Analysis of the northern pitcher plant (Sarracenia purpurea L.) phytotelm bacteriome throughout a temperate region growing season.

The insectivorous Northern Pitcher Plant, Sarracenia purpurea, recruits a dynamic biotic community in the rainwater collected by its pitcher-shaped leaves. Insect capture and degradation within the pitcher fluid (phytotelma) has been well documented as a mechanism for supplementing the plant's nitrogen, phosphorous, and micronutrient requirements. Metagenomic studies have shown a diverse microbiome in this phytotelm environment, including taxa that contribute metabolically to prey digestion.

Proteome-Wide Assessment of Clustering of Missense Variants in Neurodevelopmental Disorders Versus Cancer.

Missense de novo variants (DNVs) and missense somatic variants contribute to neurodevelopmental disorders (NDDs) and cancer, respectively. Proteins with statistical enrichment based on analyses of these variants exhibit convergence in the differing NDD and cancer phenotypes. Herein, the question of why some of the same proteins are identified in both phenotypes is examined through investigation of clustering of missense variation at the protein level.

Lysosome-related organelles contain an expansion compartment that mediates delivery of zinc transporters to promote homeostasis.

Zinc is an essential nutrient-it is stored during periods of excess to promote detoxification and released during periods of deficiency to sustain function. Lysosome-related organelles (LROs) are an evolutionarily conserved site of zinc storage, but mechanisms that control the directional zinc flow necessary for homeostasis are not well understood. In intestinal cells, the CDF-2 transporter stores zinc in LROs during excess.

HONO Measurement by Catalytic Conversion to NO on Nafion Surfaces.

A selective catalytic converter has been developed to quantify nitrous acid (HONO), a photochemical precursor to NO and OH radicals that drives the formation of ozone and other pollutants in the troposphere. The converter is made from a sulfonated tetrafluoroethylene-based fluoropolymer-copolymer (Nafion) that was found to convert HONO to NO with unity yield under specific conditions. When coupled to a commercially available NO (=NO + NO) chemiluminescence (CL) analyzer, the system measures HONO with a limit of detection as low as 64 parts-per-trillion (ppt) (1 min average) in addition to NO.

A gap-free genome assembly of Chlamydomonas reinhardtii and detection of translocations induced by CRISPR-mediated mutagenesis.

Genomic assemblies of the unicellular green alga Chlamydomonas reinhardtii have provided important resources for researchers. However, assembly errors, large gaps, and unplaced scaffolds as well as strain-specific variants currently impede many types of analysis. By combining PacBio HiFi and Oxford Nanopore long-read technologies, we generated a de novo genome assembly for strain CC-5816, derived from crosses of strains CC-125 and CC-124.

de novo variant calling identifies cancer mutation signatures in the 1000 Genomes Project.

Detection of de novo variants (DNVs) is critical for studies of disease-related variation and mutation rates. To accelerate DNV calling, we developed a graphics processing units-based workflow. We applied our workflow to whole-genome sequencing data from three parent-child sequenced cohorts including the Simons Simplex Collection (SSC), Simons Foundation Powering Autism Research (SPARK), and the 1000 Genomes Project (1000G) that were sequenced using DNA from blood, saliva, and lymphoblastoid cell lines (LCLs), respectively.

Nitrogen cycling microbiomes are structured by plant mycorrhizal associations with consequences for nitrogen oxide fluxes in forests.

Volatile nitrogen oxides (N O, NO, NO , HONO, …) can negatively impact climate, air quality, and human health. Using soils collected from temperate forests across the eastern United States, we show microbial communities involved in nitrogen (N) cycling are structured, in large part, by the composition of overstory trees, leading to predictable N-cycling syndromes, with consequences for emissions of volatile nitrogen oxides to air. Trees associating with arbuscular mycorrhizal (AM) fungi promote soil microbial communities with higher N-cycle potential and activity, relative to microbial communities in soils dominated by trees associating with ectomycorrhizal (ECM) fungi.

Oxidation of Volatile Organic Compounds as the Major Source of Formic Acid in a Mixed Forest Canopy.

Formic acid (HCOOH) is among the most abundant carboxylic acids in the atmosphere, but its budget is poorly understood. We present eddy flux, vertical gradient, and soil chamber measurements from a mixed forest and apply the data to better constrain HCOOH source/sink pathways. While the cumulative above-canopy flux was downward, HCOOH exchange was bidirectional, with extended periods of net upward and downward flux.

Microbial mechanisms and ecosystem flux estimation for aerobic NO emissions from deciduous forest soils.

Reactive nitrogen oxides (NO; NO = NO + NO + HONO) decrease air quality and impact radiative forcing, yet the factors responsible for their emission from nonpoint sources (i.e., soils) remain poorly understood.

Pilot-scale in situ bioremediation of HMX and RDX in soil pore water in Hawaii.

A nine-month in situ bioremediation study was conducted in Makua Military Reservation (MMR) in Oahu, Hawaii (USA) to evaluate the potential of molasses to enhance biodegradation of royal demolition explosive (RDX) and high-melting explosive (HMX) contaminated soil below the root zone. MMR has been in operation since the 1940's resulting in subsurface contamination that in some locations exceeds USEPA preliminary remediation goals for these chemicals. A molasses-water mixture (1 : 40 dilution) was applied to a treatment plot and clean water was applied to a control plot via seven flood irrigation events.