Genome-wide profiling of uncapped mRNA

Gene transcripts are under extensive posttranscriptional regulation, including the regulation of their stability. A major route for mRNA degradation produces uncapped mRNAs, which can be generated by decapping enzymes, endonucleases, and small RNAs. Profiling uncapped mRNA molecules is important for the understanding of the transcriptome, whose composition is determined by a balance between mRNA synthesis and degradation. In this chapter, we describe a method to profile these uncapped mRNAs at the genome scale

A Literature Review on the Relationship between Disruption and Business Model Innovation: What Choices do Incumbents have?

In many industries, incumbents face or are aware of the threat of disruption because of ongoing digital innovation. Disruption literature, prior to the late ’90s’, alluded to incumbents’ failure or success for reasons such as the technology deployed by the organisation. However, a few years after the first publication of Christensen’s theory on disruption (1995), researchers, including Christensen, began to attribute the success or failure of organisations to business models and not to technology per se. Thus, how organisations innovate their business models explain how they will fare in the market. A systematic literature review of the extant literature on disruption and business models, between 1997 and 2019 was conducted. The content analysis revealed three key relationships between disruption and business model innovation: (1) Entrants deploying disruptive business models, (2) Incumbents creating new business models, and (3) Incumbents adapting existing business models

\u3cem\u3eIn silico\u3c/em\u3e Detection of EMS-Induced Mutations in an \u3cem\u3eArabis alpina\u3c/em\u3e Population

Arabis alpine (Alpine rock-cress weed) is a flowering plant, native to mountainous environments of thenorthern hemisphere. We analyzed 1,454,931,853 next-generation sequencing (NGS) reads from 38 sequenced Arabis alpine mutant individuals which that were mutagenized using the chemical mutagen, ethyl methanesulfphonate (EMS). Using the BWA short reads mapper, BWA, 95% (1,387,167,658) of the NGS reads mapped to Arabis alpine reference genome version 4. Using the SAMtools variant- detection algorithm, SAMtools, we detected a total of 1,457,917 mutations, with an average of 38,366 mutations per sample. Overall, the predicted mutations include 971,252 high-quality single nucleotide polymorphisms (SNPs) and 168,783 high-quality insertions and deletions (INDELs)

Analysis of Natural Variation in 30 Sorghum Landraces

Sorghum is a next generation of crop species for food grain, feedstock, beverage and biofuel production. To discover highly desirable agronomic traits in sorghum, we analyzed 3.42 billion DNA sequences derived from 30 sequenced sorghum landraces using next-generation sequencing (NGS) technology. Using the BWA short reads aligner, 97% of the sequenced reads mapped successfully to the sorghum reference genome. Using the SAMtools variant-calling algorithm, we detected 68.14 million mutations, including 61.32 million DNA base substitutions or single nucleotide polymorphisms (SNPs) and 6.81 million insertions and deletions (INDELs). In our preliminary analysis using the snpEff variant annotation tool, we predicted a total of 134,207 high-impact mutations and 1.81 million moderate-impact mutations in the 30 sequenced sorghum landraces

Use of Linear Discriminant Function Analysis in Five Yield Sub-Characters Relationship Study in 134 Cowpea (Vigna unguiculata (L.) Walp) Accessions

Variations in five yield sub-characters of cowpea in 134 accessions were studied. Data were collected on number of pods per plant, pod length, pod width, peduncle length and 100-seed weight. Differences among the accessions were significant based on four of the five characters, namely pod length, pod width, peduncle length and 100-seed weight. K-means cluster analysis grouped the 134 accessions into four distinct groups. Pairwise Mahalanobis 2 distance (D) among some of the groups was highly significant. From the study the yield sub-characters pod length, pod width, peduncle length and 100-seed weight contributed most to group separation in the cowpea accessions

\u3cem\u3eVolvox_scan:\u3c/em\u3e Fast Detection of Related Mutants in Population-Scale Forward Genetic Studies

For population-scale forward genetic studies, experimental errors such as pollen contamination, sample mislabeling, and the presence of siblings in a population of independently mutagenized individuals, can negatively impact the accurate detection of induced causal DNA variants. To mitigate the phenotype to genotype gap we implemented a fast and efficient DNA mutation clustering method for the systematic identification of clusters of likely related mutants in a sequenced population. We demonstrate the utility of the software by the analysis of four large mutant populations. The standalone volvox_scan software is very flexible and has been thoroughly tested on Windows, Mac and Linux platforms

PAREsnip2: A tool for high-throughput prediction of small RNA targets from degradome sequencing data using configurable targeting rules

Small RNAs (sRNAs) are short, non-coding RNAs that play critical roles in many important biological pathways. They suppress the translation of messenger RNAs (mRNAs) by directing the RNA-induced silencing complex to their sequence-specific mRNA target(s). In plants, this typically results in mRNA cleavage and subsequent degradation of the mRNA. The resulting mRNA fragments, or degradome, provide evidence for these interactions, and thus degradome analysis has become an important tool for sRNA target prediction. Even so, with the continuing advances in sequencing technologies, not only are larger and more complex genomes being sequenced, but also degradome and associated datasets are growing both in number and read count. As a result, existing degradome analysis tools are unable to process the volume of data being produced without imposing huge resource and time requirements. Moreover, these tools use stringent, non-configurable targeting rules, which reduces their flexibility. Here, we present a new and user configurable software tool for degradome analysis, which employs a novel search algorithm and sequence encoding technique to reduce the search space during analysis. The tool significantly reduces the time and resources required to perform degradome analysis, in some cases providing more than two orders of magnitude speed-up over current methods

Physicochemical and biological properties of different Cocoa Pod Husk-based composts

The objective was to evaluate the properties of cocoa pod husk-based composts for potential application as soil amendments for crop production. The physicochemical and biological properties of the compost types were analysed. Four compost types were prepared by mixing cocoa pod husk, poultry manure and Panicum maximum in different proportions. A phytotoxicity test was carried out using maize (Zea mays L.) to test whether the compost types contain substances that inhibit seed germination or growth of the radicle. Bulk densities of the compost types were higher than 0.160 Mg m-3, an indication that the compost types as soil amendment will restrict root growth thereby inhibiting plant growth. The average pH of the compost types falls within the optimum range of 6.5 to 8.5 and thus, the composts are stabilized. The compost types had high nitrogen content, so when utilized as a soil amendment would improve the nitrogen content of soils. Copper concentrations in the compost types were far below the WHO/FAO permissible limit of 100 mg kg-1, therefore can be applied at high rates without any problem of copper accumulation in soil. Phytophthora palmivora and Phytophthora megakarya were not detected from the compost types, therefore the compost types could be used without Phytophthora disease infection. Germination percentage and germination index showed that the analyzed compost types achieved high percentages of the germinating capacity of maize seeds and had no phytotoxic substances. The cocoa pod husk-based composts showed substantially varied physicochemical and biological properties suitable to support plant growth. The results clearly showed that, CPHcomp3 made from CPH residues, poultry manure and Panicum maximum at the ratio 6: 1: 2 mixture is recommended for use as a soil amendment for crop production

A quick and cost effective method for the diagnosis of Mycobacterium ulcerans infection

BACKGROUND: Buruli ulcer (BU), a neglected tropical skin disease caused by Mycobacterium ulcerans, has been reported in over 30 countries worldwide and is highly endemic in rural West and Central Africa. The mode of transmission remains unknown and treatment is the only alternative to disease control. Early and effective treatment to prevent the morbid effects of the disease depends on early diagnosis; however, current diagnosis based on clinical presentation and microscopy has to be confirmed by PCR and other tests in reference laboratories. As such confirmed BU diagnosis is either late, inefficient, time consuming or very expensive, and there is the need for an early diagnosis tool at point of care facilities. In this paper we report on a simple, quick and inexpensive diagnostic test that could be used at point of care facilities, in resource-poor settings. METHODS: The methodology employed is based on the loop mediated isothermal amplification (LAMP) technique. Four sets of Primers, targeting the mycolactone encoding plasmid genome sequence of M. ulcerans were designed. The BU-LAMP assay was developed and tested on five M. ulcerans strains from patients in Ghana and two American Type Culture Control (ATCC) reference isolates; Ghana #970321 (D19F9) and Benin #990826 (D27D14). We also tested the assay on other closely related, mycolactone-producing mycobacterial strains; M. marinum 1218, M. marinum DL240490, M. liflandii and M. pseudoshotsii, as well as experimentally infected laboratory animal and clinical samples. RESULTS: The results revealed a high specificity of the BU-LAMP assay for selectively detecting M. ulcerans. Compared to the conventional IS-2404 PCR, the new assay is cheaper and simpler and ten times more sensitive. Test results can be obtained within 1 hour. CONCLUSIONS: This study indicates that the BU-LAMP assay could be suitable for early disease diagnosis and application in low-resource health facilities