Artificial neural network model with the parameter tuning assisted by a differential evolution technique: the study of the hold up of the slurry flow in a pipeline

This paper describes a robust hybrid artificial neural network (ANN) methodology which can offer a superior performance for the important process engineering problems. The method incorporates a hybrid artificial neural network and differential evolution technique (ANN-DE) for the efficient tuning of ANN meta parameters. The algorithm has been applied for the prediction of the hold up of the solid liquid slurry flow. A comparison with selected correlations in the literature showed that the developed ANN correlation noticeably improved the prediction of hold up over a wide range of operating conditions, physical properties, and pipe diameters

Melting dsDNA Donor Molecules Greatly Improves Precision Genome Editing in Caenorhabditis elegans

CRISPR genome editing has revolutionized genetics in many organisms. In the nematode Caenorhabditis elegans one injection into each of the two gonad arms of an adult hermaphrodite exposes hundreds of meiotic germ cells to editing mixtures, permitting the recovery of multiple indels or small precision edits from each successfully injected animal. Unfortunately, particularly for long insertions, editing efficiencies can vary widely, necessitating multiple injections, and often requiring co-selection strategies. Here we show that melting double stranded DNA (dsDNA) donor molecules prior to injection increases the frequency of precise homology-directed repair (HDR) by several fold for longer edits. We describe troubleshooting strategies that enable consistently high editing efficiencies resulting, for example, in up to 100 independent GFP knock-ins from a single injected animal. These efficiencies make C. elegans by far the easiest metazoan to genome edit, removing barriers to the use and adoption of this facile system as a model for understanding animal biology

Melting dsDNA donor molecules potentiates precision genome editing in C. elegans [preprint]

CRISPR genome editing has revolutionized genetics in many organisms. In the nematode Caenorhabditis elegans one injection into each of the two gonad arms of an adult hermaphrodite exposes hundreds of meiotic germ cells to editing mixtures, permitting the recovery of multiple indels or small precision edits from each successfully injected animal. Unfortunately, particularly for long insertions, editing efficiencies can vary widely, necessitating multiple injections, and often requiring co-selection strategies. Here we show that melting double stranded DNA (dsDNA) donor molecules prior to injection increases the frequency of precise homology-directed repair (HDR) by several fold for longer edits. We describe troubleshooting strategies that enable consistently high editing efficiencies resulting, for example, in up to 100 independent GFP knock-ins from a single injected animal. These efficiencies make C. elegans by far the easiest metazoan to genome edit, removing barriers to the use and adoption of this facile system as a model for understanding animal biology

Robust Genome Editing with Short Single-Stranded and Long, Partially Single-Stranded DNA Donors in Caenorhabditis elegans

CRISPR-based genome editing using ribonucleoprotein complexes and synthetic single-stranded oligodeoxynucleotide (ssODN) donors can be highly effective. However, reproducibility can vary, and precise, targeted integration of longer constructs-such as green fluorescent protein tags remains challenging in many systems. Here, we describe a streamlined and optimized editing protocol for the nematode Caenorhabditis elegans We demonstrate its efficacy, flexibility, and cost-effectiveness by affinity-tagging 14 Argonaute proteins in C. elegans using ssODN donors. In addition, we describe a novel PCR-based, partially single-stranded, hybrid donor design that yields high efficiency editing with large (kilobase-scale) constructs. We use these hybrid donors to introduce fluorescent protein tags into multiple loci, achieving editing efficiencies that approach those previously obtained only with much shorter ssODN donors. The principals and strategies described here are likely to translate to other systems, and should allow researchers to reproducibly and efficiently obtain both long and short precision genome edits

ISOLATION, CHARACTERIZATION AND VALIDATION OF HPLC METHOD FOR QUANTIFICATION OF BIS-[10-(2-METHYL-4H-3-THIA-4,9-DIAZABENZO[F]AZULENE)]-1,4-PIPERAZINE IN AN ANTI-PSYCHOTIC DRUG SUBSTANCE, OLANZAPINE

Objective: The main objective of present study was to Isolate, characterize and validate a reverse phase high performance liquid chromatographic method was validated for quantification of bis-[10-(2-methyl-4H-3-thia-4,9-diazabenzo[f]azulene)]-1,4-piperazine in Olanzapine drug substance; it decreases the mental disorders in human body. The method is specific, rapid, precise and accurate for the separation and determination of bis-[10-(2-methyl-4H-3-thia-4,9-diazabenzo[f]azulene)]-1,4-piperazine in Olanzapine drug substance form.Methods: The bis-[10-(2-methyl-4H-3-thia-4,9-diazabenzo[f]azulene)]-1,4-piperazine of Olanzapine was resolved on a Zorbax RX-C 8, 250 mm X 4.6 mm, 5 micron column (L-1) using a mobile phase system containing 0.03 M sodium dodecyl sulphate in water pH 2.5 with 1 N sodium hydroxide solution and acetonitrile in the ratio of (Mobile phase A-52:48 v/v) and (Mobile phase B-buffer and Acetonitrile 30:70 v/v) by using the gradient program. The mobile phase was set at a flow rate of 1.5 ml/min and the volume injected was 20μl for every injection. The detection wavelength was set at 220 nm and the column temperature was set at 35 °C.Results: The proposed method was productively applied for the quantitative determination of bis-[10-(2-methyl-4H-3-thia-4,9-diazabenzo [f]azulene)]-1,4-piperazine in Olanzapine drug substance form. The linear regression analysis data for calibration plots showed a good linear relationship over a concentration range of 0.025to 0.903 µg/ml for bis-[10-(2-methyl-4H-3-thia-4,9-diazabenzo[f]azulene)]-1,4-piperazine, 0.081-0.608 µg/ml for Olanzapine. The mean values of the correlation coefficient were 0.999 and 0.999 for bis-[10-(2-methyl-4H-3-thia-4,9-diazabenzo[f]azulene)]-1,4-piperazine and Olanzapine. The method was validated as per the ICH guidelines. The detection limit (LOD) was about 0.007 µg/ml, 0.024 µg/ml and quantitation limit (LOQ) was about 0.024 µg/ml, 0.081 µg/ml for bis-[10-(2-methyl-4H-3-thia-4,9-diazabenzo[f]azulene)]-1,4-piperazine and Olanzapine. The relative standard deviation was found to be 1.64 % and 2.18 % for bis-[10-(2-methyl-4H-3-thia-4,9-diazabenzo[f]azulene)]-1,4-piperazine and Olanzapine.Conclusion: The validated HPLC method and the statistical analysis showed that the method is repeatable and selective for the estimation of the bis-[10-(2-methyl-4H-3-thia-4,9-diazabenzo[f]azulene)]-1,4-piperazine of the Olanzapine drug substance

A co-CRISPR strategy for efficient genome editing in Caenorhabditis elegans

Genome editing based on CRISPR (clustered regularly interspaced short palindromic repeats)-associated nuclease (Cas9) has been successfully applied in dozens of diverse plant and animal species, including the nematode Caenorhabditis elegans. The rapid life cycle and easy access to the ovary by micro-injection make C. elegans an ideal organism both for applying CRISPR-Cas9 genome editing technology and for optimizing genome-editing protocols. Here we report efficient and straightforward CRISPR-Cas9 genome-editing methods for C. elegans, including a Co-CRISPR strategy that facilitates detection of genome-editing events. We describe methods for detecting homologous recombination (HR) events, including direct screening methods as well as new selection/counterselection strategies. Our findings reveal a surprisingly high frequency of HR-mediated gene conversion, making it possible to rapidly and precisely edit the C. elegans genome both with and without the use of co-inserted marker genes

The Geometry of Most Probable Trajectories in Noise-Driven Dynamical Systems

This paper presents a heuristic derivation of a geometric minimum action method that can be used to determine most-probable transition paths in noise-driven dynamical systems. Particular attention is focused on systems that violate detailed balance, and the role of the stochastic vorticity tensor is emphasized. The general method is explored through a detailed study of a two-dimensional quadratic shear flow which exhibits bifurcating most-probable transition pathways.Comment: 8 pages, 7 figure

Genotyping-by-sequencing and multilocation evaluation of two interspecific backcross populations identify QTLs for yield-related traits in pigeonpea

This study has identified single-nucleotide polymorphism (SNP) markers associated with nine yield-related traits in pigeonpea by using two backcross populations (BP) developed through interspecific crosses and evaluating them at two locations and 3 years. In both the populations, markers have shown strong segregation distortion; therefore, a quantitative trait locus (QTL) mapping mixed model was used. A total of 86 QTLs explaining 12–21% phenotypic variation were detected in BP-1. On the other hand, 107 QTLs explaining 11–29% phenotypic variation were detected in BP-2. Although most QTLs were environment and trait specific, few stable and consistent QTLs were also detected. Interestingly, 11 QTLs in BP-2 were associated with more than one trait. Among these QTLs, eight QTLs associated with days to 50% flowering and days to 75% maturity were located on CcLG07. One SNP “S7_14185076” marker in BP-2 population has been found associated with four traits, namely days to 50% flowering, days to 75% maturity, primary branches per plant and secondary branches per plant with positive additive effect. Hence, the present study has not only identified QTLs for yield-related traits, but also discovered novel alleles from wild species, which can be used for improvement of traits through genomics-assisted breeding

Serine Proteases-Like Genes in the Asian Rice Gall Midge Show Differential Expression in Compatible and Incompatible Interactions with Rice

The Asian rice gall midge, Orseolia oryzae (Wood-Mason), is a serious pest of rice. Investigations into the gall midge-rice interaction will unveil the underlying molecular mechanisms which, in turn, can be used as a tool to assist in developing suitable integrated pest management strategies. The insect gut is known to be involved in various physiological and biological processes including digestion, detoxification and interaction with the host. We have cloned and identified two genes, OoprotI and OoprotII, homologous to serine proteases with the conserved His87, Asp136 and Ser241 residues. OoProtI shared 52.26% identity with mosquito-type trypsin from Hessian fly whereas OoProtII showed 52.49% identity to complement component activated C1s from the Hessian fly. Quantitative real time PCR analysis revealed that both the genes were significantly upregulated in larvae feeding on resistant cultivar than in those feeding on susceptible cultivar. These results provide an opportunity to understand the gut physiology of the insect under compatible or incompatible interactions with the host. Phylogenetic analysis grouped these genes in the clade containing proteases of phytophagous insects away from hematophagous insects

Chronic Cough and Eosinophilic Esophagitis: An Uncommon Association

An increasing number of children, usually with gastrointestinal symptoms, is diagnosed with eosinophilic esophagitis (EE), and a particular subset of these patients complains of airway manifestations. We present the case of a 2-year-old child with chronic dry cough in whom EE was found after a first diagnosis of gastroesophageal reflux disease (GERD) due to pathological 24-hour esophageal pH monitoring. Traditional allergologic tests were negative, while patch tests were diagnostic for cow's milk allergy. We discuss the intriguing relationship between GERD and EE and the use of patch test for the allergologic screening of patients