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Abstract Kaposi’s sarcoma (KS) is a cancer affecting skin and internal organs for which the Kaposi’s sarcoma associated herpesvirus (KSHV) is a necessary cause. Previous work has pursued KS diagnosis by quantifying KSHV DNA in skin biopsies using a point-of-care (POC) device which performs quantitative loop-mediated isothermal amplification (LAMP). These previous studies revealed that extracting DNA from patient biopsies was the rate limiting step in an otherwise rapid process. In this study, a simplified, POC-compatible alkaline DNA extraction, ColdSHOT, was optimized for 0.75 mm human skin punch biopsies. The optimized ColdSHOT extraction consistently produced 40,000+ copies of DNA per 5 µl reaction from 3 mg samples—a yield comparable to standard spin column extractions—within 1 h without significant equipment. The DNA yield was estimated sufficient for KSHV detection from KS-positive patient biopsies, and the LAMP assay was not affected by non-target tissue in the unpurified samples. Furthermore, the yields achieved via ColdSHOT were robust to sample storage in phosphate-buffered saline (PBS) or Tris-EDTA (TE) buffer prior to DNA extraction, and the DNA sample was stable after extraction. The results presented in this study indicate that the ColdSHOT DNA extraction could be implemented to simplify and accelerate the LAMP-based diagnosis of Kaposi’s sarcoma using submillimeter biopsy samples.

Abstract The increasing prevalence of antibiotic resistance threatens to make currently treatable bacterial diseases deadly again. As drug resistance rises, antibiotic susceptibility testing needs to adapt to allow for widespread, individualized testing. Paper-based diagnostics offer low-cost, disposable alternatives to traditional time consuming and costly in-house methods. Here, we describe a paper-based microfluidic device, called the Bac-PAC, capable of categorizing the antibiotic susceptibly of individual strains of Carbapenem-resistant Enterobacterales. Each chip provides a colored readout with actionable susceptibility classification of three antibiotics, thus maximizing the chances of identifying a viable therapy. We verified the technology on thirty bacterial strains with two dyes using six clinically relevant antibiotics. We demonstrated that the dried tests are stable for one month and can be incubated in a rechargeable coffee mug that reduces the need for external infrastructure.

Technologies for automating animal management and monitoring tasks can improve efficiency and productivity of livestock production. We developed the e-Synch system for automated control and monitoring the estrous cycle of cattle through intravaginal hormone delivery and sensing. Thus, our objective was to evaluate luteinizing hormone (LH) concentrations after intravaginal instillation of the Gonadotropin-releasing hormone (GnRH) analogue Gonadorelin with the e-Synch system. This system consists of an intravaginal electronically controlled automated hormone delivery and sensing device integrated with an IoT platform. Lactating Holstein cows with their estrous cycle synchronized were used in two experiments (Exp). In Exp 1, at 48 h after induction of luteolysis, cows (n=5-6 per group) were randomized to receive 100 µg of Gonadorelin through intramuscular (i.m.) injection, 100 µg of Gonadorelin in a 2 mL solution delivered with e-Synch, and an empty e-Synch device. In Exp 2, at 48 h after induction of luteolysis cows (n=6-7 per group) were randomized to receive 100 µg of Gonadorelin i.m., or an intravaginal treatment with e-Synch consisting of 100 or 1,000 µg of Gonadorelin in 2 or 10 mL of solution containing 10% citric acid as absorption enhancer. Circulating concentrations of LH were analyzed with linear mixed models with or without repeated measurements. In Exp 1, cows in the i.m. Gonadorelin treatment had a surge of LH whereas cows in the other two treatments did not have a surge of LH for up to 8 h after treatment. In Exp 2, the 1,000 µg dose of Gonadorelin elicited more LH release than the 100 µg dose, regardless of solution quantity. The overall LH response as determined by area under the curve, mean, and maximum LH concentrations was similar between cows receiving 1,000 µg of Gonadorelin delivered with e-Synch and 100 μg of Gonadorelin i.m. Increasing volume of solution for delivering the same dose of Gonadorelin partially increased LH release only for the 100 µg dose. We conclude that the e-Synch system could be used to automatically release Gonadorelin in a dose and volume that induces a surge of LH of similar magnitude than after i.m. injection of 100 μg of Gonadorelin. Also, the dose of Gonadorelin delivered by e-Synch is more critical than the volume of solution used.

The objective of this manuscript was to present the e-Synch system, integrating an intravaginal electronically controlled hormone delivery and sensing device with an IoT platform for remote programming and monitoring. Secondary objectives were to demonstrate system functionality and cow responses to e-Synch. External components of e-Synch include a 3D-printed case with retention wings, a flexible wideband antenna, and silicone membrane for pressure balancing. Internal components include a central control board, battery, wireless charging coil, and two silicone hormone reservoirs connected to individual peristaltic pumps. An accelerometer and a high-accuracy temperature sensor are integrated in the custom printed circuit board (PCB). The IoT platform includes a gateway consisting of Raspberry PI 3 and a CC1352 radiofrequency module that collects sensor data at 915 mHz. Data is transferred to the Google Cloud utilizing the IoT Core service through TCP/IP, and then is pulled by the Pub/Sub service. After routing to a BigQuery table by the Dataflow service, data visualization is provided by Data Studio. Drug delivery protocols are selected using an IOS device app that connects to e-Synch through Bluetooth. Experiments with lactating Holsteins cows were conducted to demonstrate proof-of-concept system functionality and evaluate cow responses. Despite unstable communication and signal discontinuity because of signal strength attenuation by body tissue, devices (n=6) communicated with the IoT platform in 89% (24/27) of use instances. Temperature and accelerometer data were received for at least one 15 min period during an 8 h insertion period from all devices that communicated with the IoT platform. Variation in accelerometer data (± 8.565 m/s2) was consistent with cow activity during experimentation and mean vaginal temperature of 39.1 °C (range 38.6 to 39.5 °C) demonstrated sensor functionality. Hormone release was confirmed in all instances of device use except for one. Cow behavior evaluated through signs of discomfort and pain, and tail raising scores was mostly unaltered by e-Synch. Vaginal integrity and mucus scores also remained unaltered during and after device insertion. In conclusion, the e-Synch device integrated with a controlling app and IoT platform might be used to automate intravaginal hormone delivery and sensing for controlling the estrous cycle of cattle.

Gonorrhea, caused by Neisseria gonorrhoeae, is a global disease that disproportionately impacts low- and middle-income countries. Current testing methods have failed to significantly reduce disease burden, thereby allowing untreated gonorrhea infections to cause infertility and contribute to the spread of antibiotic resistance. Therefore, low-cost testing is desperately needed to combat this obligate human pathogen. Here, we developed a lateral flow assay (LFA) that identifies N. gonorrhoeae infection at the point of care (POC). The LFA utilizes whole cell bacteria without pretreatment, thus allowing for viable cell recovery after testing. While other LFAs require preheating or multiple lysing steps, our assay displays high accuracy with a single sample application step, thus making it easier for an untrained user and enabling true at-home diagnosis of gonorrhea. Furthermore, we were able to recover viable N. gonorrhoeae cells from the positive test line, thus enabling downstream antibiotic susceptibility testing. This colorimetric, paper-based, reader-free system costs $0.38 USD per test and can improve upon syndromic management currently employed in low-resource and POC settings.

Aflatoxins (AFs) are naturally occurring mycotoxins known to cause a considerable threat to food safety and affect animal and health. Rapid and reliable analytical methods are crucial for preventing AF contamination in the global food supply chain. Many conventional AF detection methods involve complex sample preparation steps, lengthy analysis times, and multiple handling stages which lead to delays in obtaining results, in addition to being unaffordable in many settings with resource constraints. Herein, we demonstrate the proof of concept of a competitive immunochromatographic (IC) strip test for quantification of total AF using commercially available antibodies and a low-cost portable CubeTM analyzer. We conducted preliminary testing of our point-of-need (PON) AF detection method with corn samples and results indicated a good agreement when compared with gold standard HPLC method. Furthermore, a detection range of 5–50 ppb with detection time of 5 min, makes this technology suitable for rapid testing and meets the regulatory requirements for AF detection in food samples. We also demonstrate the real-time data sharing capabilities of the reader to a proof-of-concept centralized and cloud-based AF databank, that we developed to provide timely monitoring for different parts of food systems. It is critical for the test data to be easily accessible within a food systems dashboard to enable early warning, data-driven decision-making, rapid interventions, and improve overall coordination between various stakeholders within the food system.

The timely diagnosis of active tuberculosis disease (TB) is crucial to interrupt the transmission and combat the spread of Mycobacterium tuberculosis (Mtb), the causative agent for TB. Here, we demonstrate the development of a specimen-direct rapid diagnostic method for TB which consists of an isothermal amplification device, Tiny Isothermal Nucleic acid quantification sYstem (TINY), coupled with helicase-dependent amplification (HDA). HDA, an isothermal amplification technique is established over TINY using pUCIDT-AMP vector carrying IS6110, the target DNA sequence for Mtb. The limit of detection of this technique for detecting the IS6110 within a threshold time of 50 min is 2.5 × 105 copies of IS6110. HDA in TINY for TB detection was evaluated using three IS6110-positive Mtb strains – H37Rv, CDC 1551, and Erdman wild-type and one IS6110-negative Mycobacterium avium. For spiked oral swabs, HDA in TINY detects IS6110 without any non-specificity in relatively short turnaround time (

Prostate cancer (PCa) is the second most diagnosed cancer among men. Targeted PCa screening may decrease PCa-specific mortality. Prostate-specific antigen (PSA) is the most reliable and widely accepted tumor biomarker for screening and monitoring PCa status. However, in many settings, quantification of serum PSA requires access to centralized laboratories. In this study, we describe a proof-of-concept rapid test combined with a highly portable CubeTM reader for quantification of total PSA from a drop of serum within 20 min. We demonstrated the application of gold nanoshells as a label for lateral flow assay with significant increase in the measured colorimetric signal intensity to achieve five times lower detection limit when compared to the traditionally used 40 nm gold nanosphere labels, without a need for any additional signal amplification steps. We first optimized and evaluated the performance of the assay with commercially available total PSA calibrators. For initial validation with commercially available ACCESS Hybritech PSA calibrator, a detection range of 0.5–150 ng/mL was achieved. We compared the performance of our total PSA test with IMMULITE analyzer for quantification of total PSA in archived human serum samples. On preliminary testing with archived serums samples and comparison with IMMULITE total PSA assay, a correlation of 0.95 (p

Abstract Background Full chloroplast genomes provide high resolution taxonomic discrimination between closely related plant species and are quickly replacing single and multi-locus barcoding regions as reference materials of choice for DNA based taxonomic annotation of plants. Bixa orellana, commonly known as “achiote” and “annatto” is a plant used for both human and animal foods and was thus identified for full chloroplast sequencing for the Center for Veterinary Medicine (CVM) Complete Chloroplast Animal Feed database. This work was conducted in collaboration with the Instituto de Medicina Tradicional (IMET) in Iquitos, Peru. There is a wide range of color variation in pods of Bixa orellana for which genetic loci that distinguish phenotypes have not yet been identified. Here we apply whole chloroplast genome sequencing of “red” and “yellow” individuals of Bixa orellana to provide high quality reference genomes to support kmer database development for use identifying this plant from complex mixtures using shotgun data. Additionally, we describe chloroplast gene content, synteny and phylogeny, and identify an indel and snp that may be associated with seed pod color. Results Fully assembled chloroplast genomes were produced for both red and yellow Bixa orellana accessions (158,918 and 158,823 bp respectively). Synteny and gene content was identical to the only other previously reported full chloroplast genome of Bixa orellana (NC_041550). We observed a 17 base pair deletion at position 58,399–58,415 in both accessions, relative to NC_041550 and a 6 bp deletion at position 75,531–75,526 and a snp at position 86,493 in red Bixa orellana. Conclusions Our data provide high quality reference genomes of individuals of red and yellow Bixa orellana to support kmer based identity markers for use with shotgun sequencing approaches for rapid, precise identification of Bixa orellana from complex mixtures. Kmer based phylogeny of full chloroplast genomes supports monophylly of Bixaceae consistent with alignment based approaches. A potentially discriminatory indel and snp were identified that may be correlated with the red phenotype.

Summary: Background: Early and accurate determination of bacterial infections as a potential cause for a patient's systemic inflammatory response is required for timely administration of appropriate treatment and antibiotic stewardship. Procalcitonin (PCT) and C-reactive protein (CRP) have both been used as biomarkers to infer bacterial infections, particularly in the context of sepsis. There is an urgent need to develop a platform for simultaneous quantification of PCT and CRP, to enable the potential use of these biomarkers at the point-of-care. Methods: A multiplexed lateral flow assay (LFA) and a fluorescence optical reader were developed. Assay performance was validated by testing spiked antigens in the buffer, followed by a validation study comparing results with conventional assays (Roche Cobas e411 Elecsys PCT and Siemens ADVIA XPT CRP) in 25 archived remnant human serum samples. Findings: A linear regression correlation of 0·97 (P

In photoreactors, non-uniform light distribution leads to regions either with an overabundance of light or insufficient light irradiation. The integration of light-guiding elements such as waveguides into photocatalytic reactors has been an emerging approach to improve light delivery. However, traditional waveguides with constant surface properties experience an exponential decay in scattering light intensity under side irradiation. This reduces the light propagation length and hinders the scale-up potential. In this work, we derive the relationship between attenuation coefficients with etching time, determine the correlation between etching time and waveguide location for uniform scattering, and experimentally validate different light scattering profiles by engineering the surface roughness distribution of waveguides. We apply a dimensionless number, the coefficient of variation, to characterize the relative light distribution uniformity for gradient-etched, uniform-etched, and unmodified waveguides. Scattering light uniformity via gradient etching is more than 13 times higher than that for uniform-etching. In addition, the light distribution for gradient etching exhibits improved uniformity than other approaches, such as tip coating, physical carving, and engineered pillars. We then evaluate the effect of different light scattering profiles on photocatalytic activities in a photodegradation test for methylene blue, with non-etched, uniform-etched, and gradient-etched waveguides serving as internal light-guiding elements. Gradient-etched waveguides show ∼4 times improvement in photodegradation activity over uniform-etched designs and ∼8 times over non-etched configurations. This result underscores gradient etching for waveguides as a viable approach for precision light delivery to increase the light distribution uniformity, thus enhancing reaction rates for photocatalytic reactors.

Background: Inflammation is a key component of immune response to infections and pathogenesis of metabolic and cardiovascular diseases. Inflammatory biomarkers, including alpha-1-acid glycoprotein (AGP), are considered prognostic tools for predicting risk, monitoring response to therapy, and adjusting nutritional biomarkers for accurate interpretation. Serum is considered a primary source of biomarkers; urine and saliva are increasingly being explored and utilized as rapidly accessible, noninvasive biofluids requiring minimal sample processing and posing fewer biohazard risks. Methods: A lateral flow immunoassay was developed for an established mobile-based platform to quantify AGP in human serum, urine, and saliva. Assay performance was assessed with purified AGP in buffer, diluted human serum samples (n = 16) banked from a trial in people living with HIV, and saliva and urine (n = 15 each) from healthy participants. Reference methods were conventional clinical chemistry analyzer or commercial ELISA. Bootstrap analysis was used to train and validate sample calibration. Findings: The correlation between the assay and reference method for serum was 0.97 (P

Migrating cells tune their energy utilization in response to their microenvironment, but how cellular energetics direct navigation remains unclear. Here, the authors report that energetic costs for motility, regulated by cell mechanics and confinement, predict the probability of migration choice.

Abstract Background Malaria continues to impose a tremendous burden in terms of global morbidity and mortality, yet even today, a large number of diagnoses are presumptive resulting in lack of or inappropriate treatment. Methods In this work, a two-colour lateral flow immunoassay (LFA) system was developed to identify infections by Plasmodium spp. and differentiate Plasmodium falciparum infection from the other three human malaria species (Plasmodium vivax, Plasmodium ovale, Plasmodium malariae). To achieve this goal, red and blue colours were encoded to two markers on a single test line of strips, for simultaneous detection of PfHRP2 (red), a marker specific for P. falciparum infection, and pLDH (blue), a pan-specific marker for infections by all species of Plasmodium. The assay performance was first optimized and evaluated with recombinant malarial proteins spiked in washing buffer at various concentrations from 0 to 1000 ng mL−1. The colour profiles developed on the single test line were discriminated and quantified: colour types corresponded to malaria protein species; colour intensities represented protein concentration levels. Results The limit of detection (the lowest concentrations of malaria antigens that can be distinguished from blank samples) and the limit of colour discrimination (the limit to differentiate pLDH from PfHRP2) were defined for the two-colour assay from the spiked buffer test, and the two limits were 31.2 ng mL−1 and 7.8 ng mL−1, respectively. To further validate the efficacy of the assay, 25 human whole blood frozen samples were tested and successfully validated against ELISA and microscopy results: 15 samples showed malaria negative; 5 samples showed P. falciparum positive; 5 samples showed P. falciparum negative, but contained other malaria species. Conclusions The assay provides a simple method to quickly identify and differentiate infection by different malarial parasites at the point-of-need and overcome the physical limitations of traditional LFAs, improving the multiplexing potential for simultaneous detection of various biomarkers.

Background: Iron deficiency (ID) and anaemia are major health concerns, particularly in young children. Screening for ID based on haemoglobin (Hb) concentration alone has been shown to lack sensitivity and specificity. The American Academy of Pediatrics (AAP) recommends soluble transferrin receptor (sTfR) as a promising approach to screen for iron deficiency. However, in most settings, assessment of iron status requires access to centralized laboratories. There is an urgent need for rapid, sensitive, and affordable diagnostics for sTfR at the point-of-care. Methods: An immunochromatographic assay-based point-of-care screening device was developed for rapid quantification of sTfR from a drop of serum within a few minutes. Performance optimization of the assay was done in sTfR-spiked buffer and commercially available sTfR calibrator, followed by a small-scale proof-of-concept validation with archived serum samples. Findings: On preliminary testing with archived serum samples and comparison with Ramco ELISA, a correlation of 0.93 (P

[This corrects the article DOI: 10.1371/journal.pone.0237507.].

Summary: In this work, we introduce HI-Light, a surface-engineered glass-waveguide-based “shell-and-tube” type photothermal reactor which is both scalable in diameter and length. We examine the effect of temperature, light irradiation, and residence time on its photo-thermocatalytic performance for CO2 hydrogenation to form CO, with a cubic phase defect-laden indium oxide, In2O3-x(OH)y, catalyst. We demonstrate the light enhancement effect under a variety of reaction conditions. Notably, the light-on performance for the cubic nanocrystal photocatalyst exhibits a CO evolution rate at 15.40 mmol gcat−1 hr−1 at 300°C and atmospheric pressure. This is 20 times higher conversion rate per unit catalyst mass per unit time beyond previously reported In2O3-x(OH)y catalyst in the cubic form under comparable operation conditions and more than 5 times higher than that of its rhombohedral polymorph. This result underscores that improvement in photo-thermocatalytic reactor design enables uniform light distribution and better reactant/catalyst mixing, thus significantly improving catalyst utilization.

OBJECTIVES/GOALS: To develop a loop-mediated isothermal amplification (LAMP) assay for the detection of cytomegalovirus (CMV) infection and drug resistance. METHODS/STUDY POPULATION: We designed core and loop primers sets utilizing the NEB LAMP Primer Design Tool. Each set contained four or six primers targeting major-immediate early genes – essential for viral entry/replication – or regions known to confer resistance to the antiviral drug ganciclovir. Optimization of reactions conditions was achieved employing DNA reference materials. Reactions were visualized through a change in color as amplification reactions accumulated. Successful reaction conditions were selected based on specific amplification products in less than 60 minutes. Limits of detection were evaluated as the main performance outcome. RESULTS/ANTICIPATED RESULTS: Genomic data were extracted and used to design a series of LAMP primers (48 total) that aimed to detect specific genomic regions of CMV. Using this strategy, we successfully designed and identified eight primer sets that showed high 100% sensitivity and 100 % specificity, when detecting > 1.00 x 10^5 copies/mL of CMV gDNA. We are in the process of characterizing a new set of primers to determine the diagnostic utility of a LAMP assay in detecting selected single-nucleotide mutations at the UL97 loci. The expected outcomes at completion include: (1) the identification of LAMP primers to detect drug-resistance mutants, (2) defining optimal conditions for successful reactions, and (3) determining limits of detection for subsequent validation with clinical specimens. DISCUSSION/SIGNIFICANCE: CMV infection remains one of the most dangerous infectious agents for immunocompromised hosts, newborns, and unborn children. This study will describe a proof-of-concept LAMP assay for the genotypic detection of drug resistance in CMV-infected individuals and hence, create new avenues for selection of effective therapies to treat CMV disease.

DNA barcoding can identify biological species and provides an important tool in diverse applications, such as conserving species and identifying pathogens, among many others. If combined with statistical tests, DNA barcoding can focus taxonomic scrutiny onto anomalous species identifications based on morphological features. Accordingly, we put nonparametric tests into a taxonomic context to answer questions about our sequence dataset of the formal fungal barcode, the nuclear ribosomal internal transcribed spacer (ITS). For example, does DNA barcoding concur with annotated species identifications significantly better if expert taxonomists produced the annotations? Does species assignment improve significantly if sequences are restricted to lengths greater than 500 bp? Both questions require a figure of merit to measure of the accuracy of species identification, typically provided by the probability of correct identification (PCI). Many articles on DNA barcoding use variants of PCI to measure the accuracy of species identification, but do not provide the variants with names, and the absence of explicit names hinders the recognition that the different variants are not comparable from study to study. We provide four variant PCIs with a name and show that for fixed data they follow systematic inequalities. Despite custom, therefore, their comparison is at a minimum problematic. Some popular PCI variants are particularly vulnerable to errors in species annotation, insensitive to improvements in a barcoding pipeline, and unable to predict identification accuracy as a database grows, making them unsuitable for many purposes. Generally, the Fractional PCI has the best properties as a figure of merit for species identification. The fungal genus Ramaria provides unusual taxonomic difficulties. As a case study, it shows that a good taxonomic background can be combined with the pertinent summary statistics of molecular results to improve the identification of doubtful samples, linking both disciplines synergistically.

Folate is a micronutrient required for the production of new cells, making it a key factor in early fetal development and ensuring normal growth and maintenance of health. The increase in consumption of folate due to increased periconceptional supplementation and fortification of grains in many countries has led to a decrease in occurrence of folate deficiency and a class of birth defects called neural tube defects. However, an opportunity remains to further improve folate status of populations in areas with limited access to fortified foods and supplementation. Screening of women of reproductive age and other vulnerable populations for folate status would increase our understanding of the magnitude of the burden of folate deficiency and inform monitoring of public health programs. Current gold standard methods for folate assessment are time-intensive and require cold chain, sophisticated laboratory infrastructure, and highly-trained personnel. Our lateral flow assay is low-cost, easy to use, and allows a user to assess folate insufficiency at the point of care in less than 40 minutes. We evaluated the sensitivity and specificity of our assay in 24 human serum samples, including 8 samples with folate concentrations less than 10.0 nmol/L and 14 samples less than 13.4 nmol/L using the Immulite 2000 commercial assay as a reference standard. The sensitivity and specificity were found to be 93% (95% CI: 54.7-100.0) and 91% (95% CI: 80.0-100.0), respectively, when using our test to determine folate insufficiency based on a cutoff of 13.4 nmol/L. Our point-of-care diagnostic test for folate concentrations could inform screening and public health programs in at-risk populations.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Resource-limited settings present unique engineering challenges for medical diagnostics. Diagnosis is often needed for those unable to reach central healthcare systems, making portability and independence from traditional energy infrastructure essential device parameters. In 2014, our group presented a microfluidic device that performed a solar-powered variant of the polymerase chain reaction, which we called solar thermal PCR. In this work, we expand on our previous effort by presenting an integrated, portable, solar thermal PCR system targeted towards the diagnosis of Kaposi's sarcoma. We call this system KS-Detect, and we now report the system's performance as a diagnostic tool using pseudo-biopsy samples made from varying concentrations of human lymphoma cell lines positive for the KS herpesvirus (KSHV). KS-Detect achieved 83% sensitivity and 70% specificity at high (≥ 10%) KSHV+ cell concentrations when diagnosing pseudo-biopsy samples by smartphone image. Using histology, we confirm that our prepared pseudo-biopsies contain similar KSHV+ cell concentrations as human biopsies positive for KS. Through our testing of samples derived from human cell lines, we validate KS-Detect as a viable, portable KS diagnostic tool, and we identify critical engineering considerations for future solar-thermal PCR devices.

Australia's Great Sandy Region is of international significance containing two World Heritage areas and patches of rainforest growing on white sand. Previous broad-scale analysis found the Great Sandy biogeographic subregion contained a significantly more phylogenetically even subset of species than expected by chance contrasting with rainforest on white sand in Peru. This study aimed to test the patterns of rainforest diversity and relatedness at a finer scale and to investigate why we may find different patterns of phylogenetic evenness compared with rainforests on white sands in other parts of the world. This study focussed on rainforest sites within the Great Sandy and surrounding areas in South East Queensland (SEQ), Australia. We undertook field collections, expanded our three-marker DNA barcode library of SEQ rainforest plants and updated the phylogeny to 95% of the SEQ rainforest flora. We sampled species composition of rainforest in fixed area plots from 100 sites. We calculated phylogenetic diversity (PD) measures as well as species richness (SR) for each rainforest community. These combined with site variables such as geology, were used to evaluate patterns and relatedness. We found that many rainforest communities in the Great Sandy area were significantly phylogenetically even at the individual site level consistent with a broader subregion analysis. Sites from adjacent areas were either not significant or were significantly phylogenetically clustered. Some results in the neighbouring areas were consistent with historic range expansions. In contrast with expectations, sites located on the oldest substrates had significantly lower phylogenetic diversity (PD). Fraser Island was once connected to mainland Australia, our results are consistent with a region geologically old enough to have continuously supported rainforest in refugia. The interface of tropical and temperate floras in part also explains the significant phylogenetic evenness and higher than expected phylogenetic diversity.

[This corrects the article DOI: 10.1371/journal.pone.0156913.].

Studies of forest dynamics plots (FDPs) have revealed a variety of negative density-dependent (NDD) demographic interactions, especially among conspecific trees. These interactions can affect growth rate, recruitment and mortality, and they play a central role in the maintenance of species diversity in these complex ecosystems. Here we use an equal area annulus (EAA) point-pattern method to comprehensively analyze data from two tropical FDPs, Barro Colorado Island in Panama and Sinharaja in Sri Lanka. We show that these NDD interactions also influence the continued evolutionary diversification of even distantly related tree species in these FDPs. We examine the details of a wide range of these interactions between individual trees and the trees that surround them. All these interactions, and their cumulative effects, are strongest among conspecific focal and surrounding tree species in both FDPs. They diminish in magnitude with increasing phylogenetic distance between heterospecific focal and surrounding trees, but do not disappear or change the pattern of their dependence on size, density, frequency or physical distance even among the most distantly related trees. The phylogenetic persistence of all these effects provides evidence that interactions between tree species that share an ecosystem may continue to promote adaptive divergence even after the species' gene pools have become separated. Adaptive divergence among taxa would operate in stark contrast to an alternative possibility that has previously been suggested, that distantly related species with dispersal-limited distributions and confronted with unpredictable neighbors will tend to converge on common strategies of resource use. In addition, we have also uncovered a positive density-dependent effect: growth rates of large trees are boosted in the presence of a smaller basal area of surrounding trees. We also show that many of the NDD interactions switch sign rapidly as focal trees grow in size, and that their cumulative effect can strongly influence the distributions and species composition of the trees that surround the focal trees during the focal trees' lifetimes.

Australian rainforests have been fragmented due to past climatic changes and more recently landscape change as a result of clearing for agriculture and urban spread. The subtropical rainforests of South Eastern Queensland are significantly more fragmented than the tropical World Heritage listed northern rainforests and are subject to much greater human population pressures. The Australian rainforest flora is relatively taxonomically rich at the family level, but less so at the species level. Current methods to assess biodiversity based on species numbers fail to adequately capture this richness at higher taxonomic levels. We developed a DNA barcode library for the SE Queensland rainforest flora to support a methodology for biodiversity assessment that incorporates both taxonomic diversity and phylogenetic relationships. We placed our SE Queensland phylogeny based on a three marker DNA barcode within a larger international rainforest barcode library and used this to calculate phylogenetic diversity (PD). We compared phylo- diversity measures, species composition and richness and ecosystem diversity of the SE Queensland rainforest estate to identify which bio subregions contain the greatest rainforest biodiversity, subregion relationships and their level of protection. We identified areas of highest conservation priority. Diversity was not correlated with rainforest area in SE Queensland subregions but PD was correlated with both the percent of the subregion occupied by rainforest and the diversity of regional ecosystems (RE) present. The patterns of species diversity and phylogenetic diversity suggest a strong influence of historical biogeography. Some subregions contain significantly more PD than expected by chance, consistent with the concept of refugia, while others were significantly phylogenetically clustered, consistent with recent range expansions.

In addition to the well characterized function of chemokines in mediating the homing and accumulation of leukocytes to tissues, some chemokines also exhibit potent antimicrobial activity. Little is known of the potential role of chemokines in bovine mammary gland health and disease. The chemokine CCL28 has previously been shown to play a key role in the homing and accumulation of IgA antibody secreting cells to the lactating murine mammary gland. CCL28 has also been shown to act as an antimicrobial peptide with activity demonstrated against a wide range of pathogens including bacteria, fungi and protozoans. Here we describe the cloning and function of bovine CCL28 and document the concentration of this chemokine in bovine milk. Bovine CCL28 was shown to mediate cellular chemotaxis via the CCR10 chemokine receptor and exhibited antimicrobial activity against a variety of bovine mastitis causing organisms. The concentration of bovine CCL28 in milk was found to be highly correlated with the lactation cycle. Highest concentrations of CCL28 were observed soon after parturition, with levels decreasing over time. These results suggest a potential role for CCL28 in the prevention/resolution of bovine mastitis.

The metabolism of birds is finely tuned to their activities and environments, and thus research on avian systems can play an important role in understanding organismal responses to environmental changes. At present, however, the physiological monitoring of bird metabolism is limited by the inability to take real-time measurements of key metabolites during flight. In this study, we present an implantable biosensor system that can be used for continuous monitoring of uric acid levels of birds during various activities including flight. The system consists of a needle-type enzymatic biosensor for the amperometric detection of uric acid in interstitial fluids. A lightweight two-electrode potentiostat system drives the biosensor, reads the corresponding output current and wirelessly transfers the data or records to flash memory. We show how the device can be used to monitor, in real time, the effects of short-term flight and rest cycles on the uric acid levels of pigeons. In addition, we demonstrate that our device has the ability to measure uric acid level increase in homing pigeons while they fly freely. Successful application of the sensor in migratory birds could open up a new way of studying birds in flight which would lead to a better understanding of the ecology and biology of avian movements.