Biomedical subjects

Jillian F Banfield

Publications and source records attributed to Jillian F Banfield.

At least 19 recordsLinked to original sources

PubMed2026

Structure and evolution-guided design of minimal RNA-guided nucleases.

The design of RNA-guided nucleases with properties not limited by evolution can expand programmable genome-editing capabilities. However, generating diverse multidomain proteins with robust enzymatic properties remains challenging. Here, we use a protein design strategy that couples a structure-guided inverse-folding model with evolution-informed residue constraints to generate active, divergent variants of TnpB, a minimal CRISPR-Cas12-like nuclease, termed SynTnpBs. High-throughput screening of artificial intelligence-generated variants yielded editors that retained or exceeded wild-type activity in bacterial, plant, and human cells. Cryo-electron microscopy-based structure determination of the most divergent variant revealed stabilizing contacts in the RNA-DNA interfaces across conformations, demonstrating the design potential of this approach. Together, these results establish a strategy for creating non-natural RNA-guided nucleases and conformationally active nucleic acid binders, enlarging the designable protein space.

Humans↗

PubMed2026

Reduced legacy precipitation decreases microbial community growth efficiency and alters soil organic carbon in a California grassland.

BACKGROUND: Changes in global patterns can leave a lasting legacy in semiarid grasslands by reshaping microbial growth dynamics and carbon cycling during the first wet-up in the autumn-a period known for intense microbial activity and significant carbon emissions. To study the lasting impacts of decreased winter rain, we implemented two precipitation regimes (100% vs. 50% mean annual precipitation) in California Mediterranean-climate grassland field plots. After the dry season, soils were rewetted in the laboratory with H218O and sampled at 0 h, 3 h, 24 h, 48 h, 72 h, and 168 h post rewet. We quantified CO2 efflux, measured microbial growth and mortality via quantitative 18O stable isotope probing and 16S rRNA gene amplicon sequencing, and characterized the soil organic carbon chemical composition, metagenomes, and metatranscriptomes. RESULTS: We found that reduced winter precipitation imposed a strong legacy effect on microbial turnover; despite maintaining similar respiration rates, microbial growth declined by ~1 order of magnitude, yielding decreased community growth efficiency (CGE = new biomass growth/respiration), and microbial mortality declined by ~2 orders of magnitude. Soil organic carbon also shifted from lipid-like, amino-sugar-like, and protein-like compounds (indicative of microbial necromass) to more oxidized lignin-like and tannin-like compounds (indicative of decomposing plant-derived compounds). Meta-omics revealed distinct metabolic strategies linked to CGE. At high-CGE, microbes appeared to consume more energetically favorable N-rich necromass (released via high microbial turnover); this allowed for increased amino acids and peptidoglycan biosynthesis and greater aromatic compound degradation, fueling further energy production and growth efficiency. At low CGE, communities had elevated carbohydrate metabolism and lipid turnover, consistent with increased investment in plant detritus degradation and membrane repair and maintenance rather than growth. CONCLUSIONS: Together, our findings demonstrate that reduced winter rainfall decreases microbial turnover following rewetting without a concurrent reduction in CO2 emissions. This shift results in persistently lower CGE, which has the potential to increase soil carbon loss as CO2. If such conditions are maintained over multiple years, these changes could reshape soil organic carbon stocks and alter the balance of grassland ecosystems under future climate scenarios. While our data suggest that sustained reductions in CGE may drive SOC decline, the magnitude and persistence of these effects depend on long-term environmental dynamics and warrant further investigation. Video Abstract.

Soil Microbiology↗

PubMed2006

Lineages of acidophilic archaea revealed by community genomic analysis.

Novel, low-abundance microbial species can be easily overlooked in standard polymerase chain reaction (PCR)-based surveys. We used community genomic data obtained without PCR or cultivation to reconstruct DNA fragments bearing unusual 16S ribosomal RNA (rRNA) and protein-coding genes from organisms belonging to novel archaeal lineages. The organisms are minor components of all biofilms growing in pH 0.5 to 1.5 solutions within the Richmond Mine, California. Probes specific for 16S rRNA showed that the fraction less than 0.45 micrometers in diameter is dominated by these organisms. Transmission electron microscope images revealed that the cells are pleomorphic with unusual folded membrane protrusions and have apparent volumes of <0.006 cubic micrometer.

Amino Acid Sequence↗

PubMed2006

Population genomics in natural microbial communities.

Little is known about the evolutionary processes that structure and maintain microbial diversity because, until recently, it was difficult to explore individual-level patterns of variation at the microbial scale. Now, community-genomic sequence data enable such variation to be assessed across large segments of microbial genomes. Here, we discuss how population-genomic analysis of these data can be used to determine how selection and genetic exchange shape the evolution of new microbial lineages. We show that once independent lineages have been identified, such analyses enable the identification of genome changes that drive niche differentiation and promote the coexistence of closely related lineages within the same environment. We suggest that understanding the evolutionary ecology of natural microbial populations through population-genomic analyses will enhance our understanding of genome evolution across all domains of life.

Archaea↗

PubMed2006

Environmental risks of nanotechnology: National Nanotechnology Initiative funding, 2000-2004.

By considering risk in the early stages of a technology, costs of identifying important health and environmental impacts after a technology has widely diffused can be avoided. Nanotechnology, involving materials and objects less than 100 nm in size, is an important case in point. In this paper we analyze the research priorities discussed by various interest groups concerned with the environmental risks of nanotechnology, evaluate the distribution of federal environmental nanotechnology R&D funding, and discuss research in this field. Overall federal environmental R&D funding to date is limited and focuses more on the positive environmental applications of nanotechnology than on basic knowledge/research, tools for nanoenvironmental research, or the potential risks of nanotechnology. The situation began to change in 2004 when a significant increase occurred in federal R&D funding for the environmental implications of engineered nanomaterials. Though literature exits on the exposure, transport, and toxicity of incidental nanoparticles, little work has been published on the environmental risks of engineered nanoparticles.

Financing, Government↗

PubMed2006

Surface chemistry controls crystallinity of ZnS nanoparticles.

Combined small-angle and high energy wide-angle X-ray scattering measurements of nanoparticle size and structure permit interior strain and disorder to be observed directly in the real-space pair distribution function (PDF). PDF analysis showed that samples of ZnS nanoparticles with similar mean diameters (3.2-3.6 nm) but synthesized and treated with different low-temperature procedures possess a dramatic range of interior disorder. We used Fourier transform infrared spectroscopy to detect the surface species and the nature of surface chemical interactions. Our results suggest that there is a direct correlation between the strength of surface-ligand interactions and interior crystallinity.

Crystallization↗

PubMed2005

Geophysical imaging of stimulated microbial biomineralization.

Understanding how microorganisms influence the physical and chemical properties of the subsurface is hindered by our inability to observe microbial dynamics in real time and with high spatial resolution. Here, we investigate the use of noninvasive geophysical methods to monitor biomineralization at the laboratory scale during stimulated sulfate reduction under dynamic flow conditions. Alterations in sediment characteristics resulting from microbe-mediated sulfide mineral precipitation were concomitant with changes in complex resistivity and acoustic wave propagation signatures. The sequestration of zinc and iron in insoluble sulfides led to alterations in the ability of the pore fluid to conduct electrical charge and of the saturated sediments to dissipate acoustic energy. These changes resulted directly from the nucleation, growth, and development of nanoparticulate precipitates along grain surfaces and within the pore space. Scanning and transmission electron microscopy (SEM and TEM) confirmed the sulfides to be associated with cell surfaces, with precipitates ranging from aggregates of individual 3-5 nm nanocrystals to larger assemblages of up to 10-20 microm in diameter. Anomalies in the geophysical data reflected the distribution of mineral precipitates and biomass over space and time, with temporal variations in the signals corresponding to changes in the aggregation state of the nanocrystalline sulfides. These results suggest the potential for using geophysical techniques to image certain subsurface biogeochemical processes, such as those accompanying the bioremediation of metal-contaminated aquifers.

Acoustics↗

PubMed2005

Characterization of titanium dioxide nanoparticles using molecular dynamics simulations.

Molecular dynamics simulations of titanium dioxide nanoparticles in the three commonly occurring phases (anatase, brookite, and rutile) are reported. The structural properties inferred by simulated X-ray diffraction patterns of the nanoparticles were investigated. The titanium-oxygen bond length as a function of size, phase, and temperature was determined and was found to be dependent on the coordination environment of the titanium and independent of phase and size. The equilibrium Ti-O bond length is 1.86 A for a four-coordinated titanium ion, 1.92 A for a five-coordinated titanium ion, and 1.94 A for an octahedral titanium ion. Smaller nanoparticles are characterized by a higher fraction of titanium ions that are four and five coordinated, due to the larger surface area-to-volume ratios. The surface energies for anatase, rutile, and brookite particles were reported. The surface energy of the nanoparticle increases and approaches a constant value as the particle gets bigger. The surface energies of small rutile particles are higher than that for anatase particles of a similar size, consistent with anatase being the more stable phase of nanocrystalline titanium dioxide.

Journal Article↗

PubMed2005

Community proteomics of a natural microbial biofilm.

Using genomic and mass spectrometry–based proteomic methods, we evaluated gene expression, identified key activities, and examined partitioning of metabolic functions in a natural acid mine drainage (AMD) microbial biofilm community. We detected 2033 proteins from the five most abundant species in the biofilm, including 48% of the predicted proteins from the dominant biofilm organism, Leptospirillum group II. Proteins involved in protein refolding and response to oxidative stress appeared to be highly expressed, which suggests that damage to biomolecules is a key challenge for survival. We validated and estimated the relative abundance and cellular localization of 357 unique and 215 conserved novel proteins and determined that one abundant novel protein is a cytochrome central to iron oxidation and AMD formation.

Amino Acids↗

PubMed2005

Size-dependent phase transformation kinetics in nanocrystalline ZnS.

Nanocrystalline ZnS was coarsened under hydrothermal conditions to investigate the effect of particle size on phase transformation kinetics. Although bulk wurtzite is metastable relative to sphalerite below 1020 degrees C at low pressure, sphalerite transforms to wurtzite at 225 degrees C in the hydrothermal experiments. This indicates that nanocrystalline wurtzite is stable at low temperature. High-resolution transmission electron microscope data indicate there are no pure wurtzite particles in the coarsened samples and that wurtzite only grows on the surface of coarsened sphalerite particles. Crystal growth of wurtzite stops when the diameter of the sphalerite-wurtzite interface reaches approximately 22 nm. We infer that crystal growth of wurtzite is kinetically controlled by the radius of the sphalerite-wurtzite interface. A new phase transformation kinetic model based on collective movement of atoms across the interface is developed to explain the experimental results.

Journal Article↗

PubMed2005

Sulfate requirement for heterotrophic growth of "Ferroplasma acidarmanus" strain fer1.

Growth of the acidophilic archaeon, "Ferroplasma acidarmanus" strain fer1, in a laboratory medium (primary constituents, FeSO4 72 mM and 0.02% yeast extract) is minimal. A survey of the annotated genome revealed metabolic transporters for Ni2+, sugars, and amino acids. Accordingly, the concentration of yeast extract was increased to 0.1% and the addition of 2 mM Ni(NH4)2(SO4)2 significantly enhanced the cultivation of strain fer1. The maximum optical density in the modified fer1 medium (mfer) was OD(492)=0.27 with 10(10) viable cells/ml as determined by a most-probable-number method, which exceeds previously reported viable cells/ml by >100-fold. Strain fer1 displayed chemolithotrophic growth with Fe2+ in mfer containing 100 mM FeSO4 or FeCl2. In the absence of Fe2+, heterotrophic growth occurred with one of the following salts (100 mM): ZnSO4, MnSO4, MgSO4, (NH4)2SO4, or Fe2(SO4)3, and did not occur with (100 mM): ZnCl2, MnCl2, MgCl2, NH4Cl, or FeCl3. Escaping headspace gas from strain fer1 cultures formed a precipitate in a zinc acetate trap. Sulfide was absent in the precipitate but zinc and sulfur were detected. These data demonstrate that SO4 is required for heterotrophic growth of strain fer1 and may have a role in the global sulfur cycle.

Archaea↗

PubMed2005

Cultivating the uncultivated: a community genomics perspective.

Current isolation methods access only a small subset of the total microbial diversity. Although an isolate traditionally has been required for genomic characterization, the advent of sequencing of entire natural microbial communities enables culture-independent genomic analysis. Information about the genetic potential of uncultivated organisms can be used to predict the form of metabolic interdependencies and nutritional requirements. We believe that this could provide the information necessary to bypass bottlenecks that have inhibited cultivation of many microorganisms. However, it might not be practical or possible to isolate all of the vast number of microbial species and strains for laboratory-based characterization. Ultimately, cultivation-independent genomic and genomically enabled approaches could provide a way to directly analyze microbial activity in its geochemical and ecological context.

Bacteria↗

PubMed2005

Community genomics in microbial ecology and evolution.

It is possible to reconstruct near-complete, and possibly complete, genomes of the dominant members of microbial communities from DNA that is extracted directly from the environment. Genome sequences from environmental samples capture the aggregate characteristics of the strain population from which they were derived. Comparison of the sequence data within and among natural populations can reveal the evolutionary processes that lead to genome diversification and speciation. Community genomic datasets can also enable subsequent gene expression and proteomic studies to determine how resources are invested and functions are distributed among community members. Ultimately, genomics can reveal how individual species and strains contribute to the net activity of the community.

DNA↗

PubMed2005

Proteogenomic approaches for the molecular characterization of natural microbial communities.

At the present time we know little about how microbial communities function in their natural habitats. For example, how do microorganisms interact with each other and their physical and chemical surroundings and respond to environmental perturbations? We might begin to answer these questions if we could monitor the ways in which metabolic roles are partitioned amongst members as microbial communities assemble, determine how resources such as carbon, nitrogen, and energy are allocated into metabolic pathways, and understand the mechanisms by which organisms and communities respond to changes in their surroundings. Because many organisms cannot be cultivated, and given that the metabolisms of those growing in monoculture are likely to differ from those of organisms growing as part of consortia, it is vital to develop methods to study microbial communities in situ. Chemoautotrophic biofilms growing in mine tunnels hundreds of meters underground drive pyrite (FeS(2)) dissolution and acid and metal release, creating habitats that select for a small number of organism types. The geochemical and microbial simplicity of these systems, the significant biomass, and clearly defined biological-inorganic feedbacks make these ecosystem microcosms ideal for development of methods for the study of uncultivated microbial consortia. Our approach begins with the acquisition of genomic data from biofilms that are sampled over time and in different growth conditions. We have demonstrated that it is possible to assemble shotgun sequence data to reveal the gene complement of the dominant community members and to use these data to confidently identify a significant fraction of proteins from the dominant organisms by mass spectrometry (MS)-based proteomics. However, there are technical obstacles currently restricting this type of "proteogenomic" analysis. Composite genomic sequences assembled from environmental data from natural microbial communities do not capture the full range of genetic potential of the associated populations. Thus, it is necessary to develop bioinformatics approaches to generate relatively comprehensive gene inventories for each organism type. These inventories are critical for expression and functional analyses. In proteomic studies, for example, peptides that differ from those predicted from gene sequences can be measured, but they generally cannot be identified by database matching, even if the difference is only a single amino acid residue. Furthermore, many of the identified proteins have no known function. We propose that these challenges can be addressed by development of proteogenomic, biochemical, and geochemical methods that will be initially deployed in a simple, natural model ecosystem. The resulting approach should be broadly applicable and will enhance the utility and significance of genomic data from isolates and consortia for study of organisms in many habitats. Solutions draining pyrite-rich deposits are referred to as acid mine drainage (AMD). AMD is a very prevalent, international environmental problem associated with energy and metal resources. The biological-mineralogical interactions that define these systems can be harnessed for energy-efficient metal recovery and removal of sulfur from coal. The detailed understanding of microbial ecology and ecosystem dynamics resulting from the proposed work will provide a scientific foundation for dealing with the environmental challenges and technological opportunities, and yield new methods for analysis of more complex natural communities.

Ecosystem↗

PubMed2005

Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp. nov. from an acidophilic microbial community.

Analysis of assembled random shotgun sequence data from a low-diversity, subsurface acid mine drainage (AMD) biofilm revealed a single nif operon. This was found on a genome fragment belonging to a member of Leptospirillum group III, a lineage in the Nitrospirae phylum with no cultivated representatives. Based on the prediction that this organism is solely responsible for nitrogen fixation in the community, we pursued a selective isolation strategy to obtain the organism in pure culture. An AMD biofilm sample naturally abundant in Leptospirillum group III cells was homogenized, filtered, and serially diluted into a nitrogen-free liquid medium. The resulting culture in the terminal dilution grew autotrophically to a maximum cell density of approximately 10(6) cells/ml, oxidizing ferrous iron as the sole energy source. 16S rRNA-internal transcribed spacer region clone library analysis confirmed that the isolate is a member of Leptospirillum group III and that the culture is axenic. We propose the name Leptospirillum ferrodiazotrophum sp. nov. for this iron-oxidizing, free-living diazotroph. This study highlights how environmental sequence data can provide insights for culturing previously uncultured microorganisms.

Bacteria↗

PubMed2005

Direct microbial reduction and subsequent preservation of uranium in natural near-surface sediment.

The fate of uranium in natural systems is of great environmental importance. X-ray absorption near-edge spectroscopy (XANES) revealed that U(VI) was reduced to U(IV) in shallow freshwater sediment at an open pit in an inactive uranium mine. Geochemical characterization of the sediment showed that nitrate, Fe(III), and sulfate had also been reduced in the sediment. Observations of the sediment particles and microbial cells by scanning and transmission electron microscopy, coupled with elemental analysis by energy dispersive spectroscopy, revealed that uranium was concentrated at microbial cell surfaces. U(IV) was not associated with framboidal pyrite or nanometer-scale iron sulfides, which are presumed to be of microbial origin. Uranium concentrations were not detected in association with algal cells. Phylogenetic analyses of microbial populations in the sediment by the use of 16S rRNA and dissimilatory sulfite reductase gene sequences detected organisms belonging to the families Geobacteraceae and Desulfovibrionaceae. Cultivated members of these lineages reduce U(VI) and precipitate iron sulfides. The association of uranium with cells, but not with sulfide surfaces, suggests that U(VI) is reduced by the enzymatic activities of microorganisms. Uranium was highly enriched (760 ppm) in a subsurface black layer in unsaturated sediment sampled from a pit which was exposed to seasonal fluctuations in the pond level. XANES analysis showed that the majority of uranium in this layer was U(IV), indicating that uranium is preserved in its reduced form after burial.

DNA, Bacterial↗

PubMed2004

Tetraether-linked membrane monolayers in Ferroplasma spp: a key to survival in acid.

Ferroplasma acidarmanus thrives in hot, extremely low pH, metal-rich solutions associated with dissolving metal sulfide ore deposits. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and thin layer chromatography analyses of F. acidarmanus membranes indicate that tetraether lipids predominate, with at least three core lipid structures. NMR measurements indicate that the cytoplasmic pH of F. acidarmanus is approximately 5.6. The optimal growth pH is approximately 1.2, and the lowest growth pH is approximately 0.0. Thus, these organisms maintain pH gradients across their membranes that approach 5 pH units. Tetraether lipids were originally thought to be specifically associated with thermophiles but are now known to be widely distributed within the archaeal domain. Our data, in combination with recently published results for thermophilic and mesothermophilic acidophilic archaea, indicate that there may be a stronger association between tetraether lipids and tolerance to acid and/or large metal ion gradients.

Acids↗

PubMed2004

Nanoparticles: strained and stiff.

Nanoparticles may contain unusual forms of structural disorder that can substantially modify materials properties and thus cannot solely be considered as small pieces of bulk material. We have developed a method to quantify intermediate-range order in 3.4-nanometer-diameter zinc sulfide nanoparticles and show that structural coherence is lost over distances beyond 2 nanometers. The zinc-sulfur Einstein vibration frequency in the nanoparticles is substantially higher than that in the bulk zinc sulfide, implying structural stiffening. This cannot be explained by the observed 1% radial compression and must be primarily due to inhomogeneous internal strain caused by competing relaxations from an irregular surface. The methods developed here are generally applicable to the characterization of nanoscale solids, many of which may exhibit complex disorder and strain.

Journal Article↗