Mark Stoeckle - Academia.edu (original) (raw)

Papers by Mark Stoeckle

PLOS ONE, Aug 27, 2012

The accuracy of DNA barcode databases is critical for research and practical applications. Here w... more The accuracy of DNA barcode databases is critical for research and practical applications. Here we apply a frequency matrix to assess sequencing errors in a very large set of avian BARCODEs. Using 11,000 sequences from 2,700 bird species, we show most avian cytochrome c oxidase I (COI) nucleotide and amino acid sequences vary within a narrow range. Except for third codon positions, nearly all (96%) sites were highly conserved or limited to two nucleotides or two amino acids. A large number of positions had very low frequency variants present in single individuals of a species; these were strongly concentrated at the ends of the barcode segment, consistent with sequencing error. In addition, a small fraction (0.1%) of BARCODEs had multiple very low frequency variants shared among individuals of a species; these were found to represent overlooked cryptic pseudogenes lacking stop codons. The calculated upper limit of sequencing error was 8610 25 errors/ nucleotide, which was relatively high for direct Sanger sequencing of amplified DNA, but unlikely to compromise species identification. Our results confirm the high quality of the avian BARCODE database and demonstrate significant quality improvement in avian COI records deposited in GenBank over the past decade. This approach has potential application for genetic database quality control, discovery of cryptic pseudogenes, and studies of low-level genetic variation.

Birds are a taxonomically well-described group of animals, yet DNA barcoding, i.e., the molecular... more Birds are a taxonomically well-described group of animals, yet DNA barcoding, i.e., the molecular characterization of species using a standardized genetic marker, has revealed unexpected patterns of genetic divergences among North American birds. We performed a comprehensive COI (cytochrome c oxidase subunit I) barcode survey of 296 species of Scandinavian birds, and compared genetic divergences among 78 transAtlantic species whose breeding ranges include both Scandinavia and North America. Ninety-four percent of the Scandinavian species showed unique barcode clusters; the remaining 6% had overlapping barcodes with one or more congeneric species, which may reflect incomplete lineage sorting or a single gene pool. Four species showed large intra-specific divergences within Scandinavia, despite no apparent morphological differentiation or indications of reproductive isolation. These cases may reflect admixture of previously isolated lineages, and may thus warrant more comprehensive phylogeographic analyses. Nineteen (24%) of 78 transAtlantic species exhibited divergent genetic clusters which correspond with regional subspecies. Three of these transAtlantic divergences were paraphyletic. Our study demonstrates the effectiveness of COI barcodes for identifying Scandinavian birds and highlights taxa for taxonomic review. The standardized DNA barcoding approach amplified the power of our regional studies by enabling independently obtained datasets to be merged with the established avian barcode library. Keywords DNA barcoding Á Genetic divergence Á Cytochrome c oxidase I Á TransAtlantic comparison Communicated by M. Wink.

Humana Press eBooks, 2012

As of February 2011, COI DNA barcode sequences (a 648-bp segment of the 5 ¢ end of the mitochondr... more As of February 2011, COI DNA barcode sequences (a 648-bp segment of the 5 ¢ end of the mitochondrial gene cytochrome c oxidase I, the standard DNA barcode for animals) have been collected from over 23,000 avian specimens representing 3,800 species, more than one-third of the world's avifauna. Here, we detail the methodology for obtaining DNA barcodes from birds, covering the entire process from fi eld collection to data analysis. We emphasize key aspects of the process and describe in more detail those that are particularly relevant in the case of birds. We provide elemental information about collection of specimens, detailed protocols for DNA extraction and PCR, and basic aspects of sequencing methodology. In particular, we highlight the primer pairs and thermal cycling profi les associated with successful amplifi cation and sequencing from a broad range of avian species. Finally, we succinctly review the methodology for data analysis, including the detection of errors (such as contamination, misidentifi cations, or amplifi cation of pseudogenes), assessment of species resolution, detection of divergent intraspecifi c lineages, and identifi cation of unknown specimens.

Journal of ornithology, Jan 10, 2010

Molecular Ecology Notes, Jan 18, 2007

DNA barcoding seeks to assemble a standardized reference library for DNA-based identification of ... more DNA barcoding seeks to assemble a standardized reference library for DNA-based identification of eukaryotic species. The utility and limitations of this approach need to be tested on well-characterized taxonomic assemblages. Here we provide a comprehensive DNA barcode analysis for North American birds including 643 species representing 93% of the breeding and pelagic avifauna of the USA and Canada. Most (94%) species possess distinct barcode clusters, with average neighbour-joining bootstrap support of 98%. In the remaining 6%, barcode clusters correspond to small sets of closely related species, most of which hybridize regularly. Fifteen (2%) currently recognized species are comprised of two distinct barcode clusters, many of which may represent cryptic species. Intraspecific variation is weakly related to census population size and species age. This study confirms that DNA barcoding can be effectively applied across the geographical and taxonomic expanse of North American birds. The consistent finding of constrained intraspecific mitochondrial variation in this large assemblage of species supports the emerging view that selective sweeps limit mitochondrial diversity.

The Journal of Immunology

In experimental visceral leishmaniasis, acquired resistance is T cell-dependent, involves IFN-gam... more In experimental visceral leishmaniasis, acquired resistance is T cell-dependent, involves IFN-gamma-activated macrophages, and is expressed in the tissues by granuloma formation. Resistance also correlates with Ag-stimulated IL-2 secretion; therefore, Leishmania donovani-infected BALB/c mice were treated with anti-IL-2 mAb or rIL-2 to determine the host defense effect of IL-2. In control mice, intracellular hepatic infection peaked at 2 wk and then declined coincident with granuloma development. In contrast, liver parasite burdens in anti-IL-2-treated mice continued to increase until after 4 wk, at which time mature granuloma formation was inhibited. Treatment of mice with continuously administered IL-2 reduced liver burdens by > 50% and led to marked accumulation of granuloma mononuclear cells. The IL-2-responsive mechanism was T cell-dependent and required both L3T4+ and Lyt-2+ cells. IL-2 enhanced IFN-gamma mRNA expression in vivo and was required for IFN-gamma secretion in vi...

Updated dataset for "Aquatic environmental DNA detects seasonal fish abundance and habitat p... more Updated dataset for "Aquatic environmental DNA detects seasonal fish abundance and habitat preference in an urban estuary (PLOS ONE 2017 e0175186). <br><br>33 additional water samples (109 total) were collected from August through December 2016, extending the original six-month study to twelve months. <br><br>Samples were analyzed as described in the original study. Briefly, one-liter water samples were filtered through a 0.45μM nylon filter, DNA was isolated using MoBio PowerSoil kit, amplified with broad-range vertebrate 12S primers, indexed with Nextera tags, and submitted to GENEWIZ for 2x150bp MiSeq sequencing. Fastq files were analyzed using DADA2 and unique sequences were submitted to GenBank using BLAST. Sequences matching fish species were selected for further analysis. The complete set of fastq files and associated data are deposited together with original dataset in NCBI Sequence Read Archive under BioProject ID PRJNA358446. New findings inclu...

Journal of Clinical Microbiology, 1995

We describe a rapid method for subtyping Mycobacterium tuberculosis based on PCR amplification of... more We describe a rapid method for subtyping Mycobacterium tuberculosis based on PCR amplification of segments located between two distinct DNA repetitive elements. This method, double-repetitive-element PCR, classified 46 clinical isolates as having 25 distinct patterns; the conventional restriction fragment length polymorphism analysis classified the same isolates as having 23 distinct patterns. The double-repetitive-element PCR is a rapid subtyping method that has a discriminating power similar to that of the restriction fragment length polymorphism method.

Journal of Virology, 1993

9E3/CEF4, which is released from transformed chicken embryo fibroblasts (CEF), is a member of the... more 9E3/CEF4, which is released from transformed chicken embryo fibroblasts (CEF), is a member of the platelet factor 4 family of inflammatory proteins and may be the avian homolog of interleukin-8. Since the function of 9E3/CEF4 is unknown, we examined the effect of the protein on mitogenicity and chemotaxis, as well as its expression, in fibroblasts and peripheral blood cells. 9E3/CEF4 mRNA was expressed in chicken peripheral blood monocytes, and its expression was stimulated by incubation of the monocytes with lipopolysaccharide or phorbol myristic acetate. Boyden double-membrane analysis of chemotaxis showed that 9E3/CEF4 was chemotactic for chicken peripheral blood mononuclear cells, as well as for heterophils. Untransformed CEF and CEF transformed with Rous sarcoma virus also migrated to 9E3/CEF4 protein, as measured by Boyden single-membrane analysis. 9E3/CEF4 was slightly mitogenic for CEF, causing a doubling of [3H]thymidine uptake when added to serum-starved CEF.9E3/CEF4 was f...

Infection and Immunity, 1994

In experimental Leishmania donovani infection in BALB/c mice, initial susceptibility gives way to... more In experimental Leishmania donovani infection in BALB/c mice, initial susceptibility gives way to T-cell-dependent acquired resistance and eventual control over visceral infection. Since various cytokines appear to underlie the host response to Leishmania infection, we examined infected liver tissue for gene expression of cytokines associated with Th1 (gamma interferon [IFN-gamma] and interleukin-2 [IL-2]) and Th2 cells (IL-4 and IL-10). By Northern (RNA) blot analysis, only IFN-gamma mRNA expression was detected in livers of infected euthymic mice. To determine whether activation of Th1 cells develops selectively in this model, qualitative PCR analysis was used. These results indicated that mRNAs for IFN-gamma, IL-2, IL-4, and IL-10 were all induced by L. donovani infection. The potentially negative Th2 cell-associated response did not appear to play a functional role, however, since resistance was acquired, anti-IL-4 monoclonal antibody treatment did not accelerate control over vi...

Molecular and Cellular Biology, 1989

We studied the expression of 9E3 mRNA, which is known to be induced in chicken embryo fibroblasts... more We studied the expression of 9E3 mRNA, which is known to be induced in chicken embryo fibroblasts by p60v-src activity and by serum. In addition to full-length 9E3 mRNA, we identified several smaller RNAs that hybridized with 9E3 cDNA. One of these RNAs hybridized with a 5' 9E3 cDNA probe but not with a 3' cDNA probe. The other hybridized with a 3' cDNA probe but lacked 5' sequences, including the entire 9E3 coding region. Only the latter RNA was polyadenylylated, as determined by RNase H digestion in the presence of oligo(dT). The level of the small RNAs increased after treatment with cycloheximide and actinomycin D, indicating that the small RNAs were produced by processing of preexisting transcripts. The derivation of the small RNAs from 9E3 mRNA rather than from a related gene was confirmed by S1 nuclease analysis. The 3' terminus of the 5' RNA and the 5' terminus of the 3' RNA mapped to the same position, which suggested that the small RNAs were ...

Nucleic Acids Research, 1992

I have previously shown that IL-1 regulates the stability of groa mRNA in fibroblasts and that de... more I have previously shown that IL-1 regulates the stability of groa mRNA in fibroblasts and that decay is associated with appearance of a smaller species of gro RNA that lacks poly(A). In this study, the relationship between the two species of gro RNA, which migrate at 1.3 and 0.9 kilobases, was characterized. Following withdrawal of IL-1 or addition of IL-1 receptor antagonist, 1.3 kilobase groa mRNA was rapidly degraded and this was associated with increased expression of the 0.9 kilobase RNA. This increase occurred in the presence of actinomycin D, indicating that the 0.9 kilobase gro RNA was a product of a preexisting transcript. In cells treated with 1 pg/mI IL-1, both species were induced but the 0.9 kilobase RNA appeared later, consistent with a precursor-product relationship. In cells treated with higher doses of IL-1, the 0.9 kilobase RNA was not expressed. Using an RNAase protection assay, the 0.9 kilobase poly(A)minus gro RNA was found to be derived from groa mRNA by removal of a 130-nucleotide sequence from the 3' non-coding region. This is one of few examples of formation of an mRNA decay intermediate in vivo; it indicates that degradation of the body of groa mRNA is initiated by site-specific nuclease attack. Characterization of the mechanism of groa mRNA degradation is a first step towards identification of the ribonuclease that controls groa mRNA stability.

Nucleic Acids Research, 1991

Expression of the cytokine gene gro, also known as melanoma growth stimulatory activity, Is induc... more Expression of the cytokine gene gro, also known as melanoma growth stimulatory activity, Is induced by inflammatory stimuli, including IL-1. To determine whether gro expression is regulated at a posttranscriptional level, the effect of IL-1 on gro mRNA stability was examined. Treatment of fibroblasts with IL-1/3 caused a dose-dependent induction otgro mRNA. When IL-1 was withdrawn, gro mRNA decayed rapidly with a half life of 1 hour. This decay occurred whether or not actinomycin D was added to block new transcription. In contrast, when IL-1 was present in the medium, the level of gro mRNA was stable over 8 hours following addition of actinomycin D. In addition, the stability of a related mRNA, IL-8, was found to be regulated by IL-1. To examine whether Northern results reflected expression of groa, or of the closely related genes, gro(3 and groy, RNA samples were analyzed by PCR. All three genes were found to be induced by IL-1 and all mRNAs were stabilized In the presence of IL-1. Northern analysis revealed a minor species of gro mRNA which lacked poly(A). The pattern of expression of this RNA suggested that it was a decay intermediate of one or more of the gro mRNAs. The findings indicate that mRNA stabilization is an important component of IL-1-induced gene expression.

Nucleic Acids Research, 1993

We have previously shown that destabllization of groa mRNA Is associated with poly(A) shortening.... more We have previously shown that destabllization of groa mRNA Is associated with poly(A) shortening. In this study, we used high-resolution Northern blots to determine the rate and extent of groa mRNA poly(A) shortening, groa mRNA was found to undergo complete deadenylation within 2 h following withdrawal of IL-1. However, the process was not uniform: at 1 h following IL-1 withdrawal, groa mRNA poly(A) lengths ranged from 0 to 180 nucleotides. There was an accumulation of deadenylated groa mRNA which suggested that there may be another step before the mRNA Is destroyed. Cyclohexlmlde was found to block groa mRNA degradation at the level of poly(A) shortening. Northern blots revealed a previously unrecognized periodic distribution of poly(A) lengths that was consistent with endonucleolytlc cleavage between complexes of poly(A)-blndlng protein. The findings Indicate that the degradation pathway of groa mRNA Is a slower version of the c-fos mRNA model, with the important additional feature that deadenylation and degradation are subject to physiologic regulation. This study provides a detailed picture of groa mRNA poly(A) shortening and establishes a basis for further investigation of the mechanism by which IL-1 stabilizes specific mRNAs.

Journal of Infectious Diseases, 1993

Isoniazid resistance in Mycobacterium tuberculosis is associated with lack of catalase-peroxidase... more Isoniazid resistance in Mycobacterium tuberculosis is associated with lack of catalase-peroxidase activity. A recent study showed that some isoniazid-resistant M. tuberculosis strains have a complete deletion of the gene (katG) encoding this enzyme. To examine what proportion of clinical isolates of M. tuberculosis have katG deletion, katG sequences in 80 randomly selected isolates from New York City were analyzed. Polymerase chain reaction was used to amplify a 282-bp segment of M. tuberculosis katG and showed that 35 (90%) of 39 isoniazid-sensitive and 31 (76%) of 41 isoniazid-resistant strains contained katG sequences (P > .1). Ten multidrug and high-level isoniazid-resistant strains with identical restriction fragment length polymorphism patterns were also analyzed. All were found to have katG sequences. These findings suggest that mechanisms other than complete deletion of katG are involved in isoniazid resistance among most clinical isolates of M. tuberculosis from New York City.

Journal of Infectious Diseases, 1993

ABSTRACT

Genes & Development, 1990

Transcription from the long terminal repeat (LTR) of Rous sarcoma virus (RSV) in rat 3Y1 fibrobla... more Transcription from the long terminal repeat (LTR) of Rous sarcoma virus (RSV) in rat 3Y1 fibroblasts was dependent on the presence of serum. Within 1 hr after addition of serum to a serum-deprived culture, there was a fivefold increase in the level of transcripts initiated at the LTR. This stimulation did not require synthesis of new proteins. The induction of transcription by serum was mostly dependent on two CCAAT boxes in the LTR. Within 1 hr after addition of serum, there was also an increase in the level of a nuclear protein that bound to the two CCAAT boxes, even in the presence of cycloheximide. This serum-induced CCAAT factor also bound CCAAT sequences from other promoters, for example, those of human heat shock protein 70, human c-Ha-ras, and human histone 1, but not to the adenovirus origin of replication or the SV40 enhancer core sequence, suggesting that it was related to CP1 or CP2. Expression from the RSV LTR was not dependent on serum in v-src-transformed cells. Using...

FEMS Immunology & Medical Microbiology, 1996

To determine if monocyte chemotactic and activating factor (MCAF) induces intracellular antimicro... more To determine if monocyte chemotactic and activating factor (MCAF) induces intracellular antimicrobial activity, human monocyte-derived macnophages were treated with MCAF and challenged with Toxoplasma gondii and Leishmania donouani. Pretreatment with MCAF induced macrophages to inhibit protozoa1 replication by approximately 50%. These findings suggest a potential host defense role for MCAF in the inflammatory response to intracellular pathogens.

Cytokine, 1996

The chicken gene, 9E3/CEF4, is a small inducible cytokine highly homologous to human IL-8 andgroα... more The chicken gene, 9E3/CEF4, is a small inducible cytokine highly homologous to human IL-8 andgroα. It is overexpressed during wound healing and in the tissues around tumours induced by Rous sarcoma virus. More is known about the expression of 9E3 in vivo than any other ...

American Journal of Respiratory and Critical Care Medicine, 1995

To examine the different roles played by migrants and permanent residents in the transmission of ... more To examine the different roles played by migrants and permanent residents in the transmission of multidrug-resistant tuberculosis (MDR-TB). D E S I G N : We conducted a population-based cohort study to assess MDR-TB transmission in Shanghai between 1 January 2009 and 31 December 2012 using genotyping and geospatial analyses. R E S U LT S : A total of 367 MDR-TB cases formed the study cohort. Significant differences between MDR-TB cases who were internal migrants and those who were permanent residents were found with regard to age, sex, region, genetic characteristics and treatment outcomes. Permanent residents had a higher transmission rate than XS and XW are senior authors.

PLOS ONE, Aug 27, 2012

Humana Press eBooks, 2012

Journal of ornithology, Jan 10, 2010

Molecular Ecology Notes, Jan 18, 2007

The Journal of Immunology

Journal of Clinical Microbiology, 1995

Journal of Virology, 1993

Infection and Immunity, 1994

Molecular and Cellular Biology, 1989

Nucleic Acids Research, 1992

Nucleic Acids Research, 1991

Nucleic Acids Research, 1993

Journal of Infectious Diseases, 1993

ABSTRACT

Genes & Development, 1990

FEMS Immunology & Medical Microbiology, 1996

Cytokine, 1996

American Journal of Respiratory and Critical Care Medicine, 1995