A5040542011- Insect symbiosis and bacterial influences
- Genomics and Phylogenetic Studies
- Parasitic Diseases Research and Treatment
- Plant Pathogenic Bacteria Studies
- Phytoplasmas and Hemiptera pathogens
- RNA and protein synthesis mechanisms
- Cocoa and Sweet Potato Agronomy
- RNA modifications and cancer
- Protist diversity and phylogeny
- Studies on Chitinases and Chitosanases
- CRISPR and Genetic Engineering
- Cancer-related molecular mechanisms research
- Plant Virus Research Studies
- Nematode management and characterization studies
- Environmental DNA in Biodiversity Studies
- Insect-Plant Interactions and Control
- Legume Nitrogen Fixing Symbiosis
- Plant Parasitism and Resistance
- Spaceflight effects on biology
- RNA Research and Splicing
- Insect Resistance and Genetics
- Reflective Practices in Education
- Health, Environment, Cognitive Aging
- Bacterial Genetics and Biotechnology
- Cancer Mechanisms and Therapy
University of Maryland, Baltimore
2014-2025
Human Genome Sciences (United States)
2021-2023
University of California, Riverside
2010-2014
University of Houston - Downtown
2010
Using a modified multilocus sequence typing (MLST) scheme for the bacterial plant pathogen Xylella fastidiosa based on same seven housekeeping genes employed in previously published MLST, we studied genetic diversity of two subspecies, X. subsp. and sandyi, which cause Pierce's disease oleander leaf scorch, respectively. Typing 85 U.S. isolates (plus one from northern Mexico) 15 different hosts 21 sandyi 4 California Texas supported their subspecific status. Analysis using MLST plus...
ABSTRACT Homologous recombination plays an important role in the structuring of genetic variation many bacteria; however, its importance adaptive evolution is not well established. We investigated association intersubspecific homologous (IHR) with shift to a novel host (mulberry) by plant-pathogenic bacterium Xylella fastidiosa . Mulberry leaf scorch was identified about 25 years ago native red mulberry eastern United States and has spread introduced white California. Comparing sequence 8...
Invasive diseases present an increasing problem worldwide; however, genomic techniques are now available to investigate the timing and geographical origin of such introductions. We employed demonstrate that bacterial pathogen causing Pierce's disease grapevine (PD) is not native US as previously assumed, but descended from a single genotype introduced Central America. PD has posed serious threat wine industry ever since its first outbreak in Anaheim, California 1880s continues inhibit grape...
ABSTRACT The bacterial pathogen, Xylella fastidiosa , infects many plant species in the Americas, making it a good model for investigating genetics of host adaptation. We used multilocus sequence typing (MLST) to identify isolates native U.S. subsp. multiplex that were largely unaffected by intersubspecific homologous recombination (IHR) and investigate how their evolutionary history influences specialization. identified 110 “non-IHR” isolates, 2 minimally recombinant “intermediate” ones...
Documenting the role of novel mutation versus homologous recombination in bacterial evolution, and especially invasion new hosts, is central to understanding long-term dynamics pathogenic bacteria. We used multilocus sequence typing (MLST) study this issue Xylella fastidiosa subsp. pauca from Brazil, a bacterium causing citrus variegated chlorosis (CVC) coffee leaf scorch (CLS). All 55 isolates typed (plus one isolate) defined three similar types (STs) dominated by ST11 (85%), while...
Abstract The newest generation of DNA sequencing technology is highlighted by the ability to generate sequence reads hundreds kilobases in length. Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving throughput per-base accuracy. We used whole-genome data produced three PacBio protocols (Sequel II CLR, Sequel HiFi, RS II) two ONT (Rapid Sequencing Ligation Sequencing) compare assemblies...
Lateral gene transfer (LGT) from bacterial Wolbachia endosymbionts has been detected in ~20% of arthropod and nematode genome sequencing projects. Many these transfers are large contain a substantial part the genome.Here, we re-sequenced three D. ananassae genomes Asia Pacific that LGTs Wolbachia. We find multiple copies transferred to Drosophila nuclear all lines. In line Indonesia, DNA nearly identical size sequence yielding an even coverage mapped reads over genome. contrast, lines Hawaii...
ABSTRACT Oxford Nanopore Technologies provides multiplexing options for DNA and cDNA sequencing, but not direct RNA sequencing. Here we describe a duplexing approach validate it by simultaneously sequencing the Saccharomyces cerevisiae rRNA from wild type knockout that have differential modifications, successfully demultiplexing data using bioinformatics approaches.
The life cycle of Plasmodium falciparum is characterized by complex regulatory changes that allow adaptation the parasites to different environmental conditions, which are especially pronounced during transmission between mammalian host and insect vector. Previous studies have shown P. uses three types ribosomal RNAs (rRNA A-, S1- S2-types) at stages its cycle. We used Oxford Nanopore Technologies (ONT) direct RNA sequencing investigate dynamics rRNA usage throughout parasite's...
Abstract Enrichment methodologies enable the analysis of minor members in multi-species transcriptomic data. We compared standard enrichment bacterial and eukaryotic mRNA to a targeted using an Agilent SureSelect (AgSS) capture for Brugia malayi , Aspergillus fumigatus Wolbachia endosymbiont B. ( w Bm). Without introducing significant systematic bias, AgSS quantitatively enriched samples, resulting more reads mapping target organism. The AgSS-enriched libraries consistently had positive...
Eukaryotic genomes can acquire bacterial DNA via lateral gene transfer (LGT).1 A prominent source of LGT is Wolbachia,2 a widespread endosymbiont arthropods and nematodes that transmitted maternally through female germline cells.3,4 The from the Wolbachia wAna to Drosophila ananassae extensive5-7 has been localized chromosome 4, contributing expansion in this lineage.6 As happened frequently with claims bacteria-to-eukaryote LGT, contribution transfers expanded size D. 4 specifically...
Here, we present a comprehensive transcriptomics data set of Brugia malayi , its Wolbachia endosymbiont w Bm, and vector host. This study samples from 16 stages across the entire B. life cycle, including stage 1 through 4 larvae, adult males females, embryos, immature microfilariae, mature microfilariae.
To better understand the transcriptomic interplay of organisms associated with lymphatic filariasis, we conducted multispecies transcriptome sequencing (RNA-Seq) on filarial nematode Brugia malayi, its Wolbachia endosymbiont wBm, and laboratory vector Aedes aegypti across entire B. malayi life cycle. In transcription noncoding 6S RNA suggests that it may be a regulator bacterial cell growth, as transcript levels correlate replication rates. For A. aegypti, transcriptional response reflects...
The 13,647-bp complete mitochondrial genome of Mansonella perstans was sequenced and is syntenic to the ozzardi . Phylogenetic analysis consistent with known phylogeny ONC5 group filarial nematodes.
Introduction Host gene and protein expression impact susceptibility to clinical malaria, but the balance of immune cell populations, cytokines genes that contributes protection, remains incompletely understood. Little is known about determinants host malaria at a time when acquired immunity developing. Methods We analyzed peripheral blood mononuclear cells (PBMCs) collected from children who differed in all small town Mali. PBMCs were aged 4-6 years start, peak end season. characterized...
Here, we present the complete genome sequence of Wolbachia endosymbiont wAna, isolated from Drosophila ananassae and derived Oxford Nanopore Illumina sequencing. We anticipate that this will aid in comparative genomics assembly D. specifically regions containing extensive lateral gene transfer events.
Brugia pahangi is a zoonotic parasite that closely related to human-infecting filarial nematodes. Here, we report the nearly complete genome of pahangi, including assemblies four autosomes and an X chromosome, with only seven gaps. The Y chromosome still not completely assembled.
Lymphatic filariasis is a devastating disease caused by filarial nematode roundworms, which contain obligate
// Mario Scarpa 1 , 2 Shivani Kapoor Eric S. Tvedte 3 Kshama A. Doshi Ying Zou 4 Prerna Singh Jonelle K. Lee Aditi Chatterjee Moaath Mustafa Ali Robin E. Bromley Julie C. Dunning Hotopp 5 Feyruz V. Rassool 6 and Maria R. Baer 7 University of Maryland Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA Department Medicine, School Institute for Genome Sciences, Pathology, Microbiology Immunology, Radiation Oncology, Veterans Affairs Medical Correspondence to: Baer, email: mbaer@umm.edu...
ABSTRACT RNA modifications, such as methylation, can be detected with Oxford Nanopore Technologies direct sequencing. One commonly used tool for detecting 5-methylcytosine (m 5 C) modifications is Tombo, which uses an “Alternative Model” to detect putative from a single sample. We examined sequencing data diverse taxa including virus, bacteria, fungi, and animals. The algorithm consistently identified at the central position of GCU motif. However, it also in same motif fully unmodified vitro...
Transcripts are potential therapeutic targets, yet bacterial transcripts remain biological dark matter with uncharacterized biodiversity. We developed and applied an algorithm to predict for Escherichia coli K12 E2348/69 strains (Bacteria:gamma-Proteobacteria) newly generated ONT direct RNA sequencing data while predicting Listeria monocytogenes Scott A RO15 (Bacteria:Firmicute), Pseudomonas aeruginosa SG17M NN2 (Bacteria:gamma-Proteobacteria), Haloferax volcanii (Archaea:Halobacteria) using...
RNA transcripts are potential therapeutic targets, yet bacterial have uncharacterized biodiversity. We developed an algorithm for transcript prediction called tp.py using it to predict (mRNA and other RNAs) in
The sequence diversity of natural and laboratory populations Brugia pahangi malayi was assessed with Illumina resequencing followed by mapping in order to identify single nucleotide variants insertions/deletions. In populations, there is a lack on chromosome X relative the autosomes (πX/πA = 0.2), which lower than expected 0.75). A reduction also observed other filarial nematodes neo-X fusions genera Onchocerca Wuchereria, but not those without Loa Dirofilaria. species fusions, abnormally...
Abstract Enrichment methodologies enable analysis of minor members in multi-species transcriptomic analyses. We compared standard enrichment bacterial and eukaryotic mRNA to targeted with Agilent SureSelect (AgSS) capture for Brugia malayi , Aspergillus fumigatus the Wolbachia endosymbiont B. (wBm). Without introducing significant systematic bias, AgSS quantitatively enriched samples, resulting more reads mapping target organism. The AgSS-enriched libraries consistently had a positive linear...