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Plant resource sharing mediated by mycorrhizal fungi has been a subject of recent debate, largely owing to the limitations of previously used isotopic tracking methods. Although CdSe/ZnS quantum dots (QDs) have been successfully used for in situ tracking of essential nutrients in plant-fungal systems, the Cd-containing QDs, due to the intrinsic toxic nature of Cd, are not a viable system for larger-scale in situ studies. We synthesized amino acid-based carbon quantum dots (CQDs; average hydrodynamic size 6 ± 3 nm, zeta potential −19 ± 12 mV) and compared their toxicity and uptake with commercial CdSe/ZnS QDs that we conjugated with the amino acid cysteine (Cys) (average hydrodynamic size 308 ± 150 nm, zeta potential −65 ± 4 mV) using yeast Saccharomyces cerevisiae as a proxy for mycorrhizal fungi. We showed that the CQDs readily entered yeast cells and were non-toxic up to 100 mg/L. While the Cys-conjugated CdSe/ZnS QDs were also not toxic to yeast cells up to 100 mg/L, they were not taken up into the cells but remained on the cell surfaces. These findings suggest that CQDs may be a suitable tool for molecular tracking in fungi (incl. mychorrhizal fungi) due to their ability to enter fungal cells.

Information on the sex- and individual-specific space use by a species elucidates demography, resource selection and individual life history. However, traditional field surveys often lack information on sex and individual identity, thereby not maximizing the potential of the effort put in. Recent advances in genetic non-invasive sampling provide cost-effective approaches to determine identity and sex from faecal DNA with high accuracy, which are advantageous for tracking individuals compared to field observations. Therefore, we describe the first single multiplex-based sex and individual identification protocol using faecal samples of the wild Asian elephant ( Elephas maximus ) collected from the vicinity of Rajaji Tiger Reserve, Uttarakhand, India. We co-amplified fluorescence-labelled microsatellites (n = 5) and a Y chromosome-linked sex marker in four replicates from faecal DNA extracts (n = 149). The mean per genotype allelic drop-out rate was 0.11 ± 0.02, while the false allele rate was 0.05 ± 0.01. The mean null allele frequency across the markers was 0.15 ± 0.02. We obtained 74.1% consensus genotypes across microsatellites and dropped samples with more than one-locus missing genotype from further analyses. The remaining dataset comprised 105 samples, 30.5% of which were females. We identified 51 unique individuals (25 males and 26 females) with a maximum of one-locus mismatch. With low genotyping error rates and adequate misidentification probabilities (P ID  = 4.2 × 10 −4 ; P IDSib  = 3.0 × 10 −2 ), the described panel provides a cost-effective method (US$ 18/sample) for molecular sexing and individual identification. Hence, the suggested multiplex panel would provide a thorough understanding of individual and sex-specific differences in habitat use across heterogeneous landscapes, facilitating effective conservation strategies.

Fecal contamination threatens human health and contributes to the eutrophication of water resources. In Oklahoma, approximately 75% of assessed stream miles in the state are listed as impaired for fecal indicator bacteria (FIB). We tested the performance of seven microbial source tracking (MST) markers in six Northeast Oklahoma streams. All samples were tested with human (HF183), bovine (COWM2, COWM3), porcine (Pig-2-Bac), avian (Av4143), Escherichia coli, and Enterococcus markers using digital PCR (dPCR), as well as culturable assays for E. coli (Colisure) and Enterococcus (Enterolert). Rural and agricultural land uses were characterized by bovine sources of bacterial contamination. Human fecal contamination was found to be prominent in developed landscapes with several indicators for chronic human fecal pollution in an urban stream. All the streams met the criterion for Enterococcus impairment in 2019 and 2020; however, we found no relationships between culturable Enterococcus and the MST markers except in the urban stream, which had chronic human fecal pollution issues. The urban stream met the criterion for E. coli impairment, and E. coli was significantly correlated with the dominant MST markers in both rural and urban streams. We find that the culturable Enterococcus assay is not specific enough to be used for FIB water quality standards. We support the continued use of culturable E. coli assays to monitor for fecal contamination, and we recommend following-up with MST to verify fecal sources so informed mitigative actions can be taken to improve stream water quality.

Neurocysticercosis (NCC) of Taenia solium has never been reported in Mongolia. A Mongolian traveler who visited China and India presented with epileptic seizures after his return to Mongolia. Magnetic resonance imaging showed multiple ring enhancing lesions with edema surrounding several lesions in his brain that were initially diagnosed to be viral encephalitis or NCC. Serology for cysticercosis using diagnostic antigens partially purified by cation-exchange chromatography and chimeric recombinant antigens and DNA analysis of a proglottid found in the patient's stool were applied for differential diagnosis. Serology showed strong positivity for NCC, and mitochondrial cox1 gene analysis revealed Indian but not Chinese haplotype of T. solium. This NCC case was considered to be caused by eggs released from adult tapeworm(s) established after eating uncooked or undercooked pork contaminated with cysticerci during his stay in India. This is a case report of taeniasis and secondary NCC associated with travel to India with an updated review of NCC in Asia. Molecular tracking of the specimen is highly informative as a way to identify where the infection was acquired.

Rising populations around coastal systems are increasing the threats to marine water quality. To assess anthropogenic fecal influence, subtidal waters were examined monthly for human- and ruminant-sourced Bacteroidales markers at 80 sites across six oceanographic basins of the Salish Sea (Washington State) from April through October, 2011. In the basins containing cities with individual populations >190,000, >50% of sites were positive for the human marker, while in the basins with high densities of dairy and cattle operations, ∼30% of sites were positive for the ruminant marker. Marker prevalence was elevated in spring (April and May) and fall (October) and reduced during summer (June through September), corresponding with seasonal precipitation. By logistic regression, the odds of human marker detection increased with percentage of adjacent catchment impervious surface, dissolved nitrate concentration, and abundance of low nucleic acid bacteria, but decreased with salinity and chlorophyll fluorescence. The odds of ruminant marker detection increased with dissolved ammonium concentration, mean flow rate for the nearest river, and adjacent shoreline length. These relationships are consistent with terrestrial to marine water flow as a transport mechanism. Thus, Bacteroidales markers traditionally used for identifying nearby sources can be used for assessing anthropogenic fecal inputs to regional marine ecosystems.

Molecular subtyping is an instrumental tool for foodborne illness surveillance and outbreak investigation. The term “molecular epidemiology‐ in the context of foodborne bacteria is usually applied to the subtyping of bacteria that cause foodborne disease and the ways in which such subtyping data contribute to understanding the transmission of those bacteria to humans. Molecular subtyping techniques can be applied to identifying the source of a particular outbreak or to a broader understanding of the role of certain foods or processes in outbreak‐related or sporadic infections. Advances in sequencing technology over the last two decades have made whole‐genome sequencing (WGS)‐based subtyping approaches the method of choice for many foodborne pathogens. Routine application of WGS in laboratory surveillance and monitoring of foodborne pathogens is transforming public health microbiology. With the increasing international trade of food and food animals, it is crucial that molecular subtyping methods for foodborne pathogens be harmonized worldwide to facilitate the rapid comparison of strains isolated in different countries. This method harmonization for comparison is best done in the framework of surveillance networks. The ongoing implementation of WGS provides an unprecedented opportunity to establish universal global standards for subtyping foodborne bacteria that will result in easily exchangeable data and global nomenclature.

Biological nitrogen fixation by microbial diazotrophs can contribute significantly to nitrogen availability in non-nodulating plant species. In this study of molecular mechanisms and gene expression relating to biological nitrogen fixation, the aerobic nitrogen-fixing endophyte Burkholderia vietnamiensis, strain WPB, isolated from Populus trichocarpa served as a model for endophyte–poplar interactions. Nitrogen-fixing activity was observed to be dynamic on nitrogen-free medium with a subset of colonies growing to form robust, raised globular like structures. Secondary ion mass spectrometry (NanoSIMS) confirmed that N-fixation was uneven within the population. A fluorescent transcriptional reporter (GFP) revealed that the nitrogenase subunit nifH is not uniformly expressed across genetically identical colonies of WPB and that only ~11% of the population was actively expressing the nifH gene. Higher nifH gene expression was observed in clustered cells through monitoring individual bacterial cells using single-molecule fluorescence in situ hybridization. Through 15N2 enrichment, we identified key nitrogenous metabolites and proteins synthesized by WPB and employed targeted metabolomics in active and inactive populations. We cocultivated WPB Pnif-GFP with poplar within a RhizoChip, a synthetic soil habitat, which enabled direct imaging of microbial nifH expression within root epidermal cells. We observed that nifH expression is localized to the root elongation zone where the strain forms a unique physical interaction with the root cells. This work employed comprehensive experimentation to identify novel mechanisms regulating both biological nitrogen fixation and beneficial plant–endophyte interactions.

The desire to understand how the brain generates and patterns behavior has driven rapid methodological innovation in tools to quantify natural animal behavior. While advances in deep learning and computer vision have enabled markerless pose estimation in individual animals, extending these to multiple animals presents unique challenges for studies of social behaviors or animals in their natural environments. Here we present Social LEAP Estimates Animal Poses (SLEAP), a machine learning system for multi-animal pose tracking. This system enables versatile workflows for data labeling, model training and inference on previously unseen data. SLEAP features an accessible graphical user interface, a standardized data model, a reproducible configuration system, over 30 model architectures, two approaches to part grouping and two approaches to identity tracking. We applied SLEAP to seven datasets across flies, bees, mice and gerbils to systematically evaluate each approach and architecture, and we compare it with other existing approaches. SLEAP achieves greater accuracy and speeds of more than 800 frames per second, with latencies of less than 3.5 ms at full 1,024 × 1,024 image resolution. This makes SLEAP usable for real-time applications, which we demonstrate by controlling the behavior of one animal on the basis of the tracking and detection of social interactions with another animal. SLEAP is a versatile deep learning-based multi-animal pose-tracking tool designed to work on videos of diverse animals, including during social behavior.

Bijvoet's method, which makes use of anomalous x-ray diffraction or dispersion, is the standard means of directly determining the absolute (stereochemical) configuration of molecules, but it requires crystalline samples and often proves challenging in structures exclusively comprising light atoms. Herein, we demonstrate a mass spectrometry approach that directly images the absolute configuration of individual molecules in the gas phase by cold target recoil ion momentum spectroscopy after laser ionizatior–induced Coulomb explosion. This technique is applied to the prototypical chiral molecule bromochlorofluoromethane and the isotopically chiral methane derivative bromodichloromethane.

A major challenge of analyzing the compositional structure of microbiome data is identifying its potential origins. Here, we introduce fast expectation-maximization microbial source tracking (FEAST), a ready-to-use scalable framework that can simultaneously estimate the contribution of thousands of potential source environments in a timely manner, thereby helping unravel the origins of complex microbial communities (https://github.com/cozygene/FEAST). The information gained from FEAST may provide insight into quantifying contamination, tracking the formation of developing microbial communities, as well as distinguishing and characterizing bacteria-related health conditions.FEAST provides a computationally efficient tool to estimate the contribution of microbial sources to a target microbial community, as demonstrated for a variety of complex environmental samples.