Cheryl D Gleasner

• Research Technologist at Los Alamos National Laboratory

Omics-based measurements enable the study of biomolecules in a high-throughput fashion, leading to the characterization and quantification of biological systems. Multi-omics methods aim to incorporate several omics measurements for a more holistic approach, which is crucial for advancing our understanding of the diversity and redundancy of biologic...

Microalgae are one of the most versatile and promising organisms for biomanufacturing. To expedite research and development, we generated an improved genome assembly and annotation of the highly productive microalga Scenedesmus obliquus UTEX393 . We measured the systems level, multi-omic responses during exposure to 15 ppt (high) vs 5 ppt (low/cont...

Recent advances in sequencing technologies have improved contiguity of de novo genome assemblies. Nevertheless, the genomes of all eukaryotic organisms which are polyploid remain unfinished, limiting understanding of genetic and structural variation in diploid or polyploid organisms. Herein, we report the methodology and analysis of a 100% complete...

Early and accurate diagnosis of respiratory pathogens and associated outbreaks can allow for the control of spread, epidemiological modeling, targeted treatment, and decision making–as is evident with the current COVID-19 pandemic. Many respiratory infections share common symptoms, making them difficult to diagnose using only syndromic presentation...

Microalgae that are of interest for biofuel production must be able to tolerate environmental changes that occur in outdoor cultivation systems. While algal cultures may experience daily temperature fluctuations and seasonal environmental changes, the underlying mechanisms that control and regulate physiological responses and adaptation to environm...

Autophagy is a critical mechanism deployed by eukaryotic cells in response to stress, including viral infection, to boost the innate antimicrobial responses. However, an increasing number of pathogens hijack the autophagic machinery to facilitate their own replication. Influenza A virus (IAV), responsible for several global pandemics, has an intric...

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The discovery of antibiotics such as penicillin and streptomycin marked a historic milestone in the 1940s and heralded a new era of antimicrobial therapy as the modern standard for medical treatment. Yet, even in those early days of discovery, it was noted that a small subset of cells (∼1 in 10 ⁵ ) survived antibiotic treatment and continued to per...

Around the world, scavenging birds such as vultures and condors have been experiencing drastic population declines. Scavenging birds have a distinct digestive process to deal with higher amounts of bacteria in their primary diet of carcasses in varying levels of decay. These observations motivate us to present an analysis of captive and healthy Cal...

Here, we report the sequence of a Staphylococcus pettenkoferi clinical isolate, strain SMA0010-04 (UGA20), which contains the PC1 beta-lactamase ( blaZ ) gene.

Here, we report the genome sequences of a Staphylococcus aureus clinical isolate, strain SMA0034-04 (UGA22), which contains one chromosome and one plasmid. We also reveal that isolate SMA0034-04 (UGA22) contains loci in the genome that encode multiple exotoxins.

We report here the genome sequence of a Staphylococcus xylosus clinical isolate, strain SMA0341-04 (UGA5), which contains one chromosome and at least one plasmid. Notably, strain SMA0341-04 (UGA5) contains the tetracycline efflux major facilitator superfamily (MFS) transporter ( tetK ) gene.

We report the complete draft genome sequences of two Staphylococcus warneri clinical isolates, strains SMA0023-04 (UGA3) and SMA0670-05 (UGA28), each of which contains one chromosome and at least one plasmid. Isolate SMA0023-04 (UGA3) contains tetracycline efflux major facilitator superfamily (MFS) transporter ( tetK ), macrolide resistance ( msrC...

Microbiology can greatly help in the quest for a sustainable solution to the problem of iron corrosion, which causes important economic losses in a wide range of fields, including the protection of cultural heritage and building materials. Using bacteria to transform reactive and unstable corrosion products into more-stable compounds represents a p...

Middle East respiratory syndrome coronavirus (MERS-CoV) is a virus that affects the respiratory system of patients. Since the virus’s first discovery in 2012, there have been a total of 1733 laboratory confirmed cases of MERS-CoV, including 628 deaths. The majority of cases have been linked to countries around the Arabian Peninsula, with the except...

Species within the Neoromicia bat genus are abundant and widely distributed in Africa. It is common for these insectivorous bats to roost in anthropogenic structures in urban regions. Additionally, Neoromicia capensis have previously been identified as potential hosts for Middle East respiratory syndrome (MERS)-related coronaviruses. This study aim...

Virome sequence data information from the Parvoviridae and Papillomaviridae families (with references and figures). (DOCX)

Neoromicia samples pooled for molecular detection of selected viruses. (PDF)

Pairwise similarities inferred from distance estimations of a 605bp conserved segment of the coronavirus RNA dependent RNA polymerase gene. The table shows pairwise sequence similarities inferred from evolutionary divergence estimates of 605 positions of compared coronaviruses. The number of base differences per site from between sequences were con...

CLC Genomics workbench bioinformatics workflow parameters. (PDF)

Alpha- and Betacoronavirus genera hemi-nested RT-PCR primers. (PDF)

Pairwise similarities inferred from distance estimations of an L gene region between selected Bunyavirales. The table shows pairwise sequence similarities inferred from evolutionary divergence estimates of 249 positions of compared Bunyavirales. The number of base differences per site from between sequences were converted to percentage of similarit...

Pairwise similarities inferred from distance estimations of full length genomes of the Circoviridae family. Sequence similarities of viruses in the Circoviridae family inferred from estimated evolutionary divergence calculated from pairwise distances. Full genomes were aligned and trimmed to 1075 overlapping positions. All ambiguous positions were...

Genome annotation of BtCoVNeo5038 with similarities to compared lineage C betacoronaviruses. The percentage similarities were inferred from pairwise distance estimates of the base pair and amino acid differences per site for each gene and of the overall genome. The estimates were calculated in MEGA7 [41] using pairwise deletion to treat gaps. All p...

Neoromicia samples collected to investigate the South African Neoromicia virome. (PDF)

Pairwise similarities inferred from distance estimations between betacoronavirus full genomes. The table shows pairwise similarities inferred from evolutionary divergence estimates of betacoronavirus full genomes. The number of base differences per site between sequences were converted to percentage similarities. Within lineage similarities are ind...

Coronavirus strains and Genbank accession numbers of sequences used in the full genome phylogeny. (PDF)

What is MERS-CoV? Transmission Sequencing and Data Analysis Summary References

We report herein the development, functional and molecular characterization of an isogenic, paired bladder cancer cell culture model system for studying platinum drug resistance. The 5637 human bladder cancer cell line was cultured over ten months with stepwise increases in oxaliplatin concentration to generate a drug resistant 5637R sub cell line....

Differentially expressed known transcripts. (PDF)

Differentially expressed novel transcripts. (TIFF)

Differentially expressed transcripts for 5637 and 5637R cells. (TIFF)

We report here the genome sequence of an effective chromium-reducing bacterium, Bacillus cereus strain S612. The size of the draft genome sequence is approximately 5.4 Mb, with a G+C content of 35%, and it is predicted to contain 5,450 protein-coding genes.

The genome of strain GS3372 is the first publicly available strain of Aeribacillus pallidus. This endospore-forming thermophilic strain was isolated from a deep geothermal reservoir. The availability of this genome can contribute to the clarification of the taxonomy of the closely related Anoxybacillus, Geobacillus, and Aeribacillus genera. Copyrig...

Bacillus alveayuensis strain 24KAM51 was isolated from a marine hydrothermal vent in Milos, Greece. Its genome depicts interesting features of halotolerance and resistance to heavy metals. Copyright © 2015 Filippidou et al.

Anoxybacillus geothermalis strain GSsed3 is an endospore-forming thermophilic bacterium isolated from filter deposits in a geothermal site. This novel species has a larger genome size (7.2 Mb) than that of any other Anoxybacillus species, and it possesses genes that support its phenotypic metabolic characterization and suggest an intriguing link to...

Anthropogenic N deposition alters patterns of C and N cycling in temperate forests, where forest floor litter decomposition is a key process mediated by a diverse community of bacteria and fungi. To track forest floor decomposer activity we generated metatranscriptomes that simultaneously surveyed the actively expressed bacterial and eukaryote gene...

We report here the genome sequence of Thauera sp. strain SWB20, isolated from a Singaporean wastewater treatment facility using gel microdroplets (GMDs) and single-cell genomics (SCG). This approach provided a single clonal microcolony that was sufficient to obtain a 4.9-Mbp genome assembly of an ecologically relevant Thauera species.

We report draft genomes of Enterobacter cloacae strain S611, an endophytic bacterium isolated from surface-sterilized germinating wheat seeds. We present the assembly and annotation of its genome, which may provide insights into the metabolic pathways involved in adaptation.

Sequencing bacterial genomes has traditionally required large amounts of genomic DNA (~1 μ g). There have been few studies to determine the effects of the input DNA amount or library preparation method on the quality of sequencing data. Several new commercially available library preparation methods enable shotgun sequencing from as little as 1 ng...

Supplementary data describe the NEBNext Ultra workflow (Figure S1), statistics for all NEBNext and TruSeq libraries (Table S1), and statistics for all assemblies generated with IDBA (Table 2a) and Allpaths (Table 2a) algorithms.

In vitro selection has been an essential tool in the development of recombinant antibodies against various antigen targets. Deep sequencing has recently been gaining ground as an alternative and valuable method to analyze such antibody selections. The analysis provides a novel and extremely detailed view of selected antibody populations, and allows...

We report the genome sequence of a seed-borne bacterium, Pseudomonas putida strain S610. The size of the draft genome sequence is approximately 4.6 Mb, which is the smallest among all P. putida strains sequenced to date.

Primer design for highly variable DNA sequences is difficult, and experimental success requires attention to many interacting constraints. The advent of next-generation sequencing methods allows the investigation of rare variants otherwise hidden deep in large populations, but requires attention to population diversity and primer localization in re...

Halorhodospira halophila is among the most halophilic organisms known. It is an obligately photosynthetic and anaerobic purple sulfur bacterium that exhibits autotrophic growth up to saturated NaCl concentrations. The type strain H. halophila SL1 was isolated from a hypersaline lake in Oregon. Here we report the determination of its entire genome i...

The majority of microbial genomic diversity remains unexplored. This is largely due to our inability to culture most microorganisms in isolation, which is a prerequisite for traditional genome sequencing. Single-cell sequencing has allowed researchers to circumvent this limitation. DNA is amplified directly from a single cell using the whole-genome...

In May of 2011, an enteroaggregative Escherichia coli O104:H4 strain that had acquired a Shiga toxin 2-converting phage caused a large outbreak of bloody diarrhea in Europe which was notable for its high prevalence of hemolytic uremic syndrome cases. Several studies have described the genomic inventory and phylogenies of strains associated with the...

Figure showing alignments of individual prophages. (PDF)

RAST annotations and three-way comparisons, including ortholog-by-ortholog analysis of Shiga toxin phage proteins. (XLSX)

Supplementary Tables S1–S5. (DOCX)

Detailed strain phenotypes. (XLSX)

Optical maps and comparison to finished sequences. (JPG)

Identity of SNPs between strains and TY-2482. (XLSX)

Omnilog data summaries (separate tabs for average AUC values for each strain; unfiltered fold-change/significance; and filtered fold-change/significance). (XLSX)

Microbial hydrolysis of polysaccharides is critical to ecosystem functioning and is of great interest in diverse biotechnological applications, such as biofuel production and bioremediation. Here we demonstrate the use of a new, efficient approach to recover genomes of active polysaccharide degraders from natural, complex microbial assemblages, usi...

Frequency of glycoside hydrolase genes in Verrucomicrobia genomes. (A) Relationship between the abundance of glycoside hydrolase genes and genome size in the publicly available Verrucomicrobia genomes. (B) Relationship between the abundance of glycoside hydrolase genes and the genome size in the five sequenced Verrucomicrobia SAGs. (C) The number o...

Signal peptide prediction for laminarinase protein sequence. Prediction of signal peptide was performed with SignalP 3.0 Server. Cleavage site is indicated at the N-terminus of the protein sequence, which is used to direct the protein through the cellular membrane. (TIF)

Abundance of polysaccharide-positive Verrucomicrobia phylotypes among ETS- and esterase-positive, coastal SAGs. (DOC)

Evidence for the xylanase gene in the single amplified genome AAA168-F10. (A) Active site, including the catalytic residues responsible for xylan hydrolysis, derived from Conserved Domain Protein, SWISS-MODEL, and PROSITE databases. (B) Neighbor-joining phylogenetic tree of amino acid sequences, applying Kimura evolutionary model and indicating boo...

Principal coordinate analysis (PCoA) of weighted pairwise UniFrac distances between SSU rRNA gene sequences from the various coastal bacterial fractions. Included are high nucleic acid content (HNA), low nucleic acid content (LNA), ETS-active and esterase-active cells. A Neighbor-Joining tree employing Jukes-Cantor substitution model served as the...

Peptidase genes encoded by the single amplified genome AAA168-F10. A total of 67 peptidase families were found. Peptidases acting on polypeptides (e.g., family M1) and oligopeptides (e.g., S9), carboxy/aminopeptidases (e.g., M14/M42), dipeptidyl-peptidases (e.g., S15) and endopeptidases (e.g., S01B) are encoded on the AAA168-F10 genome. Annotation...

Summary of single amplified genomes (SAGs) from which the 16S rRNA gene was recovered. (DOC)

Glycoside hydrolase enzymes encoded by SAG AAA168-F10. (DOC)

Taxonomic composition of freshwater single amplified genomes (SAGs). Bacterioplankton were probed with the nucleic acid stain SYTO-9, representing a random subset of the total microbial assemblage, and with fluoresceinamine-labeled polysaccharides laminarin and xylan. (TIF)

Phylogenetic composition of polysaccharide-positive Gammaproteobacteria, Acidobacteria, Bacteroidetes, Planctomycetes, OP10, and OP11. (A) Maximum likelihood phylogenetic analysis of the SSU rRNA gene sequences. Bootstrap (1000 replicates) values ≥50 are displayed. Each phylotype, indicated in red (coastal) or blue (freshwater) is formed by SAGs wi...

Comparative genome analysis of the five sequenced single amplified genomes (SAGs) of the Verrucomicrobia phylotype AAA168-F10. Plotted are values of the average nucleotide identity (ANI) and the tetranucleotide frequency signature for each of the pairwise genome comparisons. (TIF)

Assembly statistics. (DOC)

While sequencing methods were available in the late 1970s, it was not until the human genome project and a significant influx of funds for such research that this technology became high throughput. The fields of microbiology and microbial ecology, among many others, have been tremendously impacted over the years, to such an extent that the determin...

Human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) evade containment by CD8+ T lymphocytes through focused epitope mutations. However, because of limitations in the numbers of viral sequences that can be sampled, traditional sequencing technologies have not provided a true representation of the plasticity of these viruses or...

Integration of previously reported and newly available basic clinical data regarding SUMA, WEAU, and CH40 with 454 sampling timeline. (0.17 MB DOC)

Inner PCR/sequencing primers (forward, F; reverse, R). (0.09 MB DOC)

Annotated example of format for Table S3, which includes aligned amino-acid sequences of the epitope regions with variant frequencies, organized by subtype, escape form, and time point. The subject ID, and count of the number of variants with a given protein sequence are shown. The epitope is in bold, and the array of secondary mutations that are f...

Aligned amino-acid sequences of the epitope regions with variant frequencies, organized by subtype, escape form, and time point. (0.38 MB DOC)

Estimates of accumulation rates of dominant viral variants. (0.05 MB DOC)

Summary of subtype consensus frequencies in 4 chronically infected subjects from an earlier study [supplement ref. 10, Tsibris et al.]. (0.05 MB DOC)

Phylogenetic trees of ENV V3 DNA sequences (all timepoint samples combined for each subject). (A) WEAU, (B) CH40,and (C) SUMA, pooled from all samples, with branch color indicating sample timepoint (blue, 1st timepoint; green, 2nd; red. 3rd). Branch widths are proportional to the log-ratio of abundance in the sample; trees are rooted by the most co...

Amplification protocol. The protocol was designed with the intent of reducing loss of diversity during PCR amplification by (1) limiting the number of cycles (2) using large amounts of template, and (3) using multiple small amplification reactions which were pooled for sequencing. (0.77 MB TIF)

Additional methods and description of all supplementary figures and tables. (0.19 MB PDF)

Conventional sequencing variants and previously available immunological data regarding escape. (0.19 MB DOC)

Poisson compatibility within major escape lineages. (0.09 MB DOC)

Modeling results for first time point samples for WEAU, CH40 and SUMA. (0.08 MB DOC)

Frequencies of not-transmitted B consensus amino acids. (0.06 MB DOC)

Phylogenetic trees for ENV V3 DNA sequences, by time point. (A) WEAU, (B) CH40, and (C) SUMA. Branch widths are proportional to the log-ratio of abundance in the sample; trees are rooted by the most common sequence (the transmitted/founder virus); times are in days from symptoms (WEAU, SUMA) or from screening (CH40). (1.87 MB EPS)

Distributions of accumulation rates of viral variants generated during acute infection. In the cases when the frequency of a variant was below the level of detection (i.e., less than 1 sequence per sample), we added the value of 1/N to the variant frequency at that time point. Equation 3 was used to estimate the rate of escape ! for every viral var...

We used ultra-deep sequencing to obtain tens of thousands of HIV-1 sequences from regions targeted by CD8+ T lymphocytes from longitudinal samples from three acutely infected subjects, and modeled viral evolution during the critical first weeks of infection. Previous studies suggested that a single virus established productive infection, but these...