scholarly journals Food authentication from shotgun sequencing reads with an application on high protein powders

2019 ◽  
Vol 3 (1) ◽  
Author(s):  
Niina Haiminen ◽  
Stefan Edlund ◽  
David Chambliss ◽  
Mark Kunitomi ◽  
Bart C. Weimer ◽  
...  
Keyword(s):  
Sequence Data ◽  
Shotgun Sequencing ◽  
High Protein ◽  
Absolute Difference ◽  
Food Authentication ◽  
Food Ingredients ◽  
Bioinformatic Pipeline ◽  
Three Samples ◽  
Eukaryotic Species ◽  
Median Absolute Difference

AbstractHere we propose that using shotgun sequencing to examine food leads to accurate authentication of ingredients and detection of contaminants. To demonstrate this, we developed a bioinformatic pipeline, FASER (Food Authentication from SEquencing Reads), designed to resolve the relative composition of mixtures of eukaryotic species using RNA or DNA sequencing. Our comprehensive database includes >6000 plants and animals that may be present in food. FASER accurately identified eukaryotic species with 0.4% median absolute difference between observed and expected proportions on sequence data from various sources including sausage meat, plants, and fish. FASER was applied to 31 high protein powder raw factory ingredient total RNA samples. The samples mostly contained the expected source ingredient, chicken, while three samples unexpectedly contained pork and beef. Our results demonstrate that DNA/RNA sequencing of food ingredients, combined with a robust analysis, can be used to find contaminants and authenticate food ingredients in a single assay.

scholarly journals Evaluation of point-of-care glucose testing accuracy using locally-smoothed median absolute difference curves

2008 ◽  
Vol 389 (1-2) ◽  
pp. 31-39 ◽  
Author(s):  
Gerald J. Kost ◽  
Nam K. Tran ◽  
Victor J. Abad ◽  
Richard F. Louie
Keyword(s):  
Point Of Care ◽  
Absolute Difference ◽  
Glucose Testing ◽  
Testing Accuracy ◽  
Median Absolute Difference

scholarly journals Coexistence of Fosfomycin and Colistin Resistance in Klebsiella pneumoniae : Whole-Genome Shotgun Sequencing

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Balaji Veeraraghavan ◽  
Susmitha K. Perumalla ◽  
Naveen Kumar Devanga Ragupathi ◽  
Agila Kumari Pragasam ◽  
Dhiviya Prabaa Muthuirulandi Sethuvel ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Sequence Data ◽  
Draft Genome ◽  
Shotgun Sequencing ◽  
Whole Genome ◽  
Colistin Resistance ◽  
Genome Sequences ◽  
Major Threat ◽  
Carbapenem Resistant ◽  
Whole Genome Shotgun Sequencing

Resistance to colistin is a major threat that limits therapeutic choices for treating carbapenem-resistant Klebsiella pneumoniae infections. Herein, we report the draft genome sequences of two colistin-resistant K. pneumoniae isolates (BA41763 and B6753). The sequence data indicate that BA41763 and B6753 contain genomes of ~5.9 and 5.7 Mb in size with several plasmids.

scholarly journals Multiomic Strategies Reveal Diversity and Important Functional Aspects of Human Gut Microbiome

2018 ◽  
Vol 2018 ◽  
pp. 1-13 ◽  
Author(s):  
Ravi Ranjan ◽  
Asha Rani ◽  
Patricia W. Finn ◽  
David L. Perkins
Keyword(s):  
Sequence Data ◽  
Bacterial Species ◽  
Abundant Species ◽  
Shotgun Sequencing ◽  
Sequencing Analysis ◽  
Sequencing Data ◽  
Illumina Platform ◽  
Shotgun Metagenomics ◽  
Functional Aspects ◽  
Detectable Bias

It is well accepted that dysbiosis of microbiota is associated with disease; however, the biological mechanisms that promote susceptibility or resilience to disease remain elusive. One of the major limitations of previous microbiome studies has been the lack of complementary metatranscriptomic (functional) data to complement the interpretation of metagenomics (bacterial abundance). The purpose of this study was twofold, first to evaluate the bacterial diversity and differential gene expression of gut microbiota using complementary shotgun metagenomics (MG) and metatranscriptomics (MT) from same fecal sample. Second, to compare sequence data using different Illumina platforms and with different sequencing parameters as new sequencers are introduced, and to determine if the data are comparable on different platforms. In this study, we perform ultradeep metatranscriptomic shotgun sequencing for a sample that we previously analyzed with metagenomics shotgun sequencing. We performed sequencing analysis using different Illumina platforms, with different sequencing and analysis parameters. Our results suggest that use of different Illumina platform did not lead to detectable bias in the sequencing data. The analysis of the sample using MG and MT approach shows that some species genes are highly represented in the MT than in the MG, indicating that some species are highly metabolically active. Our analysis also shows that ~52% of the genes in the metagenome are in the metatranscriptome and therefore are robustly expressed. The functions of the low and rare abundance bacterial species remain poorly understood. Our observations indicate that among the low abundant species analyzed in this study some were found to be more metabolically active compared to others, and can contribute distinct profiles of biological functions that may modulate the host-microbiota and bacteria-bacteria interactions.

scholarly journals Genome Sequence ofStachybotrys chartarumStrain 51-11

2015 ◽  
Vol 3 (5) ◽  
Author(s):  
Doris A. Betancourt ◽  
Timothy R. Dean ◽  
Jean Kim ◽  
Josh Levy
Keyword(s):  
Genome Sequence ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Shotgun Sequencing ◽  
Health Impacts ◽  
Stachybotrys Chartarum ◽  
Illumina Hiseq

TheStachybotrys chartarumstrain 51-11 genome was sequenced by shotgun sequencing utilizing Illumina HiSeq 2000 and PacBio technologies. SinceS. chartarumhas been implicated as having health impacts within water-damaged buildings, any information extracted from the genomic sequence data relating to toxins or the metabolism of the fungus might be useful.

Parkin and relatives: the RBR family of ubiquitin ligases

2004 ◽  
Vol 17 (3) ◽  
pp. 253-263 ◽  
Author(s):  
Ignacio Marín ◽  
J. Ignasi Lucas ◽  
Ana-Citlali Gradilla ◽  
Alberto Ferrús
Keyword(s):  
Functional Data ◽  
Autosomal Recessive ◽  
Protein Quality ◽  
Sequence Data ◽  
Multiple Roles ◽  
Control Mechanisms ◽  
Parkin Gene ◽  
Ubiquitin Protein Ligase ◽  
Autosomal Recessive Juvenile Parkinsonism ◽  
Eukaryotic Species

Mutations in the parkin gene cause autosomal-recessive juvenile parkinsonism. Parkin encodes a ubiquitin-protein ligase characterized by having the RBR domain, composed of two RING fingers plus an IBR/DRIL domain. The RBR family is defined as the group of genes whose products contain an RBR domain. RBR family members exist in all eukaryotic species for which significant sequence data is available, including animals, plants, fungi, and several protists. The integration of comparative genomics with structural and functional data allows us to conclude that RBR proteins have multiple roles, not only in protein quality control mechanisms, but also as indirect regulators of transcription. A recently formulated hypothesis, based on a case of gene fusion, suggested that RBR proteins may be often part of cullin-containing ubiquitin ligase complexes. Recent data on Parkin protein agrees with that hypothesis. We discuss the involvement of RBR proteins in several neurodegenerative diseases and cancer.

scholarly journals Iron-Rich Salt and Antioxidants from Sea Sponge with Added Moringa Leaves as Potential Food Ingredients in Efforts to Alleviate Anemia

2021 ◽  
Vol 1 (1) ◽  
pp. 1-11
Author(s):  
Fahrul Nurkolis ◽  
Dian Aruni Kumalawati ◽  
Reza Sukma Dewi ◽  
Maizer Said Nahdi ◽  
Defny Silvia Wewengkang ◽  
...  
Keyword(s):  
Antioxidant Activity ◽  
Moisture Content ◽  
Deficiency Anemia ◽  
Food Ingredients ◽  
Three Samples ◽  
High Prevalence ◽  
Using Data ◽  
The One ◽  
Theoretical Science ◽  
And Control

Based on the high prevalence of anemia of more than 24% population affected, the natural potential of Indonesia such as Sponge and Moringa leaves to be a salt product high in iron, and interconnection between this theoretical science and Islamic studies related to the utilization of natural materials, we want to explore how potential be a product that can be one of the efforts to alleviate anemia. Initial data collection to explore sponge types and types of plants rich in iron was done using data search portal NCBI (National Center for Biotechnology Information, USA) in the last five years starting from 2016/03/30 to 2021/03/28. Samples were formulated based on the comparison of seawater, sponge (Spongia sp), and moringa leaves in a composition as follows: Sample A (1:1:0.05),  sample B (1:1:0.25), sample C (1:1:0.5) and control that did not use the addition of Moringa leaves (1:1). The analysis included testing antioxidant activity using DPPH, moisture content, NaCl, impurities sulfate, magnesium, calcium, and iron levels which were all done in three repetitions of each sample or triplicates and using analytical methods from the Association of Official Analytical Chemists (AOAC).Sponge sp is a type of sea sponge that is easy to find in the Indonesian country and can be combined with moringa leaves whose availability is also abundant in Indonesia, as a potential salt high in iron. This study obtained salt granules as much as 0.92 ± 0.22 kg. There was no difference in the results of salt granules from each sample, and there was no difference in the level of fineness of salt granules, namely 20-35 mesh or equivalent to crude salt. However, there were differences in the level of chemical it contains. Samples B, C, and control correspond to SNI 3556:2016 based on percentage of  moisture content, Fe, calcium impurities, sulfate impurities, and magnesium impurities in all three samples. However, it is known that sample C is the one that has the highest iron levels compared to B and control samples, which means that sample C is the best sample and has antioxidant activity that is in line with the purpose of this study, which is an effort to alleviate iron deficiency anemia. This salt is also a salt that is Halal Tayyiban, which means not only halal but also good and healthy if consumed.

scholarly journals Bamboo tea: reduction of taxonomic complexity and application of DNA diagnostics based onrbcLandmatKsequence data

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2781 ◽  
Author(s):  
Thomas Horn ◽  
Annette Häser
Keyword(s):  
Sequence Data ◽  
Distinct Species ◽  
The European Union ◽  
Food Ingredients ◽  
Novel Foods ◽  
Dna Sequence Data ◽  
Bamboo Leaves ◽  
Diagnostic Potential ◽  
Phylogenetic Framework ◽  
Safety Assessments

BackgroundNames used in ingredient lists of food products are trivial and in their nature rarely precise. The most recent scientific interpretation of the term bamboo (Bambusoideae,Poaceae) comprises over 1,600 distinct species. In the European Union only few of these exotic species are well known sources for food ingredients (i.e., bamboo sprouts) and are thus not considered novel foods, which would require safety assessments before marketing of corresponding products. In contrast, the use of bamboo leaves and their taxonomic origin is mostly unclear. However, products containing bamboo leaves are currently marketed.MethodsWe analysed bamboo species and tea products containing bamboo leaves using anatomical leaf characters and DNA sequence data. To reduce taxonomic complexity associated with the term bamboo, we used a phylogenetic framework to trace the origin of DNA from commercially available bamboo leaves within the bambusoid subfamily. For authentication purposes, we introduced a simple PCR based test distinguishing genuine bamboo from other leaf components and assessed the diagnostic potential ofrbcLandmatKto resolve taxonomic entities within the bamboo subfamily and tribes.ResultsBased on anatomical and DNA data we were able to trace the taxonomic origin of bamboo leaves used in products to the generaPhyllostachysandPseudosasafrom the temperate “woody” bamboo tribe (Arundinarieae). Currently availablerbcLandmatKsequence data allow the character based diagnosis of 80% of represented bamboo genera. We detected adulteration by carnation in four of eight tea products and, after adapting our objectives, could trace the taxonomic origin of the adulterant toDianthus chinensis(Caryophyllaceae), a well known traditional Chinese medicine with counter indications for pregnant women.

Shotgun barcode baiting: capturing barcoding genes from environmental samples for species identification

2021 ◽  
Author(s):  
Kevin Nota ◽  
Ludovic Orlando ◽  
Alexis Marchesini ◽  
Matteo Girardi ◽  
Cristiano Vernesi ◽  
...  
Keyword(s):  
Environmental Samples ◽  
Sequence Data ◽  
Fragment Size ◽  
Gc Content ◽  
Pcr Amplification ◽  
Shotgun Sequencing ◽  
Taxonomic Resolution ◽  
Universal Method ◽  
Dna Fragments ◽  
Target Capture

<p>The current main methodologies for identifying DNA fragments in ancient environmental samples are metabarcoding and shotgun sequencing which present strong advantages and limitations. Target capture is a promising method for enriching shotgun libraries for target organisms and might be able to combine the advantages from metabarcoding and shotgun sequencing into a single method. Target capture operates by hybridising DNA fragments in a sample to synthetic RNA-baits which share enough homology (≥85 %). These RNA-baits contain a magnetic molecule which is used to pull the hybridised fragments of interest to a magnet, allowing for the non-hybridised molecules to be washed away. The RNA-baits are designed according to prior knowledge of target sequences. Target capture does not require a PCR amplification step to amplify fragments using taxon-specific primers, and it might, therefore, be less prone to PCR amplification biases.</p><p>We designed a bait-set for capturing two barcoding plastidial genes <em>mat</em>K and <em>rbc</em>L for all the species in four major plant orders: Asterales, Fagales, Pinales, and Poales. These orders are species-rich and/or difficult to identify to low taxonomic levels (family, genus or species) using metabarcoding. Our objectives were: 1) to design a universal method for trimming and selecting sequences for bait design using online sequence repositories, 2) to investigate a potential capture bias of species with a low GC-content (proportion of guanine and cytosine nucleotides) and 3) to investigate taxonomic resolution of target capture compared to metabarcoding. Because species with an overall low GC content (<32%) might be less efficiently captured than species with a higher GC content, we used mock communities with a known proportion of amplicons fragment size distribution and GC content. Further, we used sequence data simulations to investigate taxonomic resolution using varies species pools.</p>

Locally Smoothed Median Absolute Difference Curves and the First Global Performance Cooperative

2009 ◽  
Vol 8 (2) ◽  
pp. 45-52
Author(s):  
Gerald J. Kost ◽  
Nam K. Tran ◽  
Jorge R. Sifontes ◽  
Dan M. Mecozzi ◽  
Richard F. Louie ◽  
...  
Keyword(s):  
Absolute Difference ◽  
Global Performance ◽  
Median Absolute Difference

scholarly journals Validation of the CrIS fast physical NH<sub>3</sub> retrieval with ground-based FTIR

2017 ◽  
Vol 10 (7) ◽  
pp. 2645-2667 ◽  
Author(s):  
Enrico Dammers ◽  
Mark W. Shephard ◽  
Mathias Palm ◽  
Karen Cady-Pereira ◽  
Shannon Capps ◽  
...  
Keyword(s):  
Relative Difference ◽  
Atmospheric Composition ◽  
Absolute Difference ◽  
Lower Sensitivity ◽  
Composition Change ◽  
Atmospheric Concentration ◽  
The Absolute ◽  
Cross Track ◽  
Median Absolute Difference ◽  
Total Column

Abstract. Presented here is the validation of the CrIS (Cross-track Infrared Sounder) fast physical NH3 retrieval (CFPR) column and profile measurements using ground-based Fourier transform infrared (FTIR) observations. We use the total columns and profiles from seven FTIR sites in the Network for the Detection of Atmospheric Composition Change (NDACC) to validate the satellite data products. The overall FTIR and CrIS total columns have a positive correlation of r  =  0.77 (N  =  218) with very little bias (a slope of 1.02). Binning the comparisons by total column amounts, for concentrations larger than 1.0  ×  1016 molecules cm−2, i.e. ranging from moderate to polluted conditions, the relative difference is on average ∼ 0–5 % with a standard deviation of 25–50 %, which is comparable to the estimated retrieval uncertainties in both CrIS and the FTIR. For the smallest total column range (< 1.0  × 1016 molecules cm−2) where there are a large number of observations at or near the CrIS noise level (detection limit) the absolute differences between CrIS and the FTIR total columns show a slight positive column bias. The CrIS and FTIR profile comparison differences are mostly within the range of the single-level retrieved profile values from estimated retrieval uncertainties, showing average differences in the range of  ∼ 20 to 40 %. The CrIS retrievals typically show good vertical sensitivity down into the boundary layer which typically peaks at  ∼ 850 hPa (∼ 1.5 km). At this level the median absolute difference is 0.87 (std  =  ±0.08) ppb, corresponding to a median relative difference of 39 % (std  =  ±2 %). Most of the absolute and relative profile comparison differences are in the range of the estimated retrieval uncertainties. At the surface, where CrIS typically has lower sensitivity, it tends to overestimate in low-concentration conditions and underestimate in higher atmospheric concentration conditions.

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