A5024021461- Microbial Community Ecology and Physiology
- Marine Biology and Ecology Research
- Genomics and Phylogenetic Studies
- Microbial Metabolic Engineering and Bioproduction
- Plant Molecular Biology Research
- Methane Hydrates and Related Phenomena
- Marine and coastal ecosystems
- Photosynthetic Processes and Mechanisms
- Protist diversity and phylogeny
- Single-cell and spatial transcriptomics
- Enzyme Catalysis and Immobilization
- Immune Cell Function and Interaction
- Reproductive System and Pregnancy
- Marine Bivalve and Aquaculture Studies
- Forensic and Genetic Research
- RNA Research and Splicing
- Plant Reproductive Biology
- Phytase and its Applications
- Plant Gene Expression Analysis
- Legume Nitrogen Fixing Symbiosis
- Molecular Biology Techniques and Applications
- Philosophy, Science, and History
- Microbial Natural Products and Biosynthesis
- T-cell and B-cell Immunology
- Biosensors and Analytical Detection
Los Medanos College
2020-2021
Joint Genome Institute
2018-2019
University of California, San Diego
2010-2019
University of Hawaiʻi at Mānoa
2016-2017
University of Hawaii System
2017
Georgetown University
2006-2007
Georgetown University Medical Center
2007
Highlights•RNA expression profiling of >12,000 single Arabidopsis root cells by Drop-seq•Recovered major tissue types and cell stages identified specific marker genes•Sucrose alters type proportions but does not profoundly change identities•Identified ∼800 genes dynamically expressed across endodermis developmentSummarySingle-cell transcriptome heterogeneous tissues can provide high-resolution windows into developmental dynamics environmental responses, its application to plants has been...
Summary Relatively little information is available for the composition of microbial communities present in hadal environments, deepest marine locations. Here we a description phylogenetic diversity particle‐associated (> 3 µm) and free‐living (3–0.22 microorganisms pelagic trench environment. Small subunit ribosomal RNA gene sequences were recovered from members Bacteria , Archaea Eukarya obtained depth 6000 m Puerto Rico Trench (PRT). Species richness estimates bacterial fraction greater...
Plant xylem cells conduct water and mineral nutrients. Although most plant are totipotent, unusual undergo terminal differentiation. Many genes regulating this process well characterized, including the Vascular-related NAC Domain 7 (VND7), MYB46, MYB83 transcription factors, which proposed to act in interconnected feedforward loops (FFLs). Less is known regarding molecular mechanisms underlying transition cell Here, we generate whole-root single-cell data, demonstrate that VND7 initiates...
Bacterial production of long-chain omega-3 polyunsaturated fatty acids (PUFAs), such as eicosapentaenoic acid (EPA, 20:5n-3) and docosahexaenoic (DHA, 22:6n-3), is constrained to a narrow subset marine γ-proteobacteria. The genes responsible for de novo bacterial PUFA biosynthesis, designated pfaEABCD, encode large, multi-domain protein complexes akin type I iterative polyketide synthases, herein referred "Pfa synthases". In addition the archetypal Pfa synthase gene products from bacteria,...
Abstract Concentrated seabed deposits of polymetallic nodules, which are rich in economically valuable metals (e.g., copper, nickel, cobalt, manganese), occur over vast areas the abyssal Pacific Ocean floor. Little is currently known about diversity microorganisms inhabiting habitats. In this study, sediment, nodule, and water column samples were collected from Clarion‐Clipperton Zone Eastern North Pacific. The diversities prokaryote microeukaryote communities associated with these habitats...
Abstract The cycling of carbon (C) by benthic organisms is a key ecosystem function in the deep sea. Pulse‐chase experiments are designed to quantify this process, yet few studies have been carried out using abyssal (3500–6000 m) sediments and only handful undertaken situ. We undertook eight situ pulse‐chase three strata (4050–4200 m water depth) separated tens hundreds kilometers eastern Clarion‐Clipperton Fracture Zone (CCFZ). These demonstrated that bacteria dominated consumption...
Phosphate fertilizers are essential for high-yield agriculture yet costly and environmentally damaging. Microbes that release soluble phosphate from naturally occurring sources in the soil appealing, as they may reduce need such fertilizers. In this study, we used synthetic biology approaches to create a collection of engineered root-associated microbes with ability phytate. We demonstrate these strains improve plant growth under phosphorus-limited conditions. This represents first step...
Marine bacteria regulate fluxes of matter and energy essential for pelagic benthic organisms may also be involved in the formation maintenance commercially valuable abyssal polymetallic nodules. Future mining these nodule fields is predicted to have substantial effects on biodiversity physicochemical conditions mined areas. Yet, identity distributions bacterial populations deep-sea sediments associated nodules has received relatively little attention. We examined communities using...
Genetic polymorphism of KIR2DL4 results in alleles with either 9 or 10 consecutive adenines exon 6, which encodes the transmembrane domain. "10A" encode a membrane-expressed receptor that is constitutively expressed on resting CD56bright NK cells and CD56dim after culture. However, some individuals 10A allele, cannot be detected their cells. "9A" have been predicted to secreted due splicing out region. In this publication, we show those allele who lack detectable express D0-domain excised....
Summary Bacterial production of long‐chain fatty acids via a polyketide synthase‐related mechanism has thus far only been investigated in isolate‐based studies. Here, the genetic capacity for was using culture‐independent approach. PCR primers targeting keto‐acyl synthase (KS) domain pfaA gene involved omega‐3 polyunsaturated acid (PUFA) biosynthesis were used to construct clone libraries investigate KS sequence diversity disparate marine habitats. Of 446 sequences recovered, 123 (27.6%)...
Nitrogen frequently limits oceanic photosynthesis and the availability of inorganic nitrogen sources in surface oceans is shifting with global change. We evaluated potential for abrupt increases N to induce cascading effects on dissolved organic matter (DOM) microbial communities ocean. collected water from 5 m depth central North Pacific amended duplicate 20 liter polycarbonate carboys nitrate or ammonium, tracking planktonic carbon fixation, DOM production, composition community structure...
Abstract Single-cell transcriptome analysis of heterogeneous tissues can provide high-resolution windows into the genomic basis and spatiotemporal dynamics developmental processes. Here we demonstrate feasibility high-throughput single-cell RNA sequencing plant tissue using Drop-seq approach. Profiling >4,000 individual cells from Arabidopsis root provides transcriptomes marker genes for a diversity cell types illuminates gene expression changes that occur across endodermis development.
Various marine gamma-proteobacteria produce omega-3 polyunsaturated fatty acids, such as eicosapentaenoic acid (20:5, EPA) and docosahexaenoic (22:6, DHA), which are incorporated into membrane phospholipids. Five genes, designated pfaABCDE, encode the polyketide/fatty synthase necessary for production of these long-chain acids. In addition to de novo biosynthesis EPA DHA, "Pfa synthase" is also involved with a hydrocarbon product (31:9, PUHC) in conjunction oleABCD pathway. this work, we...
Bacteria and archaea are key contributors to deep-sea biogeochemical cycles food webs. The disruptions these microbial communities may experience during following polymetallic nodule mining in the Clarion-Clipperton Zone (CCZ) of North Pacific Ocean could therefore have broad ecological effects. Our goals this synthesis characterize current understanding biodiversity biogeography bacteria CCZ identify gaps baseline data sampling approaches, prior onset region. This is part a large effort...
Abstract Genomic DNA sequencing was used to identify alleles of KIR2DL4 from 78 unrelated individuals involved in hematopoietic stem cell transplants. Eight known were observed. Three new alleles, KIR2DL4*00203, *00502, *0080104, which differ at the nucleotide but not protein sequence level, also identified.
Summary Plant xylem cells conduct water and mineral nutrients. Although most plant are totipotent, unusual undergo terminal differentiation. Many genes regulating this process well characterized, including the VASCULAR-RELATED NAC DOMAIN7 (VND7), MYB46 MYB83 transcription factors which proposed to act in interconnected feed-forward loops. Much less is known regarding dynamic behavior underlying transition cell Here we utilize whole root single data mathematically model relationship. These...