Tsvetan R Bachvaroff's research while affiliated with University of Maryland Center for Environmental Science and other places
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Publications (80)
Dinoflagellates are unicellular organisms that are implicated in harmful algal blooms (HABs) caused by potent toxins that are produced through polyketide synthase (PKS) pathways. However, the exact mechanisms of toxin synthesis are unknown due to a lack of genomic segregation of fat, toxins, and other PKS-based pathways. To better understand the un...
Dinoflagellates play important roles in ecosystems as primary producers and consumers making natural products that can benefit or harm environmental and human health but are also potential therapeutics with unique chemistries. Annotations of dinoflagellate genes have been hampered by large genomes with many gene copies that reduce the reliability o...
Eyestalk-derived neuropeptides, primarily the crustacean hyperglycemic hormone (CHH) neuropeptide family, regulate vitellogenesis in decapod crustaceans. The red deep-sea crab, Chaceon quinquedens, a cold-water species inhabiting depths between 200 and 1800 meters, has supported a small fishery, mainly harvesting adult males in the eastern US for o...
Many marine sponges harbor dense communities of microbes that aid in the chemical defense of these nonmotile hosts. Metabolites that comprise this chemical arsenal can have pharmaceutically-relevant activities such as antibacterial, antiviral, antifungal and anticancer properties. Previous investigation of the Caribbean giant barrel sponge Xestospo...
Photosynthetic dinoflagellates synthesize many toxic but also potential therapeutic compounds therapeutics via polyketide/non-ribosomal peptide synthesis, a common means of producing natural products in bacteria and fungi. Although canonical genes are identifiable in dinoflagellate transcriptomes, the biosynthetic pathways are obfuscated by high co...
Harvesting the adult male Jonah crab, Cancer borealis, mainly based on the size, has become an economically significant fishery, particularly in the Southern New England region of the US since 2000. Many decapod crustacean fisheries including C. borealis rely on harvesting adult males. Understanding the size related-sexual maturity and the seasonal...
The crustacean molting process is regulated by an interplay of hormones produced by the eyestalk ganglia and Y-organs (YO). Molt-inhibiting hormone and crustacean hyperglycemic hormone released by the sinus gland of the eyestalk ganglia (EG) inhibit the synthesis and secretion of ecdysteroid by the YO, hence regulating hemolymph levels during the m...
Many dinoflagellate species make toxins in a myriad of different molecular configurations but the underlying chemistry in all cases is presumably via modular synthases, primarily polyketide synthases. In many organisms modular synthases occur as discrete synthetic genes or domains within a gene that act in coordination thus forming a module that pr...
The blue crab, Callinectes sapidus (Rathbun, 1896) is an economically, culturally, and ecologically important species found across the temperate and tropical North and South American Atlantic coast. A reference genome will enable research for this high-value species. Initial assembly combined 200x coverage Illumina paired-end reads, a 60x 8 kb mate...
Due to the increasing prevalence of Dinophysis spp. and their toxins on every US coast in recent years, the need to identify and monitor for problematic Dinophysis populations has become apparent. Here we present morphological analyses, using light and scanning electron microscopy, and rDNA sequence analysis, using a ~2 kb sequence of ribosomal ITS...
Background:
Antioxidative enzymes contribute to a parasite's ability to counteract the host's intracellular killing mechanisms. The facultative intracellular oyster parasite, Perkinsus marinus, a sister taxon to dinoflagellates and apicomplexans, is responsible for mortalities of oysters along the Atlantic coast of North America. Parasite trophozo...
Marine actinomycetes (order Actinomycetales ) are of interest as a promising source of pharmaceuticals. The genomes of three novel sponge-associated actinomycetes exhibiting antimycobacterial activity, Brevibacterium sp. strain XM4083, Micrococcus sp. strain R8502A1, and Micromonospora sp. strain XM-20-01, were sequenced in an effort to identify co...
The blue crab Callinectes sapidus reovirus 1 (CsRV1), a double-stranded RNA virus, belongs to the Class III virus family Reoviridae and infects marine invertebrates, including the blue crab C. sapidus. Callinectes sapidus reovirus 1 levels correlate with disease progression, and high levels of infection usually result in death. To understand CsRV1...
In the ocean, dinoflagellates are associated with a microbial community that provides some of their essential nutrients. In the laboratory, most dinoflagellates are cultured in seawater supplemented with nutrients, although little effort has been made to maintain them axenically. This can complicate the study of their physiological processes such a...
Histogram of AT % in Amoebophrya sp. ex Karlodinium veneficum transcriptome data.
(PDF)
Gene ontology terms associated with sequences containing typical stop codons.
(PDF)
Amoebophrya is part of an enigmatic, diverse, and ubiquitous marine alveolate lineage known almost entirely from anonymous environmental sequencing. Two cultured Amoebophrya strains grown on core dinoflagellate hosts were used for transcriptome sequencing. BLASTx using different genetic codes suggests that Amoebophyra sp. ex Karlodinium veneficum u...
Dinoflagellates make up a diverse array of fatty acids and polyketides. A necessary precursor for their synthesis is malonyl-CoA formed by carboxylating acetyl CoA using the enzyme acetyl-CoA carboxylase (ACC). To date, information on dinoflagellate ACC is limited. Through transcriptome analysis in Amphidinium carterae, we found three full-length h...
Assignments of peptides via MS/MS analysis of protein from isolated scintillons of Lingulodinium polyedrum.
Tabs show assignments of proteins from two independent scintillon preparations. Samples shown in ‘MS results 1’ tab were initially treated with 100 ng trypsin at 30°C; those in ‘MS results 2’ tab were initially treated with 100 ng trypsin at...
In 1972, J. Woodland Hastings and colleagues predicted the existence of a proton selective channel (HV1) that opens in response to depolarizing voltage across the vacuole membrane of bioluminescent dinoflagellates and conducts protons into specialized luminescence compartments (scintillons), thereby causing a pH drop that triggers light emission. H...
Sequence of longest open reading frame of contig 26784 in MMETSP1032 assembly, and sequence of codon-optimized gene of LpHV1.
(DOCX)
Alignment of predicted amino acid sequences of putative dinoflagellate HV1s.
Sequences were found by BLAST searches of RNA-seq projects [35,36] and were aligned with MSA-Probs [72]. Dinoflagellate sequences are shown aligned with sequence logos of individual transmembrane helices obtained from an alignment of animal HV1s [12]. The sequence logos ar...
Primers and predicted product sizes for qPCR.
(DOCX)
Fluorescence images from pre-serum or no-antibody control treatments of fixed whole cells.
Cells and images were prepared as for Fig 6.
(TIF)
Fluorescence images from pre-serum or no-antibody control treatments of fixed isolated scintillons.
Scintillons and images were prepared as for Fig 7.
(TIF)
Significance
We created a dataset of dinoflagellate transcriptomes to resolve internal phylogenetic relationships of the group. We show that the dinoflagellate theca originated once, through a process that likely involved changes in the metabolism of cellulose, and suggest that a late origin of dinosterol in the group is at odds with dinoflagellate...
Insulin-like peptides (ILPs) have regulatory roles in reproduction, development and metabolism in invertebrates. The mode of ILP actions has not been well studied in invertebrates in regard to the role of binding partners, i.e., ILP binding protein (ILPBP). In this study, the full-length cDNA of Callinectes sapidus ILPBP (Cas-ILPBP, 960 bp) has bee...
Most eukaryotic mRNAs are translated by a cap-dependent mechanism, which requires recognition of the 5′ cap structure of the mRNA by eIF4E. Due to its crucial role in translation, eIF4E is a major target of regulation. One of the most prominent mechanisms regulating eIF4E activity is through its interaction with numerous proteins termed eIF4E-inter...
Analysis of eIF4E sequences from the more than twenty fish genomes currently available, as well as those of select tetrapods, echinoderm (Strongylocentrotus purpuratus), tunicate (Ciona intestinalis), and cephalocordate (Branchiostoma lanceolatum), has allowed a glimpse of the origins and evolution of the eIF4E and 4E-BP families in vertebrates. Me...
The blue crab, Callinectes sapidus (Rathbun 1896), which is a commercially important trophic link in coastal ecosystems of the western Atlantic, is infected in both North and South America by C. sapidus Reovirus 1 (CsRV1), a double stranded RNA virus. The 12 genome segments of a North American strain of CsRV1 were sequenced using Ion Torrent techno...
Isoprenoid metabolism occupies a central position in the anabolic metabolism of all living cells. In plastid-bearing organisms, two pathways may be present for de novo isoprenoid synthesis, the cytosolic mevalonate pathway (MVA) and nuclear-encoded, plastid-targeted non-mevalonate pathway (DOXP). Using transcriptomic data we find that dinoflagellat...
Dinoflagellates are eukaryotes with unusual cell biology and appear to rely on translational rather than transcriptional control of gene expression. The eukaryotic translation initiation factor 4E (eIF4E) plays an important role in regulating gene expression because eIF4E binding to the mRNA cap is a control point for translation. eIF4E is part of...
Ichthyotoxic Karlodinium veneficum has become a persistent problem in the eutrophic Swan River Estuary (SRE) near Perth, Western Australia. Karlotoxin (KmTx) concentrations and K. veneficum were sampled from March to July 2005, spanning a bloom confirmed by microscopy and genetics (ITS sequence), and a fish kill coincident with end of the bloom. Th...
Galectins are highly conserved lectins that are key to multiple biological functions, including pathogen recognition and regulation of immune responses. We previously reported that CvGal1, a galectin expressed in phagocytic cells (hemocytes) of the eastern oyster (Crassostrea virginica), is "hijacked" by the parasite Perkinsus marinus to enter the...
Galectins constitute a conserved and widely distributed lectin family characterized by their binding affinity for ß-galactosides and a unique binding site sequence motif in the carbohydrate recognition domain (CRD). In spite of their structural conservation, galectins display a remarkable functional diversity, by participating in developmental proc...
Dinoflagellates are unusual eukaryotes with large genomes and a reduced role for transcriptional regulation compared to other eukaryotes. The mRNA in dinoflagellates is trans-spliced with a 5'-spliced-leader sequence, yielding a 22-nucleotide 5'-sequence with a methylated nucleotide cap. Since the control of gene expression is primarily post-transc...
Metagenomic methods provide a powerful means to investigate complex ecological phenomena. Developed originally for study of Bacteria and Archaea, the application of these methods to eukaryotic microorganisms is yet to be fully realized. Most prior environmental molecular studies of eukaryotes have relied heavily on PCR amplification with eukaryote-...
Bacillus sp. strain RP1137 is a bacterium that is able to rapidly and efficiently aggregate biofuel-producing microalgae. By 16S rRNA
gene sequencing, it was found to be related to the industrially important Bacillus megaterium. Here, we report the draft genome sequence of Bacillus sp. strain RP1137.
Bacillus sp. strain RP1137 is a bacterium that is able to rapidly and efficiently aggregate biofuel-producing microalgae. By 16S rRNA gene sequencing, it was found to be related to the industrially important Bacillus megaterium. Here, we report the draft genome sequence of Bacillus sp. strain RP1137.
Background
The genetic element s2m seems to represent one of very few examples of mobile genetic elements in viruses. The function remains obscure and a scattered taxonomical distribution has been reported by numerous groups.
Methods
We have searched GenBank in order to identify all viral accessions that have s2m(−like) sequence motifs. Rigorous p...
The greatest diversity of eukaryotic species is within the microbial eukaryotes, the protists, with plants and fungi/metazoa representing just two of the estimated seventy five lineages of eukaryotes. Protists are a diverse group characterized by unusual genome features and a wide range of genome sizes from 8.2 Mb in the apicomplexan parasite
Babes...
The greatest diversity of eukaryotic species is within the microbial eukaryotes, the protists, with plants and fungi/metazoa representing just two of the estimated seventy five lineages of eukaryotes. Protists are a diverse group characterized by unusual genome features and a wide range of genome sizes from 8.2 Mb in the apicomplexan parasite Babes...
Tab-delimited text file containing annotation and summary data for the 160 orthologs used in the phylogenetic analysis.
(TXT)
Concaterpillar ML trees derived from compatible partitions of the multigene alignment. Set numbers were determined by Concaterpillar and are listed in the figure by descending size.
(TIF)
The tremendous diversity of land plants all descended from a single charophyte green alga that colonized the land somewhere between 430 and 470 million years ago. Six orders of charophyte green algae, in addition to embryophytes, comprise the Streptophyta s.l. Previous studies have focused on reconstructing the phylogeny of organisms tied to this k...
Recent recognition that tintinnids are infected by dinophycean as well as syndinean parasites prompts taxonomic revision of dinoflagellate species that parasitize these ciliates. Long overlooked features of the type species Duboscquella tintinnicola are used to emend the genus and family Duboscquellidae, resulting in both taxa being moved from the...
The genus Euduboscquella is one of a few described genera within the syndinean dinoflagellates, an enigmatic lineage with abundant diversity in marine
environmental clone libraries based on small subunit (SSU) rRNA. The region composed of the SSU through to the partial large
subunit (LSU) rRNA was determined from 40 individual tintinnid ciliate lor...
Dinoflagellates and apicomplexans are a strongly supported monophyletic group in rDNA phylogenies, although this phylogeny is not without controversy, particularly between the two groups. Here we use concatenated protein-coding genes from expressed sequence tags or genomic data to construct phylogenies including "typical" dinophycean dinoflagellate...
Dinoflagellates have unique nuclei and intriguing genome characteristics with very high DNA content making complete genome sequencing difficult. In dinoflagellates, many genes are found in multicopy gene families, but the processes involved in the establishment and maintenance of these gene families are poorly understood. Understanding the dynamics...
The dinoflagellate Tintinnophagus acutus n. g., n. sp., an ectoparasite of the ciliate Tintinnopsis cylindrica Daday, superficially resembles Duboscquodinium collini Grassé, a parasite of Eutintinnus fraknoii Daday. Dinospores of T. acutus are small transparent cells having a sharply pointed episome, conspicuous eyespot, posteriorly positioned nucl...
Parasitic dinoflagellates of the genus Amoebophrya play important roles in the ecology of estuaries and open ocean environments. Little is known of the cell and molecular biology of Amoebophrya, but the genus is intermediate on phylogenetic trees between apicomplexans and typical dinophycean dinoflagellates. Here, we constructed four cDNA libraries...
Dinoflagellates are a highly diverse and environmentally important group of protists with relatively poor resolution of phylogenetic relationships, particularly among heterotrophic species. We examined the phylogeny of several dinophysiacean dinoflagellates using samples collected from four Atlantic sites. As a rule, 3.5 kb of sequence including th...
Athecate, pseudocolony-forming dinoflagellates have been classified within two genera of polykrikoids, Polykrikos and Pheopolykrikos, and different views about the boundaries and composition of these genera have been expressed in the literature. The photosynthetic polykrikoid Pheopolykrikos hartmannii, for instance, was originally described within...
LSU rDNA phylogeny. Gamma-corrected maximum likelihood tree (-lnL = 4115.21736, α = 0.742, 4 rate categories) inferred using the GTR model of substitution on an alignment of 47 LSU rDNA sequences and 358 unambiguously aligned sites. Numbers at the branches denote bootstrap percentages using maximum likelihood – GTR (top) and Bayesian posterior prob...
Concatenated SSU and LSU rDNA phylogeny. Gamma-corrected maximum likelihood tree (-lnL = 10274.67788, α = 0.496, 4 rate categories) inferred using the GTR model of substitution on an alignment of 17 combined SSU and LSU rDNA sequences and 2549 unambiguously aligned sites. Numbers at the branches denote bootstrap percentages using maximum likelihood...
We examined the influence of N or P depletion, alternate N- or P-sources, salinity, and temperature on karlotoxin (KmTx) production in strains of Karlodinium veneficum (D. Ballant.) J. Larsen, an ichthyotoxic dinoflagellate that shows a high degree of variability of toxicity in situ. The six strains examined represented KmTx 1 (CCMP 1974, MD 2) and...
Karlodinium veneficum (D. Ballant.) J. Larsen strains, 16 from the U.S. Atlantic eastern seaboard and two from New Zealand (CAWD66 and CAWD83), were used to characterize toxin profiles during batch culture. All 18 strains were determined as the same species based on ITS sequence analyses, a positive signal in a chloroplast real-time PCR assay and p...
Dinoflagellates represent a major lineage of unicellular eukaryotes with unparalleled diversity and complexity in morphological features. The monophyly of dinoflagellates has been convincingly demonstrated, but the interrelationships among dinoflagellate lineages still remain largely unresolved. Warnowiid dinoflagellates are among the most remarkab...
Karlodinium veneficum is a common member of the phytoplankton in coastal ecosystems, usually present at relatively low cell abundance (102 to 103 mL−1), but capable of forming blooms of 104 to 105 cells mL−1 under appropriate conditions. We present evidence consistent with the hypothesis that prey abundance, particularly the abundance of nano-plank...
Dinoflagellate genomes present unique challenges including large size, modified DNA bases, lack of nucleosomes, and condensed chromosomes. EST sequencing has shown that many genes are found as many slightly different variants implying that many copies are present in the genome. As a preliminary survey of the genome our goal was to obtain genomic se...
Karlodinium veneficum is a cosmopolitan dinoflagellate with a worldwide distribution in mesohaline temperate waters. The toxins from K. veneficum, or karlotoxins (KmTxs), which have been implicated in fish kill events, have been purified from monoalgal cultures, and shown to possess hemolytic, cytotoxic and ichthyotoxic activities. Three karlotoxin...
The parasitic dinoflagellate Amoebophrya sp. ex Karlodinium veneficum was used to test two hypotheses: (1) infection of cells decreases with increasing host toxicity and (2) parasitism causes the catabolism of host toxin. To test the first hypothesis, host strains differing in toxin content were inoculated with dinospores of Amoebophrya sp. derived...
Photosynthetic eukaryotes contain primary, secondary or tertiary plastids, depending on the source of the organelle (a cyanobacterium or a photosynthetic eukaryote). Plastid phylogeny is relatively well investigated, but molecular phylogenies have conflicted as a function of gene choice, taxon-representations, and analytical method. To better under...
Karlodinium veneficum is a common member of temperate, coastal phytoplankton assemblages that occasionally forms blooms associated with fish kills. Here, we tested the hypothesis that the cytotoxic and ichthyotoxic compounds produced by K. veneficum, karlotoxins, can have anti-grazing properties against the heterotrophic dinoflagellate, Oxyrrhis ma...
Serial transfer of plastids from one eukaryotic host to another is the key process involved in evolution of secondhand plastids. Such transfers drastically change the environment of the plastids and hence the selection regimes, presumably leading to changes over time in the characteristics of plastid gene evolution and to misleading phylogenetic in...
Peridinin-pigmented dinoflagellates contain secondary plastids that seem to have undergone more nearly complete plastid genome reduction than other eukaryotes. Many typically plastid-encoded genes appear to have been transferred to the nucleus, with a few remaining genes found on minicircles. To understand better the evolution of the dinoflagellate...
The chlorophyll c-containing algae comprise four major lineages: dinoflagellates, haptophytes, heterokonts, and cryptophytes. These four lineages have sometimes been grouped together based on their pigmentation, but cytological and rRNA data had suggested that they were not a monophyletic lineage. Some molecular data support monophyly of the plasti...
The complete nucleotide sequence of the plastid genome of the haptophyte Emiliania huxleyi has been determined. E. huxleyi is the most abundant coccolithophorid and has a key role in the carbon cycle. It is also implicated in the production of dimethylsulphide (DMS), which is involved in cloud nucleation and may affect the global climate. Here, we...
The complete nucleotide sequence of the mitochondrial genome of Emiliania huxleyi (Haptophyta) was determined. E. huxleyi is the most abundant coccolithophorid, key in many marine ecosystems, and plays a vital role in the global carbon cycle.
The mitochondrial genome contains genes encoding three subunits of cytochrome c oxidase, apocytochrome b, s...
The peridinin-pigmented plastids of dinoflagellates are very poorly understood, in part because of the paucity of molecular data available from these endosymbiotic organelles. To identify additional gene sequences that would carry information about the biology of the peridinin-type dinoflagellate plastid and its evolutionary history, an analysis wa...
The complete nucleotide sequence of the mitochondrial genome of Emiliania huxleyi (Haptophyta) was determined. E. huxleyi is the most abundant coccolithophorid, key in many marine ecosystems, and plays a vital role in the global carbon cycle. The mitochondrial genome contains genes encoding three subunits of cytochrome c oxidase, apocytochrome b, s...
Citations
... One multi-modular PKS termed the "Triple KS" for its three apparent ketosynthase modules and first described by Williams et al., is of particular interest in that it is ubiquitously present in dinoflagellate transcriptomes, indicating a core function [13,22]. Although the genes for classic lipid synthesis have been described elsewhere [23], other common processes that could be mediated by PKSs include PUFA synthesis and the "hairpin" structure that is found in many toxins across a wide range of Dinoflagellate species (Figure In addition to PKSs, non-ribosomal peptide synthetases (NRPS) and NRPS/PKS hybrids are also present in dinoflagellates [13]. ...
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... Approximately 70-72 % of reads map to a bacterial genome. All the genomic data that were obtained from the sequencing were assembled by using the K-mer size 55 de-Bruijin graph method [53], in which the set of DNA sequences can be analyzed using many popular algorithms such as Allpaths-LG3 and Abyss39. The graph has K-mers that can join the nodes. ...
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