Jessica GrantSmith College · Biological Sciences
Jessica Grant
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Publications (82)
![photo-lyase and mitochondrial 16S rRNA genes [18-19] did not detect S....](publication/355580456/figure/fig3/AS:1083085231796230@1635239050979/photo-lyase-and-mitochondrial-16S-rRNA-genes-18-19-did-not-detect-S-japonicum-DNA-in_Q320.jpg)
Background
Elimination and control of Schistosoma japonicum , the most virulent of the schistosomiasis-causing blood flukes, requires the development of sensitive and specific diagnostic tools capable of providing an accurate measurement of the infection prevalence in endemic areas. Typically, detection of S . japonicum has occurred using the Kato-...
Eukaryotic parasites are significant contributors to childhood illness in Niger. While helminthiases have received national attention through mass deworming efforts, the epidemiology of intestinal protozoa in Niger remains underexamined. This study employed real-time PCR diagnostics to describe the prevalence of two schistosomes, four soil-transmit...
Though bulk stool remains the gold standard specimen type for enteropathogen diagnosis, rectal swabs may offer comparable sensitivity with greater ease of collection for select pathogens. This study sought to evaluate the validity and reproducibility of rectal swabs as a sample collection method for the molecular diagnosis of Giardia duodenalis. Pa...
Background
Optimization of polymerase chain reaction (PCR)-based diagnostics requires the careful selection of molecular targets that are both highly repetitive and pathogen-specific. Advances in both next-generation sequencing (NGS) technologies and bioinformatics-based analysis tools are facilitating this selection process, informing target choic...
There is growing interest in local elimination of soil-transmitted helminth (STH) infection in endemic settings. In such settings, highly sensitive diagnostics are needed to detect STH infection. We compared double-slide Kato-Katz, the most commonly used copromicroscopic detection method, to multi-parallel quantitative polymerase chain reaction (qP...
Eukaryotic parasites are significant contributors to childhood illness in Niger. While helminthiases have received national attention through mass deworming efforts, the epidemiology of intestinal protozoa in Niger remains underexamined. This study employed real-time PCR diagnostics to describe the prevalence of two schistosomes, four soil-transmit...
Background
Optimization of polymerase chain reaction (PCR)-based diagnostics requires the careful selection of molecular targets that are both highly repetitive and pathogen-specific. Advances in both next-generation sequencing (NGS) technologies and bioinformatics-based analysis tools are facilitating this selection process, informing target choic...
The balance of expense and ease of use vs. specificity and sensitivity in diagnostic assays for helminth disease is an important consideration, with expense and ease often winning out in endemic areas where funds and sophisticated equipment may be scarce. In this review, we argue that molecular diagnostics, specifically new assays that have been de...
An active area of research investigates whether soil-transmitted helminths (STH) can be locally eliminated in endemic settings. In such settings, highly sensitive diagnostics are needed to detect STH infection. We compared double-slide Kato-Katz, the most commonly used copromicroscopic detection method, to multi-parallel quantitative polymerase cha...
Background
Proper collection and storage of fecal samples is necessary to guarantee the subsequent reliability of DNA-based soil-transmitted helminth diagnostic procedures. Previous research has examined various methods to preserve fecal samples for subsequent microscopic analysis or for subsequent determination of overall DNA yields obtained follo...
Analysis of deviance table for GLM at -20°C.
This table shows that there was no significant effect on the integrity of the samples over time (F = 0.079, p = 0.780) for those samples stored at -20°C.
(XLSX)
Coefficients from the GLM along with their standard errors (SE) at 32°C.
The first column shows the method of preservation employed (indexed by j). In the second column, the value in the first row is exp(α0) and the values in all subsequent rows are exp(α1j). These are exponentiated coefficients associated with each treatment upon initial applicati...
Average Cq values from quantitative real-time PCR testing for IAC and N. americanus.
Note that only a small subset of the samples underwent preliminary testing before determining that an additional purification step was required. For potassium dichromate, Cq values were significantly improved after the purification step, whereas for other preservat...
Mean Cq values from the quantitative real-time PCR testing of all N. americanus biological replicates (n = 9) for each preservative, temperature and time point (total n = 628).
(XLSX)
Analysis of deviance table for GLM at 4°C.
At 4°C we fit the full model specified in Eq 1. The marginal significance of the interaction term (F = 1.825; p = 0.083) suggests that there is only weak evidence that these methods differ in their preservation ability over time. That is, at 4°C, the differences in Cq are attributable to the application of...
Background:
Molecular-based surveys have indicated that Ancylostoma ceylanicum, a zoonotic hookworm, is likely the second most prevalent hookworm species infecting humans in Asia. Most current PCR-based diagnostic options for the detection of Ancylostoma species target the Internal Transcribed Spacer (ITS) regions of the ribosomal gene cluster. Th...
Ancylostoma spp. determination on field samples from Orán, Argentina using semi-nested PCR-RFLP analysis.
The testing was performed in the same manner as described in Fig 1 (main manuscript). The banding pattern demonstrates the presence of A. duodenale in these samples and validates the negative results from the newly described real-time PCR assay...
Ancylostoma spp. mixed infections and average Ct values from real-time PCR testing for A. ceylanicum.
(XLSX)
Average Ct values from real-time PCR testing for A. duodenale and A. ceylanicum with samples from Orán, Argentina.
DNA extracts from Orán, Argentina, were tested from two separate laboratories (Baylor College of Medicine (BCM), USA and Smith College, USA) in duplicate using real-time PCR assays specific for A. duodenale and A. ceylanicum. The avera...
Average Ct values from real-time PCR testing for A. duodenale and A. ceylanicum with samples from Timor-Leste.
DNA extracts from Timor-Leste were tested from two separate laboratories (QIMR, Australia and Smith College, USA) in duplicate using real-time PCR assays specific for Ancylostoma duodenale and Ancylostoma ceylanicum. The average Ct values...
A sequestered germline in Metazoa has been argued to be an obstacle to lateral gene transfer (LGT), though few studies have specifically assessed this claim. Here we test the hypothesis that the origin of a sequestered germline reduced LGT events in Bilateria (i.e. triploblast lineages) as compared to early-diverging Metazoa (i.e. Ctenophora, Cnida...
Background
The soil transmitted helminths are a group of parasitic worms responsible for extensive morbidity in many of the world’s most economically depressed locations. With growing emphasis on disease mapping and eradication, the availability of accurate and cost-effective diagnostic measures is of paramount importance to global control and elim...
Comparative assay results for patient-obtained sample from Timor-Leste.
All samples were tested in duplicate utilizing both real-time PCR assays (QIMR and Smith) and results are provided as mean Ct values.
(XLSX)
This study reveals extensive phenotypic convergence based on the non-monophyly of genera and morphospecies of testate (shelled) amoebae. Using two independent markers, small subunit ribosomal DNA (ssu-rDNA) and mitochondrial cytochrome oxidase I (COI), we demonstrate discordance between morphology and molecules for 'core Nebela' species (Arcellinid...
Most eukaryotic lineages are microbial, and many have only recently been sampled for phylogenetic studies or remain in the "dark area" of the tree of life where there are no molecular data. To assess relationships among eukaryotic lineages, we perform a taxon-rich phylogenomic analysis including 232 eukaryotes selected to maximize taxonomic diversi...
The isolate ATCC® 50979™ is a small amoebozoan whose actin gene was previously characterized, but did not allow a stable phylogenetic placement. This isolate was originally mis-identified upon deposition, and subsequently mis-illustrated in a recent publication. Here, we provide both a detailed morphological description as well as additional molecu...
Lateral gene transfer (LGT) has impacted the evolutionary history of eukaryotes, though to a lesser extent than in bacteria
and archaea. Detecting LGT and distinguishing it from single gene tree artifacts is difficult, particularly when considering
very ancient events (i.e., over hundreds of millions of years). Here, we use two independent lines of...
Background
Understanding the evolutionary relationships of all eukaryotes on Earth remains a paramount goal of modern biology, yet analyzing homologous sequences across 1.8 billion years of eukaryotic evolution is challenging. Many existing tools for identifying gene orthologs are inadequate when working with heterogeneous rates of evolution and en...
We initiate in silico rigidity-theoretical studies of biological assemblies and small crystals for protein structures. The goal is to determine if, and how, the interactions among neighboring cells and subchains affect the flexibility of a molecule in its crystallized state. We use experimental X-ray crystallography data from the Protein Data Bank...
Background: Characterizing genome-scale data from diverse eukaryotes is essential for gene discovery and for inferring major transitions across the eukaryotic tree of life. Yet, the bulk of eukaryotic diversity remains undersampled, particularly for free-living microbial lineages. Analysis of transcriptome data generated from high throughput (e.g....
Genomic content varies over the course of the life cycle in many lineages across the eukaryotic tree of life. Such variation is thought to be widespread in Foraminifera, a microbial lineage within the Rhizaria, as complex nuclear dynamics have been observed in the life cycle of diverse species. Perhaps the most striking example is the elimination o...
The first analyses of gene sequence data indicated that the eukaryotic tree of life consisted of a long stem of microbial
groups “topped” by a crown-containing plants, animals, and fungi and their microbial relatives. Although more recent multigene
concatenated analyses have refined the relationships among the many branches of eukaryotes, the root...
We initiate in silico rigidity-theoretical studies of protein crystal structures, with the goal to determine if, and how, the interactions among neighboring crystal cells affect the flexibility of biological unit. We use an efficient graph-based algorithm for rigidity analysis, and other tools available through the KINARI-Web server developed in ou...
We describe the amoeboid isolate ATCC© 50593™ as a new taxon, Telaepolella tubasferens n. g. n. sp. This multinucleated amoeba has filose pseudopods and is superficially similar to members of the vampyrellids (Rhizaria) such as Arachnula impatiens Cien-kowski, 1876, which was the original identification upon deposition. However, previous multigene...
Diagrams of all 18 reconstructions performed.
(PDF)
Leaf Stability values obtained for each taxon in each different reconstruction. Taxa are ranked by their average Leaf Stability.
(XLS)
A summary of previously proposed relationships between the Amoebozoa.
(TIF)
Root to tip branch lengths for each taxon in each reconstruction. Taxa are ordered from shorter to longer average branch lengths.
(XLS)
List of organisms, abbreviations and accession numbers for SSU-rDNA and actin genes used in concatenated analyses. Each organism is specified as to wheater it was included or not in a particular set of analyses with an x.
(XLS)
Evolutionary relationships within Amoebozoa have been the subject of controversy for two reasons: 1) paucity of morphological characters in traditional surveys and 2) haphazard taxonomic sampling in modern molecular reconstructions. These along with other factors have prevented the erection of a definitive system that resolves confidently both high...
An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations underlying the diversity of microbial and macroscopic (e.g., plants and animals) eukaryotes. Previous work has divided eukaryotic diversity into a small number of high-level "supergroups," many of which receive strong support in phylogenomic analyses....
Six eukaryotic supergroups have been proposed based on both morphological and molecular data. However, some of these supergroups are contentious and the deep relationships among them are poorly resolved. This is due to a limited number of morphological characters and few molecular markers in current use. The lack of resolution in most multigene ana...
Our knowledge of the diversity of amoeboid protists is rapidly expanding as new and old habitats are more fully explored. In 2003, while investigating the cause of an amoeboid disease afflicting lobsters on the East Coast, samples were examined for the presence of amoebae from the carapace washings of the American lobster, Homarus americanus. Durin...
The colorless amoeboid eukaryote genus Leukarachnion represents one of a long list of microbial lineages for which there have been few taxonomic studies. In this study, we analyze molecular data to assess the placement of a species of Leukarachnion on the eukaryotic tree of life and we report fine structural data to provide additional information o...
Placing amoeboid lineages on the eukaryotic tree of life is difficult due to the paucity of comparable morphological characters and the limited molecular data available for many groups. This situation has led to the lumping of distantly related lineages into large inclusive groups, such as Sarcodina, that do not reflect evolutionary relationships....
Our understanding of the eukaryotic tree of life and the tremendous diversity of microbial eukaryotes is in flux as additional genes and diverse taxa are sampled for molecular analyses. Despite instability in many analyses, there is an increasing trend to classify eukaryotic diversity into six major supergroups: the 'Amoebozoa', 'Chromalveolata', '...
Figure 8. Likelihood analysis of the 92-taxon data set of SSU-rDNA + nucleotide sequences of actin, alpha-tubulin and beta-tubulin performed with RaxML. See text and Figure 2 for additional notes.
Figure 4. Likelihood analysis of the 105-taxon data set of SSU-rDNA + nucleotide sequences of actin, alpha-tubulin and beta-tubulin performed with RaxML. See text and Figure 2 for additional notes.
Figure 5. Bayesian analyses of the 105-taxon data set of SSU-rDNA + nucleotide sequences of actin, alpha-tubulin and beta-tubulin performed with MrBayes. See text and Figure 2 for additional notes.
Figure 12. Bayesian analysis of 93 actin amino acid sequences that are in the 105 multigene taxon analysis, performed with MrBayes. See text and Figure 2 for additional notes.
Figure 13. Bayesian analysis of 96 alpha-tubulin amino acid sequences that are in the 105 multigene taxon analysis, performed with MrBayes. See text and Figure 2 for additional notes.
Table 1. Table of taxa sampled and sources of genes.
Figure 6. Bayesian analyses of the 105-taxon data set of amino acid sequences of actin, alpha-tubulin and beta-tubulin performed with MrBayes. See text and Figure 2 for additional notes.
Figure 7. Likelihood analysis of the 105-taxon data set of amino acid sequences of actin, alpha-tubulin and beta-tubulin performed with PhyML. See text and Figure 2 for additional notes.
Figure 9. Bayesian analyses of the 92-taxon data set of SSU-rDNA + nucleotide sequences of actin, alpha-tubulin and beta-tubulin performed with MrBayes. See text and Figure 2 for additional notes.
Figure 10. Bayesian analyses of the 92-taxon data set of amino acid sequences of actin, alpha-tubulin and beta-tubulin performed with MrBayes. See text and Figure 2 for additional notes.
Figure 11. Likelihood analysis of the 92-taxon data set of amino acid sequences of actin, alpha-tubulin and beta-tubulin performed with PhyML. See text and Figure 2 for additional notes.
Figure 14. Bayesian analysis of 98 beta-tubulin amino acid sequences that are in the 105 multigene taxon analysis, performed with MrBayes. See text and Figure 2 for additional notes.
We combine a morphological description with a multigene analysis to assess the phylogenetic placement of a poorly known amoeboid taxon Corallomyxa within the eukaryotic tree of life. A detailed morphological analysis including transmission electron microscopy and light microscopy of Corallomyxa sp. ATCC s 50975 TM demonstrates that this isolate is...
We combine a morphological description with a multigene analysis to assess the phylogenetic placement of a poorly known amoeboid taxon Corallomyxa within the eukaryotic tree of life. A detailed morphological analysis including transmission electron microscopy and light microscopy of Corallomyxa sp. ATCC((R)) 50975trade mark demonstrates that this i...
Questions
Questions (2)
Hi all,
I am trying to design a qPCR test to distinguish between closely related sequences. I have some regions that vary between the taxa I am trying to identify but they are still ~75-85% identical over the length of the primer regions. Does anyone have experience that would let them say whether I am likely to amplify my taxon of interest and not its close relatives with sequences so similar?
Cheers,
Jessica
I have three (or possibly four) time points. How many replicates from each time point is sufficient and how many reads should I aim for per sample?
I am looking at sequencing the V4 region of 16S and some centers offer a reasonably priced service (around $50/sample) but only guarantee ~10,000 reads/sample. My pilot project was sequenced on a miseq 2x150 and cost well over $1500 for 6 samples with between 0.5 - 1M reads per sample. Can I get away with fewer reads if I can then afford more replicates?
