ORCID Profile
0000-0002-5192-7047
Current Organisations
U.S. Food and Drug Administration
,
National Museum of Natural History
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Publisher: Elsevier BV
Date: 2005
Publisher: ZappyLab, Inc.
Date: 25-03-2022
DOI: 10.17504/PROTOCOLS.IO.3BYL4BWERVO5/V1
Abstract: This protocol details methods for the preparation of SARS-CoV-2 sequencing library using VSS primers from library preparation from NEBNext® ARTIC SARS-CoV-2 Companion Kit (Oxford Nanopore Technologies®), NEB #E7660S/L 24/96 reactions adapted for wastewater s les. Standard Protocol with PCR Bead Cleanup: This protocol includes a cleanup and normalization step for each s le after cDNA synthesis. Performing the cleanup and normalization step creates library pools where the reads for each library are more evenly distributed. These pools will likely achieve sufficient and equal coverage in less run time, but they take more hands-on time This protocol also includes options for barcoding with dual indexing or single indexing of the s les.
Publisher: Elsevier BV
Date: 04-2023
Publisher: Magnolia Press
Date: 21-01-2021
DOI: 10.11646/ZOOTAXA.4915.2.11
Abstract: Hernáez et al. (2020) described a new species of ghost shrimp, Neocallichirus pinheiroi, from northeastern coast of Brazil, Western Atlantic. Although the description and figures presented by Hernáez et al. (2020) fully characterize the new species, the journal issue in which the description appeared was published online only, and the article in which N. pinheiroi appeared did not include a ZooBank registration number (LISD), required for validation of new names in electronic-only publications [vide Art. 8.5.3 of the amended Code of the International Commission on Zoological Nomenclature (ICZN, 1999, 2012)]. As result, the name Neocallichirus pinheiroi Hernáez, Windsor, Paula & Santana, 2020, is not available according the International Code of Zoological Nomenclature (ICZN, 1999, 2012). Therefore, the present note serves to validate the name Neocallichirus pinheiroi by fulfilling the ICZN conditions for nomenclatural availability.
Publisher: Pensoft Publishers
Date: 07-2019
DOI: 10.3897/ZOOKEYS.858.33826
Abstract: The United States Food and Drug Administration (FDA) has recently adopted DNA barcoding for the purpose of determining the species identity of commercial seafood products. This effort has revealed instances of incongruence between current scientifically accepted taxon names and those utilized by the seafood industry in product labelling. One such case is that of “ Portunushaanii ”, a name utilized by the seafood industry to label commercial products under the market name “red swimming crab.” However, carcinologists currently regard P.haanii as synonym of Portunusgladiator Fabricius, 1798, which itself is the subject of debate over whether it is a secondary homonym of Cancer gladiator Fabricius, 1793. Further complicating matters, DNA barcode sequences from commercial products match GenBank sequences identified as Portunuspseudoargentatus Stephenson, 1961. Here the complicated taxonomic history of the Portunusgladiator complex is reviewed and a resolution proposed based on combined morphological descriptions and molecular phylogenetic analyses. It is demonstrated that, given the provisions of the International Code of Zoological Nomenclature and the current elevation of Monomia Gistel, 1848, to full genus rank, its type species, Portunusgladiator Fabricius, 1798, should be treated as a valid and available taxon name. It is also shown, upon examination and comparison of types and topotypic material that Monomiahaanii (Stimpson, 1858) is a distinct taxon from M.gladiator , and Portunuspseudoargentatus Stephenson, 1961, is a junior subjective synonym of M.haanii (Stimpson, 1858). Furthermore, it is shown that crab meat sold in the US currently labeled as “ Portunushaanii ” and/or “red swimming crab” is in fact M.haanii using comparative analysis of DNA barcode sequences between museum-vouchered reference specimens, whole crabs provided directly by a seafood importer, and processed commercial products purchased at retail.
Publisher: Regional Euro-Asian Biological Invasions Centre Oy (REABIC)
Date: 2020
Publisher: Cold Spring Harbor Laboratory
Date: 12-12-2022
DOI: 10.1101/2022.12.09.519815
Abstract: For much of terrestrial bio ersity, the evolutionary pathways of adaptation from marine ancestors are poorly understood, and have usually been viewed as a binary trait. True crabs, the decapod crustacean infraorder Brachyura, comprise over 7,600 species representing a striking ersity of morphology and ecology, including repeated adaptation to non-marine habitats. Here, we reconstruct the evolutionary history of Brachyura using new and published sequences of 10 genes for 344 tips spanning 88 of 109 families. Using 36 newly vetted fossil calibrations, we infer that brachyurans most likely erged in the Triassic, with family-level splits in the late Cretaceous and early Paleogene. By contrast, the root age is underestimated with automated s ling of 328 fossil occurrences explicitly incorporated into the tree prior, suggesting such models are a poor fit under heterogeneous fossil preservation. We apply recently defined trait-by-environment associations to classify a gradient of transitions from marine to terrestrial lifestyles. We estimate that crabs left the marine environment at least seven and up to 17 times convergently, and returned to the sea from non-marine environments at least twice. Although the most highly terrestrial- and many freshwater-adapted crabs are concentrated in Thoracotremata, Bayesian threshold models of ancestral state reconstruction fail to identify shifts to higher terrestrial grades due to the degree of underlying change required. Lineages throughout our tree inhabit intertidal and marginal marine environments, corroborating the inference that the early stages of terrestrial adaptation have a lower threshold to evolve. Our framework and extensive new fossil and natural history datasets will enable future comparisons of non-marine adaptation at the morphological and molecular level. Crabs provide an important window into the early processes of adaptation to novel environments, and different degrees of evolutionary constraint that might help predict these pathways.
Publisher: ZappyLab, Inc.
Date: 25-01-2022
DOI: 10.17504/PROTOCOLS.IO.B4BSQSNE
Abstract: This SARS-CoV-2 targeted, and rapid viral RNA library preparation and sequencing kit provides an approximately five hour turn-around time from viral RNA s le to sequencing.The kit includes cDNA synthesis, enrichment, and library lification and indexing.The enhanced protocol removes the need for normalization and quantification prior to lification and indexing.RNA input is 5 ul, regardless of SC2 viral load in the s le extract.Amplification is performed using two primer pools that produces licons that are 300 bp in size, so no fragmentation is necessary prior to sequencing on Illumina platforms.10 bp unique dual indices are provided in the kit, and with a cycle read length of 149 for each paired-end read, the sequencing time is just over 28 hours.
Publisher: ZappyLab, Inc.
Date: 09-03-2022
DOI: 10.17504/PROTOCOLS.IO.B545Q8Y6
Abstract: PURPOSE: This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewater. Protocols developed for this project cover wastewater collection, concentration, RNA extraction, RT-qPCR, library prep, genome sequencing, quality control checks, and data submission to NCBI. This modified protocol details methods for cDNA synthesis and library preparation for sequencing of wastewater s les containing SARS-CoV-2. The protocol is based primarily on the NEBNext® ARTIC SARS-CoV-2 Library Prep Kit (Illumina®), NEB #E7650S/L 24/96 reactions, with a few modifications. Primarily, VarSkip Short primers are used in place of the ARTIC V3 primers. These primers are available in the NEBNext®ARTIC SARS-CoV-2 FS Library Prep Kit (Illumina®) however, for optimal variant detection from wastewater, sequenced fragments should be as large as possible, so we discourage fragmentation prior to end prep. There are a couple of decision points in this protocol. Examining cDNA licon s les on an Agilent TapeStation system or similar fragment analyzer is extremely helpful in making these decisions. Version Updates: V2- Quality checks of cleaned licons on low viral titer and high viral titer s les has been added as a decision point before proceeding to sequencing.
Publisher: ZappyLab, Inc.
Date: 16-12-2021
DOI: 10.17504/PROTOCOLS.IO.B2YZQFX6
Abstract: This procedure outlines the protocol for sequencing of VarSkip Short SARS-CoV-2 cDNA licons using the Illumina DNA Prep library preparation kit for sequencing on an Illumina MiSeq sequencer.
Publisher: CSIRO Publishing
Date: 2017
DOI: 10.1071/IS13011_CO
Abstract: Mithracid crabs comprise a primarily subtidal reef- and rubble-dwelling group inhabiting both tropical and subtropical seas. Despite their relative ubiquity in many hard-substrate environments, there has been little consensus about their phylogenetic relationships or whether their group rank should be that of subfamily or family. We have used a combined molecular dataset of two nuclear (18S, H3) and three mitochondrial (12S, 16S, COI) genes to build a preliminary molecular phylogeny of Majoidea in order to examine the membership of Mithracidae. We then built a second molecular phylogeny based on three mitochondrial genes to assess the internal composition of the family, and conducted comparative morphological examinations of genera and species that resolved in unexpected positions on the phylogram. Four genera are designated under new or resurrected names on the basis of molecular and morphological characters, while memberships of several other existing genera are modified. Following review of molecular and morphological characters, the genera Coelocerus, Cyclocoeloma, Cyphocarcinus, Leptopisa, Micippa, Picrocerodes, Stenocionops and Tiarinia are provisionally excluded from Mithracidae s.s., while Hemus and Pitho are included in it. A key to genera of Mithracidae is provided.
Publisher: ZappyLab, Inc.
Date: 05-01-2022
DOI: 10.17504/PROTOCOLS.IO.B3INQKDE
Abstract: The Zymo Environ Water RNA kit has been tested and evaluated for the application of SARS-CoV-2 wastewater surveillance. This kit was designed for water, wastewater, sludge, sewage, biofilm and other similar s le sources. As such, minimal optimization was required for this application. The kit incorporates an enrichment step that is accomplished with the use of Water Concentrating Buffer (WCB), which promotes the pelleting of viral capsids and protein-associated RNA, increasing SARS-CoV-2 RNA yields by more than 8-fold compared to without WCB. DNA/RNA Shield™ allows for safe handling as it has been validated for inactivation of pathogens including SARS-CoV-2. The kit yields highly concentrated, PCR inhibitor-free high quality RNA, applicable for many downstream applications including RT-qPCR, RT-ddPCR, and NGS.
Publisher: ZappyLab, Inc.
Date: 20-01-2022
DOI: 10.17504/PROTOCOLS.IO.B34RQQV6
Abstract: This procedure outlines the protocol for sequencing of VarSkip Short SARS-CoV-2 cDNA licons using the Illumina DNA Prep library preparation kit for sequencing on an Illumina MiSeq sequencer.
Publisher: CSIRO Publishing
Date: 2014
DOI: 10.1071/IS13011
Abstract: Mithracid crabs comprise a primarily subtidal reef- and rubble-dwelling group inhabiting both tropical and subtropical seas. Despite their relative ubiquity in many hard-substrate environments, there has been little consensus about their phylogenetic relationships or whether their group rank should be that of subfamily or family. We have used a combined molecular dataset of two nuclear (18S, H3) and three mitochondrial (12S, 16S, COI) genes to build a preliminary molecular phylogeny of Majoidea in order to examine the membership of Mithracidae. We then built a second molecular phylogeny based on three mitochondrial genes to assess the internal composition of the family, and conducted comparative morphological examinations of genera and species that resolved in unexpected positions on the phylogram. Four genera are designated under new or resurrected names on the basis of molecular and morphological characters, while memberships of several other existing genera are modified. Following review of molecular and morphological characters, the genera Coelocerus, Cyclocoeloma, Cyphocarcinus, Leptopisa, Micippa, Picrocerodes, Stenocionops and Tiarinia are provisionally excluded from Mithracidae s.s., while Hemus and Pitho are included in it. A key to genera of Mithracidae is provided.
Publisher: ZappyLab, Inc.
Date: 31-03-2022
DOI: 10.17504/PROTOCOLS.IO.B6YGRFTW
Abstract: PURPOSE: This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewater. Protocols developed for this project cover wastewater collection, concentration, RNA extraction, RT-qPCR, library prep, genome sequencing, quality control checks, and data submission to NCBI. This modified protocol details methods for cDNA synthesis and library preparation for sequencing of wastewater s les containing SARS-CoV-2. The protocol is based primarily on the NEBNext® ARTIC SARS-CoV-2 Library Prep Kit (Illumina®), NEB #E7650S/L 24/96 reactions, with a few modifications. Primarily, VarSkip Short primers are used in place of the ARTIC V3 primers. These primers are available in the NEBNext®ARTIC SARS-CoV-2 FS Library Prep Kit (Illumina®) however, for optimal variant detection from wastewater, sequenced fragments should be as large as possible, so we discourage fragmentation prior to end prep. There are a couple of decision points in this protocol. Examining cDNA licon s les on an Agilent TapeStation system or similar fragment analyzer is extremely helpful in making these decisions. Version Updates: V3- Controlled vocabulary for positiveControl and negativeControl has been added to the S le Sheet.
Publisher: ZappyLab, Inc.
Date: 06-12-2022
DOI: 10.17504/PROTOCOLS.IO.14EGN26QQG5D/V1
Abstract: This protocol uses the Ceres Nanotrap® particle-based virus capture and concentration method for 10mL of wastewater followed by extraction with the Zymo Environ™ Water RNA extraction kit with a Zymo DNase step.
Publisher: ZappyLab, Inc.
Date: 30-03-2022
DOI: 10.17504/PROTOCOLS.IO.B6WFRFBN
Abstract: This SARS-CoV-2 targeted, a rapid viral RNA library preparation kit compatible with Illumina sequencers, provides an approximately five hour turn-around time from viral RNA s le to sequencing. The kit includes cDNA synthesis, SARS-CoV-2 enrichment, and library lification and indexing reagents. The Enhanced protocol removes the need for normalization and quantification prior to lification and indexing. RNA input is 5 μl, regardless of SC2 viral load in the s le extract. Amplification is performed using two primer pools that produce overlapping licons that are approximately 250 bp in size as a result, no fragmentation is necessary prior to sequencing on Illumina platforms. 10 bp unique dual indexes (UDIs) are provided in the kit, and with a cycle read length of 149 for each paired-end read, the sequencing time is just over 28 hours. Version Updates: V2- Recommending 1:10 dilution of index primer on low viral titer s les to reduce short fragments. Controlled vocabulary for the use of positive control and negative template control has been added to the S le Sheet following miseq loading guidelines.
Publisher: ZappyLab, Inc.
Date: 30-03-2022
DOI: 10.17504/PROTOCOLS.IO.RM7VZY39RLX1/V3
Abstract: This SARS-CoV-2 targeted, a rapid viral RNA library preparation kit compatible with Illumina sequencers, provides an approximately five hour turn-around time from viral RNA s le to sequencing. The kit includes cDNA synthesis, SARS-CoV-2 enrichment, and library lification and indexing reagents. The Enhanced protocol removes the need for normalization and quantification prior to lification and indexing. RNA input is 5 μl, regardless of SC2 viral load in the s le extract. Amplification is performed using two primer pools that produce overlapping licons that are approximately 250 bp in size as a result, no fragmentation is necessary prior to sequencing on Illumina platforms. 10 bp unique dual indexes (UDIs) are provided in the kit, and with a cycle read length of 149 for each paired-end read, the sequencing time is just over 28 hours. Version Updates: V2- Recommending 1:10 dilution of index primer on low viral titer s les to reduce short fragments. Controlled vocabulary for the use of positive control and negative template control has been added to the S le Sheet following miseq loading guidelines.
Publisher: ZappyLab, Inc.
Date: 25-03-2022
DOI: 10.17504/PROTOCOLS.IO.B6RMRD46
Abstract: This protocol details methods for the preparation of SARS-CoV-2 sequencing library using VSS primers from library preparation from NEBNext® ARTIC SARS-CoV-2 Companion Kit (Oxford Nanopore Technologies®), NEB #E7660S/L 24/96 reactions adapted for wastewater s les. Standard Protocol with PCR Bead Cleanup: This protocol includes a cleanup and normalization step for each s le after cDNA synthesis. Performing the cleanup and normalization step creates library pools where the reads for each library are more evenly distributed. These pools will likely achieve sufficient and equal coverage in less run time, but they take more hands-on time This protocol also includes options for barcoding with dual indexing or single indexing of the s les.
Publisher: Informa UK Limited
Date: 20-12-2019
Publisher: Oxford University Press (OUP)
Date: 24-09-2020
Abstract: Multiple paternity is widespread across animal and plant taxa and can increase genetic ersity and enhance fitness, especially in unpredictable environments. A prior study of the intertidal zone porcelain crab, Petrolisthes cinctipes (Randall, 1840), found that most females carried polyandrous broods. We tested the hypothesis that multiple paternity in P. cinctipes enhances fitness through increased average brood tolerance to temperature stress. Embryonic survival of split broods (N = 27) was measured under ambient conditions and following a single one-hour heat shock at 30 °C. Two microsatellite loci were used to genotype embryos and mothers in order to distinguish multiple from single paternity in each brood. Mean overall hatching percentage did not differ between singly and multiply sired broods however, when exposed to a heat-shock, single-sired broods experienced 11% lower hatching success. Though relative fitness was higher in single-sired broods under non-stressful conditions, extrapolation of our results to conditions where temperatures are at least 30 °C (present-day extremes for the California coast) for & 2 days of the embryonic brood period, multiply sired broods have a relative fitness that is approximately 24 times higher after 15 generations. Maternal quality (size) and the timing of the heat shock relative to developmental timing also influence the brood response to heat shock. Our results suggest that multiple paternity reduces embryo survival variance between ambient and heat-shock conditions and that polyandrous behavior could be an advantage for P. cinctipes in the thermally variable high-intertidal zone. We conclude that multiple paternity is an important strategy for increasing fitness by genetic ersification in organisms that experience severe and unpredictable levels of environmental stress.
Publisher: Pensoft Publishers
Date: 18-02-2019
DOI: 10.3897/ZOOKEYS.825.32271
Abstract: Three new species and a new genus of majoid crabs from deep waters in the eastern Pacific are described and illustrated using morphological and molecular data. A new species of inachoidid, Collodesanartius sp. n. is described from Peru, which resembles C.tenuirostris Rathbun, 1893, in the general appearance of the carapace, but is distinguished by the details of tubercles on the carapace and thoracic sternum, proportions of the pereopod articles, and bathymetric distribution. A new epialtid, Nibiliamachala sp. n. , is described from Ecuador Nibilia A Milne-Edwards, 1878 has, until now, been considered to be monotypic, occurring only in the western Atlantic. This new species, from the eastern Pacific, closely resembles N.antilocapra (Stimpson, 1871) in the general morphology, but can be distinguished by the number of spines on the carapace and pereopods. Another epialtid, Solincaaulix gen. n. et sp. n , is establish for material collected from Ecuador and Peru, and can be easily identified from other taxa by the presence of a deep furrow between the very inflated branchial regions.
Publisher: FapUNIFESP (SciELO)
Date: 2022
Publisher: ZappyLab, Inc.
Date: 20-01-2022
DOI: 10.17504/PROTOCOLS.IO.B34QQQVW
Abstract: PURPOSE: This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewater. Protocols developed for this project cover wastewater collection, concentration, RNA extraction, RT-qPCR, library prep, genome sequencing, quality control checks, and data submission to NCBI. This modified protocol details methods for cDNA synthesis and library preparation for sequencing of wastewater s les containing SARS-CoV-2. The protocol is based primarily on the NEBNext® ARTIC SARS-CoV-2 Library Prep Kit (Illumina®), NEB #E7650S/L 24/96 reactions, with a few modifications. Primarily, VarSkip Short primers are used in place of the ARTIC V3 primers. These primers are available in the NEBNext®ARTIC SARS-CoV-2 FS Library Prep Kit (Illumina®) however, for optimal variant detection from wastewater, sequenced fragments should be as large as possible, so we discourage fragmentation prior to end prep. There are a couple of decision points in this protocol. Examining cDNA licon s les on an Agilent TapeStation system or similar fragment analyzer is extremely helpful in making these decisions.
Publisher: ZappyLab, Inc.
Date: 25-04-2022
DOI: 10.17504/PROTOCOLS.IO.RM7VZY52XLX1/V1
Abstract: This protocol details methods for the preparation of RTqPCR for the CDC's N1 fragment of the nucleocopsid gene of SARS-CoV-2 using the Promega GoTaq® Enviro Wastewater SARS-CoV-2 System (AM2110). Total Nucleic Acid (TNA) from the Promega Maxwell® RSC Enviro TNA Kit (Cat.# AS1831) is used as input. This system is a one-step RT-qPCR. In addition to the N1 primer robe, it includes an internal process control, Pepper Mild Mottle Virus (PMMoV), to allow for normalization and an internal lification control (IAC). The GoTaq® Enviro Master Mix, provided in this kit, uses proprietary enzymes and formulations that tolerate reverse transcriptase and PCR inhibitors such as humic acids, that can be present in nucleic acid s les purified from wastewater.
Publisher: Informa UK Limited
Date: 2017
Publisher: ZappyLab, Inc.
Date: 16-12-2021
DOI: 10.17504/PROTOCOLS.IO.B2YUQFWW
Abstract: PURPOSE: This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewater. Protocols developed for this project cover wastewater collection, concentration, RNA extraction, RT-qPCR, library prep, genome sequencing, quality control checks, and data submission to NCBI. This modified protocol details methods for cDNA synthesis and library preparation for sequencing of wastewater s les containing SARS-CoV-2. The protocol is based primarily on the NEBNext® ARTIC SARS-CoV-2 Library Prep Kit (Illumina®), NEB #E7650S/L 24/96 reactions, with a few modifications. Primarily, VarSkip Short primers are used in place of the ARTIC V3 primers. These primers are available in the NEBNext®ARTIC SARS-CoV-2 FS Library Prep Kit (Illumina®) however, for optimal variant detection from wastewater, sequenced fragments should be as large as possible, so we discourage fragmentation prior to end prep. There are a couple of decision points in this protocol. Examining cDNA licon s les on an Agilent TapeStation system or similar fragment analyzer is extremely helpful in making these decisions.
Publisher: ZappyLab, Inc.
Date: 31-03-2022
DOI: 10.17504/PROTOCOLS.IO.5JYL89N26V2W/V3
Abstract: PURPOSE: This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewater. Protocols developed for this project cover wastewater collection, concentration, RNA extraction, RT-qPCR, library prep, genome sequencing, quality control checks, and data submission to NCBI. This modified protocol details methods for cDNA synthesis and library preparation for sequencing of wastewater s les containing SARS-CoV-2. The protocol is based primarily on the NEBNext® ARTIC SARS-CoV-2 Library Prep Kit (Illumina®), NEB #E7650S/L 24/96 reactions, with a few modifications. Primarily, VarSkip Short primers are used in place of the ARTIC V3 primers. These primers are available in the NEBNext®ARTIC SARS-CoV-2 FS Library Prep Kit (Illumina®) however, for optimal variant detection from wastewater, sequenced fragments should be as large as possible, so we discourage fragmentation prior to end prep. There are a couple of decision points in this protocol. Examining cDNA licon s les on an Agilent TapeStation system or similar fragment analyzer is extremely helpful in making these decisions. Version Updates: V3- Controlled vocabulary for positiveControl and negativeControl has been added to the S le Sheet.
Publisher: Pensoft Publishers
Date: 20-05-2020
DOI: 10.3897/ZSE.96.50360
Abstract: A new genus of majoid spider crab, Pohleus gen. nov. is established for Pericera septemspinosa Stimpson, 1871 and Pericera heptacantha Bell, 1836, based on morphology and molecular data from the partial sequences of the 12S and 16S mitochondrial genes and the 18S small subunit rRNA nuclear locus. The species are re-described and illustrated, based on material from several localities of the western Atlantic and eastern Pacific oceans. The carapace, antennal and pterygostomial spines, male thoracic sternum and first gonopods are distinctive characters, distinguishing Pohleus gen. nov. from species assigned to Macrocoeloma Miers, 1879, where P. septemspinosus and P. heptacanthus are currently included.
Publisher: American Society for Microbiology
Date: 08-08-2019
DOI: 10.1128/MRA.00576-19
Abstract: Curcuma longa L. is a native species of Asia that is commonly known as turmeric. It is a spice also used in traditional medicine to treat a wide range of illnesses. Here, we present the fully annotated chloroplast genome of Curcuma longa .
Publisher: Brill
Date: 2013
Publisher: ZappyLab, Inc.
Date: 31-01-2022
DOI: 10.17504/PROTOCOLS.IO.B4HTQT6N
Abstract: This SARS-CoV-2 targeted, a rapid viral RNA library preparation kit compatible with Illumina sequencers, provides an approximately five hour turn-around time from viral RNA s le to sequencing. The kit includes cDNA synthesis, SARS-CoV-2 enrichment, and library lification and indexing reagents. The Enhanced protocol removes the need for normalization and quantification prior to lification and indexing. RNA input is 5 μl, regardless of SC2 viral load in the s le extract. Amplification is performed using two primer pools that produce overlapping licons that are approximately 250 bp in size as a result, no fragmentation is necessary prior to sequencing on Illumina platforms. 10 bp unique dual indexes (UDIs) are provided in the kit, and with a cycle read length of 149 for each paired-end read, the sequencing time is just over 28 hours.
Publisher: PeerJ
Date: 05-11-2019
DOI: 10.7717/PEERJ.7827
Abstract: Callinectes sapidus Rathbun, 1896 is a western Atlantic species with a disjointed natural geographic range from Massachusetts, USA to Venezuela (distribution area 1) and from Alagoas, Brazil to northern Argentina (distribution area 2). It is the only species of portunid crab commercially harvested in the continental United States but is also imported into the US from several Latin American countries, Venezuela and Mexico in particular. In the United States, crab products labeled as “blue crab” and “Product of the USA” may not legally contain other species of crab or C. sapidus not harvested in the United States. The present study documents nucleotide variation within the barcode region of cytochrome c oxidase I (COI) in 417 reference specimens of C. sapidus collected from throughout its natural range. The goal of this study is to determine if this variation can be utilized to detect mislabeled C. sapidus products sold in interstate commerce by comparing genetic signatures in reference specimens to those observed in commercial crabmeat labeled as “Product of the USA” and “Product of Venezuela.” In reference specimens, we observed high levels of genetic variation in the barcode region. However, three lineages were consistently observed with significant pairwise F st values between the lineages. Lineage 1 was observed throughout the natural geographic range but predominated in the continental US and was the only lineage observed in the major crabmeat-producing states (MD, LA, VA, NC). Lineage 2 primarily occurred in the Caribbean region of distribution area 1 but was also infrequently encountered in the South Atlantic Bight region of the US coast. Finally, Lineage 3 was only observed in Brazilian waters and had the lowest haplotype and nucleotide ersity values. Lineages 1 and 2 were separated by a mean pairwise distance ( p -distance) of 3.15%, whereas Lineage 3 had a mean p -distance of 2.55% and 1.35% to Lineages 1 and 2, respectively. Within lineage mean p -distances were 0.45%, 0.19%, and 0.07% for Lineages 1, 2, and 3, respectively. Among all vouchered reference specimens collected from the continental United States, Mexico, Puerto Rico, and Venezuela, we identified 22 phylogenetically informative sites that drive observed lineage ergences. Haplotypes identified from barcode COI sequences from commercial C. sapidus products labeled as originating from the US all aligned with haplotypes from Lineage 1 reference specimens and haplotypes from commercial products labeled as originating from Venezuela all aligned with Lineage 2, suggesting that these lineages may be useful for indicating whether products originate from the continental US or are imported when package labeling is in question.
Location: United States of America
Location: United States of America
No related grants have been discovered for Amanda Windsor.