Preparation of Aspergillus niger 426 naringinases for debittering citrus juice using of agro-industrial residues

Naringin (4,5,7-trihydroxy flavanone-7-rhamnoglucoside), considered as the main bitter component of grapefruit, requires the use of enzymes to reduce the level of this substance during juice processing. For this reason, it has been the focus of many studies. To increase the production of naringinase by Aspergillus niger cultivated in solid-state fermentation (SSF), it was verified whether the influence of agro-industrial residues as fermentation substrates and, finally, selected the best of the three inducers, or their mixtures to remove the bitterness of grapefruit juice. Cultivation with 2.3 g of grapefruit peel, 2.5 g of rice bran, and 5.2 g of wheat bran and medium supplementation with a mixture of naringin, rutin, and hesperidin in the concentration of (g / L): 2, 5, 4.5, and 3.0, respectively, leading to a maximum activity of 28 U / mL. The results indicate that the sequencing procedure, which allowed the definition of an optimal mixture of components, is a new way for microorganisms to have a high naringinase yield, in particular by SSF, since our data showed a 96% increase in the production of naringinase.

Third Backcross Generation Indonesian Indigenous Chicken Kampong Broiler-Type (Kambro) SOX5 Gene Polymorphism

The comb is an accessory organ on the head of chicken which is influenced by testosterone hormone and can be used as an indicator of chicken’s fertility. Comb shape is related to climate adaptation and associated with a dominant mutation in chicken chromosome 1. Therefore this research was aimed to study the association between Pea-comb shape and SOX5 gene polymorphism in the population of progenies (BC-III Kambro) derived from a crossbreed between females Pelung and males second backcross generation Kampong Broiler-Type (BC-II Kambro). Chicken (Gallus gallus) SOX5 gene was acquired from NCBI GenBank with the Ref. Seq. 418195. Primers used to amplify the SOX5 gene are (F):5’-AGGTAGCCATGGTGACAAGC-3’,(R):5’-GATCTGTGAGGCAGCCAGTT-3’. Progenies showed 100% Pea-comb shape, while parental generation composed of Pea-comb shape and Single-comb shape. PCR-RFLP and endonuclease restriction enzyme HindIII were unable to determine the genotype of the female parent with Pea-comb. The result of SOX5 gene polymorphism showed the comb shape uniformity between progenies and parental of Kambro backcross generation. This study concluded that the genotype of Pea-comb shape female Pelung was undetermined and there was no polymorphism of the SOX5 gene between pea and single comb. PCR-RFLP using endonuclease restriction enzyme HindIII produced both target products and non-target/artifact products. The sequencing procedure was required to provide nucleotide sequences.

Using texts to sequence the introduction of new vocabulary in an eap course

This paper examines the feasibility of allowing the texts that are used in a course to sequence the target vocabulary of a course, in this paper the vocabulary of academic study as represented by the University Word List. It was found that such an approach would only allow the learners to meet a little over half of the 836 word vocabulary and that a three-step sequencing procedure would be needed to effectively meet all of the wanted vocabulary. The three steps would involve (1) using adapted texts to gradually introduce the very common academic words, (2) using unsimplified texts to meet the next 200-300 words, and (3) relying on extensive reading and planned decontextualised learning to meet the remaining lower frequency items.

Using texts to sequence the introduction of new vocabulary in an eap course

This paper examines the feasibility of allowing the texts that are used in a course to sequence the target vocabulary of a course, in this paper the vocabulary of academic study as represented by the University Word List. It was found that such an approach would only allow the learners to meet a little over half of the 836 word vocabulary and that a three-step sequencing procedure would be needed to effectively meet all of the wanted vocabulary. The three steps would involve (1) using adapted texts to gradually introduce the very common academic words, (2) using unsimplified texts to meet the next 200-300 words, and (3) relying on extensive reading and planned decontextualised learning to meet the remaining lower frequency items.

*-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments

Background Over the past few years the variety of experimental designs and protocols for sequencing experiments increased greatly. To ensure the wide usability of the produced data beyond an individual project, rich and systematic annotation of the underlying experiments is crucial. Findings We first developed an annotation structure that captures the overall experimental design as well as the relevant details of the steps from the biological sample to the library preparation, the sequencing procedure, and the sequencing and processed files. Through various design features, such as controlled vocabularies and different field requirements, we ensured a high annotation quality, comparability, and ease of annotation. The structure can be easily adapted to a large variety of species. We then implemented the annotation strategy in a user-hosted web platform with data import, query, and export functionality. Conclusions We present here an annotation structure and user-hosted platform for sequencing experiment data, suitable for lab-internal documentation, collaborations, and large-scale annotation efforts.

DeepSimulator: a deep simulator for Nanopore sequencing

ABSTRACTMotivationOxford Nanopore sequencing is a rapidly developed sequencing technology in recent years. To keep pace with the explosion of the downstream data analytical tools, a versatile Nanopore sequencing simulator is needed to complement the experimental data as well as to benchmark those newly developed tools. However, all the currently available simulators are based on simple statistics of the produced reads, which have difficulty in capturing the complex nature of the Nanopore sequencing procedure, the main task of which is the generation of raw electrical current signals.ResultsHere we propose a deep learning based simulator, DeepSimulator, to mimic the entire pipeline of Nanopore sequencing. Starting from a given reference genome or assembled contigs, we simulate the electrical current signals by a context-dependent deep learning model, followed by a base-calling procedure to yield simulated reads. This workflow mimics the sequencing procedure more naturally. The thorough experiments performed across four species show that the signals generated by our context-dependent model are more similar to the experimentally obtained signals than the ones generated by the official context-independent pore model. In terms of the simulated reads, we provide a parameter interface to users so that they can obtain the reads with different accuracies ranging from 83% to 97%. The reads generated by the default parameter have almost the same properties as the real data. Two case studies demonstrate the application of DeepSimulator to benefit the development of tools in de novo assembly and in low coverage SNP detection.AvailabilityThe software can be accessed freely at: https://github.com/lykaust15/deep_simulator.

The Number of Target Molecules of the Amplification Step Limits Accuracy and Sensitivity in Ultradeep-Sequencing Viral Population Studies

ABSTRACT The invention of next-generation sequencing (NGS) techniques marked the coming of a new era in the detection of the genetic diversity of intrahost viral populations. A good understanding of the genetic structure of these populations requires, first, the ability to identify the different isolates or variants and, second, the ability to accurately quantify them. However, the initial amplification step of NGS studies can impose potential quantitative biases, modifying the variant relative frequencies. In particular, the number of target molecules (NTM) used during the amplification step is vastly overlooked although of primary importance, as it sets the limit of the accuracy and sensitivity of the sequencing procedure. In the present article, we investigated quantitative biases in an NGS study of populations of a multipartite single-stranded DNA (ssDNA) virus at different steps of the procedure. We studied 20 independent populations of the ssDNA virus faba bean necrotic stunt virus (FBNSV) in two host plants, Vicia faba and Medicago truncatula. FBNSV is a multipartite virus composed of eight genomic segments, whose specific and host-dependent relative frequencies are defined as the “genome formula.” Our results show a significant distortion of the FBNSV genome formula after the amplification and sequencing steps. We also quantified the genetic bottleneck occurring at the amplification step by documenting the NTM of two genomic segments of FBNSV. We argue that the NTM must be documented and carefully considered when determining the sensitivity and accuracy of data from NGS studies. IMPORTANCE The advent of next-generation sequencing (NGS) techniques now enables study of the genetic diversity of viral populations. A good understanding of the genetic structure of these populations first requires the ability to identify the different isolates or variants and second requires the ability to accurately quantify them. Prior to sequencing, viral genomes need to be amplified, a step that potentially imposes quantitative biases and modifies the viral population structure. In particular, the number of target molecules (NTM) used during the amplification step is of primary importance, as it sets the limit of the accuracy and sensitivity of the sequencing procedure. In this work, we used 20 replicated populations of the multipartite faba bean necrotic stunt virus (FBNSV) to estimate the various limitations of ultradeep-sequencing studies performed on intrahost viral populations. We report quantitative biases during rolling-circle amplification and the NTM of two genomic segments of FBNSV.