after anthesis and increased sink demand probably met by current photosynthesis of organs other than leaves, like ear green tissues. An erratum to this article is available at .     

Opportunism: a panacea for implementation of whole-genome sequencing studies in nutrigenomics research?

Observational studies have consistently shown associations between mild deficiencies in folate and vitamin B₁₂ with increased risk of a myriad of common diseases. These findings have invariably translated into null outcomes in intervention trials due in part to our ignorance of the specific genomic and environmental factors that underpin population variability in requirements to these B-vitamins. Although genome-wide association studies have shed initial light on the genetic architecture of variability in status of these vitamins, particularly vitamin B₁₂, the causal mechanisms remain uncharacterised. A recent study by Grarup et al. (PLoS Genet 9(6):e1003530, 2013) used next-generation whole-genome sequencing to gain further insight into the genetic architecture of vitamin B₁₂ and folate status in the general population. Their study represents the analysis of approximately ten times greater number of genetic variants and nearly four times the number of individuals compared to the largest previous GWAS study of these B-vitamins. In light of this, we purport that although the study may be viewed as the state of the art in the roadmap to personalised or precision nutrition, the lack of insight provided by the study serves as a cautionary reminder of the importance of study design, particularly when leveraging large-scale data, such as those from whole-genome sequences. We believe that the precedent set by such large-scale “proof of principle” type projects will wrongly enforce a negative outlook for nutrigenomics research and present alternative study designs, which although less opportunistic are far more likely to be informative and yield novel results.