Fibre optic absorbance meter with low limit of detection for waterborne cations

We report an evanescent wave based fibre optic absorbance meter that enables the colorimetric detection of waterborne cations with water insoluble chromoionophoric sensitisers. This establishes an alternative to the PVC membrane based transducers that are conventionally used for this purpose. Here, a water insoluble sensitiser is coated as a thin film on an unclad section of a multimode optical fibre to overlap with the evanescent field of a light beam propagating along the fibre core. The colorimetric response of the sensitiser when in contact with waterborne cation leads to increased absorption of virtual photons associated with the evanescent field. The resulting intensity loss of the propagating beam is detected by a bespoke newly designed self- referenced evanescent wave absorbance meter with beam intensity modulation and Lock-in amplification. We validate our transducer with the well characterised water insoluble sensitizer, 1-(2-pyridylazo)-2-naphthol (PAN), for the detection of aqueous Zn2+ cations. We find a limit of detection (LoD) of 54 nM Zn2+, 28 times lower compared to a PVC membrane based sensor using same sensitiser for same cation (Albero et al., Journal of Pharmaceutical and Biomedical Analysis 29 (2002), 779). Our evanescent wave absorbance meter can easily be adapted to other colorimetric sensitisers, including chromoionophoric complex forming macrocycles

Genome Sequence of the Wheat Stem Sawfly, Cephus cinctus, Representing an Early-Branching Lineage of the Hymenoptera, Illuminates Evolution of Hymenopteran Chemoreceptors.

The wheat stem sawfly, Cephus cinctus, is a major pest of wheat and key ecological player in the grasslands of western North America. It also represents the distinctive Cephoidea superfamily of sawflies (Symphyta) that appeared early during the hymenopteran radiation, but after three early-branching eusymphytan superfamilies that form the base of the order Hymenoptera. We present a high-quality draft genome assembly of 162 Mb in 1,976 scaffolds with a scaffold N50 of 622 kb. Automated gene annotation identified 11,210 protein-coding gene models and 1,307 noncoding RNA models. Thirteen percent of the assembly consists of ∼58,000 transposable elements partitioned equally between Class-I and Class-II elements. Orthology analysis reveals that 86% of Cephus proteins have identifiable orthologs in other insects. Phylogenomic analysis of conserved subsets of these proteins supports the placement of the Cephoidea between the Eusymphyta and the parasitic woodwasp superfamily Orussoidea. Manual annotation and phylogenetic analysis of families of odorant, gustatory, and ionotropic receptors, plus odorant-binding proteins, shows that Cephus has representatives for most conserved and expanded gene lineages in the Apocrita (wasps, ants, and bees). Cephus has also maintained several insect gene lineages that have been lost from the Apocrita, most prominently the carbon dioxide receptor subfamily. Furthermore, Cephus encodes a few small lineage-specific chemoreceptor gene family expansions that might be involved in adaptations to new grasses including wheat. These comparative analyses identify gene family members likely to have been present in the hymenopteran ancestor and provide a new perspective on the evolution of the chemosensory gene repertoire

Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential

Rye (Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is allogamous and only recently domesticated, thus giving cultivated ryes access to a diverse and exploitable wild gene pool. To further enhance the agronomic potential of rye, we produced a chromosome-scale annotated assembly of the 7.9-gigabase rye genome and extensively validated its quality by using a suite of molecular genetic resources. We demonstrate applications of this resource with a broad range of investigations. We present findings on cultivated rye's incomplete genetic isolation from wild relatives, mechanisms of genome structural evolution, pathogen resistance, low-temperature tolerance, fertility control systems for hybrid breeding and the yield benefits of rye-wheat introgressions.Peer reviewe

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Introduction: Wheat (Triticum aestivum L.) is the most widely cultivated crop on Earth, contributing about a fifth of the total calories consumed by humans. Consequently, wheat yields and production affect the global economy, and failed harvests can lead to social unrest. Breeders continuously strive to develop improved varieties by fine-tuning genetically complex yield and end-use quality parameters while maintaining stable yields and adapting the crop to regionally specific biotic and abiotic stresses. Rationale: Breeding efforts are limited by insufficient knowledge and understanding of wheat biology and the molecular basis of central agronomic traits. To meet the demands of human population growth, there is an urgent need for wheat research and breeding to accelerate genetic gain as well as to increase and protect wheat yield and quality traits. In other plant and animal species, access to a fully annotated and ordered genome sequence, including regulatory sequences and genome-diversity information, has promoted the development of systematic and more time-efficient approaches for the selection and understanding of important traits. Wheat has lagged behind, primarily owing to the challenges of assembling a genome that is more than five times as large as the human genome, polyploid, and complex, containing more than 85% repetitive DNA. To provide a foundation for improvement through molecular breeding, in 2005, the International Wheat Genome Sequencing Consortium set out to deliver a high-quality annotated reference genome sequence of bread wheat. Results: An annotated reference sequence representing the hexaploid bread wheat genome in the form of 21 chromosome-like sequence assemblies has now been delivered, giving access to 107,891 high-confidence genes, including their genomic context of regulatory sequences. This assembly enabled the discovery of tissue- and developmental stage–related gene coexpression networks using a transcriptome atlas representing all stages of wheat development. The dynamics of change in complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. Aspects of the future value of the annotated assembly for molecular breeding and research were exemplarily illustrated by resolving the genetic basis of a quantitative trait locus conferring resistance to abiotic stress and insect damage as well as by serving as the basis for genome editing of the flowering-time trait. Conclusion: This annotated reference sequence of wheat is a resource that can now drive disruptive innovation in wheat improvement, as this community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding. Importantly, the bioinformatics capacity developed for model-organism genomes will facilitate a better understanding of the wheat genome as a result of the high-quality chromosome-based genome assembly. By necessity, breeders work with the genome at the whole chromosome level, as each new cross involves the modification of genome-wide gene networks that control the expression of complex traits such as yield. With the annotated and ordered reference genome sequence in place, researchers and breeders can now easily access sequence-level information to precisely define the necessary changes in the genomes for breeding programs. This will be realized through the implementation of new DNA marker platforms and targeted breeding technologies, including genome editing

Spectrophotometric determination of Hg(II) in water samples by dispersive liquid liquid microextraction with use ionic liquid after derivatization with a water soluble Fe(II) phthalocyanine

Caglar, Yasemin/0000-0001-8462-0925; Biyiklioglu, Zekeriya/0000-0001-5138-214XWOS: 000427292800009This study reports the synthesis of water soluble iron(II) phthalocyanine and a facile method for spectrophotometric determination of Hg(II) in environmental water samples by ionic liquid based dispersive liquid-liquid microextraction (IL-DLLME). In the method, 1-heptyl-3-methylimidazolium hexafluorophosphate (250 A mu L) as extraction solvent, acetonitrile (750 A mu L) as dispersive solvent and Triton X-100 (200 A mu L) as anti-sticking agent were used. After the extraction of the Hg(II) complex (Hg(II):q-Fe(II)-Pc) into thin droplets of ionic liquid, the sample was centrifuged for 4 min at 2000 rpm. The upper aqueous phase was removed and the residue diluted to 250 A mu L with methanol and transferred to a 250 A mu L cell for spectrophotometric detection at 280 nm. The linear range of the method is 0.05-1 A mu g/mL. The limits of detection and quantification is 0.01 and 0.03 A mu g/mL, respectively. The RSD for the developed method was calculated as 0.78% at 0.50 A mu g/mL Hg(II).Scientific and Technological Research Council of Turkey (TUBITAK)Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [115Z076]We are grateful for the financial support of the Scientific and Technological Research Council of Turkey (TUBITAK). Grant Number: 115Z076

Anthracene Substituted Co (II) and Cu (II) phthalocyanines; Preparations, Investigation of Catalytical and Electrochemical Behaviors

Biyiklioglu, Zekeriya/0000-0001-5138-214X; Caglar, Yasemin/0000-0001-8462-0925WOS: 000441870500016An approach to investigation of catalytical behaviors of Co (II) and Cu (II) phthalocyanines is reported that is based on changing any parameter to effect these behaviors. Towards this end, new anthracene substituted Co (II) and Cu (II) phthalocyanines were prepared and characterized spectroscopic methods. New cobalt (II) and copper (II) phthalocyanines were used as catalyst for oxidation of different phenolic compounds (such as 2,3-dichlorophenol, 4-methoxyphenol, 4-nitrophenol, 2,3,6-trimethylphenol) with different oxidants. Then, electrochemical characterization of cobalt (H) and copper (II) phthallocyanines were determined by using cyclic voltammetry (CV) and square wave voltammetry (SWV) techniques. Although copper (II) phthalocyanine showed similar Pc based electron transfer processes, cobalt (II) phthalocyanine showed metal and ligand based reduction reactions as expected.Research Fund of Karadeniz Technical University [5302]Research Fund of Karadeniz Technical University, Grant/Award Number: 530