Microfluidic approach to correlate C. elegans neuronal functional aging and underlying changes of gene expression in mechanosensation.

The aging process has broad physiological impacts, including a significant decline in sensory function, which threatens both physical health and quality of life. One ideal model to study aging, neuronal function, and gene expression is the nematode Caenorhabditis elegans, which has a short lifespan and relatively simple, thoroughly mapped nervous system and genome. Previous works have identified that mechanosensory neuronal structure changes with age, but importantly, the actual age-related changes in the function and health of neurons, as well as the underlying genetic mechanisms responsible for these declines, are not fully understood. While advanced techniques such as single-cell RNA-sequencing have been developed to quantify gene expression, it is difficult to relate this information to functional changes in aging due to a lack of tools available. To address these limitations, we present a platform capable of measuring both physiological function and its associated gene expression throughout the aging process in individuals. Using our pipeline, we investigate the age-related changes in function of the mechanosensing ALM neuron in C. elegans, as well as some relevant gene expression patterns (mec-4 and mec-10). Using a series of devices for animals of different ages, we examined subtle changes in neuronal function and found that while the magnitude of neuronal response to a large stimulus declines with age, sensory capability does not significantly decline with age; further, gene expression is well maintained throughout aging. Additionally, we examine PVD, a harsh-touch mechanosensory neuron, and find that it exhibits a similar age-related decline in magnitude of neuronal response. Together, our data demonstrate that our strategy is useful for identifying genetic factors involved in the decline in neuronal health. We envision that this framework could be applied to other systems as a useful tool for discovering new biology.

Oral Microbiome and Alzheimer's Disease.

The accumulation of amyloid-beta plaques in the brain is a central pathological feature of Alzheimer's disease. It is believed that amyloid responses may be a result of the host immune response to pathogens in both the central nervous system and peripheral systems. Oral microbial dysbiosis is a chronic condition affecting more than 50% of older adults. Recent studies have linked oral microbial dysbiosis to a higher brain Aß load and the development of Alzheimer's disease in humans. Moreover, the presence of an oral-derived and predominant microbiome has been identified in the brains of patients with Alzheimer's disease and other neurodegenerative diseases. Therefore, in this opinion article, we aim to provide a summary of studies on oral microbiomes that may contribute to the pathogenesis of the central nervous system in Alzheimer's disease.

Analysis of Eight Types of Plant-based Milk Alternatives from the United States Market for Target Minerals and Trace Elements.

A wide variety of commercial plant-based foods that are marketed and sold as alternatives for milk (plant-based milk alternatives or PBMAs) are available to consumers. In this study, PBMAs from the United States (n=85) were subjected to analysis for target minerals (magnesium, phosphorus, selenium, and zinc) to compare their variability across PBMA types, brands, and production lots. Samples were also screened for the environmental contaminant elements arsenic, cadmium, and lead. The eight PBMA types sampled were produced from almond, cashew, coconut, hemp, oat, pea, rice, and soy. Elemental analysis was conducted using microwave-assisted acid digestion followed by inductively coupled plasma-mass spectrometry. The results showed that pea PBMAs contained the highest mean amounts of phosphorus, selenium, and zinc, while soy PBMAs were highest in magnesium. Mean amounts of minerals were lower than those found in milk for the majority of PBMA types. There was significant variation (P<0.05) in amounts of minerals across the majority of product brands. The amounts of phosphorus and magnesium varied across production lots (P<0.05), but the absolute value of these differences was low. Total arsenic was highest in rice PBMAs; amounts of cadmium and lead across PBMAs were generally found at low or non-quantifiable amounts. These results underscore the importance of generating analytical data on the elemental composition of products within the rapidly growing category of PBMA.

Validation and interlaboratory comparison of anticoagulant rodenticide analysis in animal livers using ultra-performance liquid chromatography-mass spectrometry.

Anticoagulant rodenticides (ARs) are used to control rodent populations. Poisoning of non-target species can occur by accidental consumption of commercial formulations used for rodent control. A robust method for determining ARs in animal tissues is important for animal postmortem diagnostic and forensic purposes. We evaluated an ultra-performance liquid chromatography coupled with mass spectrometry (UPLC-MS) method to quantify 8 ARs (brodifacoum, bromadiolone, chlorophacinone, coumachlor, dicoumarol, difethialone, diphacinone, warfarin) in a wide range of animal (bovine, canine, chicken, equine, porcine) liver samples, including incurred samples. We further evaluated UPLC-MS in 2 interlaboratory comparison (ILC) studies; one an ILC exercise (ICE), the other a proficiency test (PT). The limits of detection of UPLC-MS were 0.3-3.1 ng/g, and the limits of quantification were 0.8-9.4 ng/g. The recoveries obtained using UPLC-MS were 90-115%, and relative SDs were 1.2-13% for each of the 8 ARs for the 50, 500, and 2,000 ng/g spiked liver samples. The overall accuracy from the laboratories participating in the 2 ILC studies (4 and 11 laboratories for ICE and PT studies, respectively) were 86-118%, with relative repeatability SDs of 3.7-11%, relative reproducibility SDs of 7.8-31.2%, and Horwitz ratio values of 0.5-1.5. Via the ILC studies, we verified the accuracy of UPLC-MS for AR analysis in liver matrices and demonstrated that ILC can be utilized to evaluate performance characteristics of analytical methods.

Market Basket Survey of the Micronutrients Vitamin A, Vitamin D, Calcium, and Potassium in Eight Types of Commercial Plant-Based Milk Alternatives from United States Markets.

We performed a market basket survey of plant-based milk alternatives (PBMAs) from the US market for vitamin A, vitamin D, calcium, and potassium to identify the amount and variability of these micronutrients across various PBMAs. The PBMA types included in this analysis were almond, cashew, coconut, hemp, oat, pea, rice, and soy (n=90 total product units). Analyses for vitamin A (as retinyl palmitate), vitamin D2/D3, and minerals were performed using high-performance liquid chromatography, liquid chromatography-tandem mass spectrometry, and inductively coupled plasma-mass spectrometry, respectively. A majority of PBMA types had significant differences (P<0.05) in the amounts of target micronutrients across brands. The coefficient of variation (%CV) for micronutrient concentrations within one lot of a single brand ranged from 4.1-42.2% for vitamin A, 1.5-44.1% for vitamin D, 1.7%-37.6% for calcium, and 0.7%-39.0% for potassium. The variability of these micronutrients should be taken into account when considering the nutritional value of PBMAs.

The power, potential, benefits, and challenges of implementing high-throughput sequencing in food safety systems.

The development and application of modern sequencing technologies have led to many new improvements in food safety and public health. With unprecedented resolution and big data, high-throughput sequencing (HTS) has enabled food safety specialists to sequence marker genes, whole genomes, and transcriptomes of microorganisms almost in real-time. These data reveal not only the identity of a pathogen or an organism of interest in the food supply but its virulence potential and functional characteristics. HTS of amplicons, allow better characterization of the microbial communities associated with food and the environment. New and powerful bioinformatics tools, algorithms, and machine learning allow for development of new models to predict and tackle important events such as foodborne disease outbreaks. Despite its potential, the integration of HTS into current food safety systems is far from complete. Government agencies have embraced this new technology, and use it for disease diagnostics, food safety inspections, and outbreak investigations. However, adoption and application of HTS by the food industry have been comparatively slow, sporadic, and fragmented. Incorporation of HTS by food manufacturers in their food safety programs could reinforce the design and verification of effectiveness of control measures by providing greater insight into the characteristics, origin, relatedness, and evolution of microorganisms in our foods and environment. Here, we discuss this new technology, its power, and potential. A brief history of implementation by public health agencies is presented, as are the benefits and challenges for the food industry, and its future in the context of food safety.

Enabling high-throughput single-animal gene-expression studies with molecular and micro-scale technologies.

Gene expression and regulation play diverse and important roles across all living systems. By quantifying the expression, whether in a sample of single cells, a specific tissue, or in a whole animal, one can gain insights into the underlying biology. Many biological questions now require single-animal and tissue-specific resolution, such as why individuals, even within an isogenic population, have variations in development and aging across different tissues and organs. The popular techniques that quantify the transcriptome (e.g. RNA-sequencing) process populations of animals and cells together and thus, have limitations in both individual and spatial resolution. There are single-animal assays available (e.g. fluorescent reporters); however, they suffer other technical bottlenecks, such as a lack of robust sample-handling methods. Microfluidic technologies have demonstrated various improvements throughout the years, and it is likely they can enhance the impact of these single-animal gene-expression assays. In this perspective, we aim to highlight how the engineering/method-development field have unique opportunities to create new tools that can enable us to robustly answer the next set of important questions in biology that require high-density, high-quality gene expression data.

An automated platform to monitor long-term behavior and healthspan in Caenorhabditis elegans under precise environmental control.

Health and longevity in all organisms are strongly influenced by the environment. To fully understand how environmental factors interact with genetic and stochastic factors to modulate the aging process, it is crucial to precisely control environmental conditions for long-term studies. In the commonly used model organism Caenorhabditis elegans, existing assays for healthspan and lifespan have inherent limitations, making it difficult to perform large-scale longitudinal aging studies under precise environmental control. To address these constraints, we developed the Health and Lifespan Testing Hub (HeALTH), an automated, microfluidic-based system for robust longitudinal behavioral monitoring. Our system provides long-term (i.e. entire lifespan) spatiotemporal environmental control. We demonstrate healthspan and lifespan studies under a variety of genetic and environmental perturbations while observing how individuality plays a role in the aging process. This system is generalizable beyond aging research, particularly for short- or long-term behavioral assays, and could be adapted for other model systems.

Mitigating osteonecrosis of the jaw (ONJ) through preventive dental care and understanding of risk factors.

It is well established that alterations in phosphate metabolism have a profound effect on hard and soft tissues of the oral cavity. The present-day clinical form of osteonecrosis of the jaw (ONJ) was preceded by phosphorus necrosis of the jaw, ca. 1860. The subsequent removal of yellow phosphorus from matches in the early 20th century saw a parallel decline in "phossy jaw" until the early 2000s, when similar reports of unusual jaw bone necrosis began to appear in the literature describing jaw necrosis in patients undergoing chemotherapy and concomitant steroid and bisphosphonate treatment. Today, the potential side effect of ONJ associated with medications that block osteoclast activity (antiresorptive) is well known, though the mechanism remains unclear and the management and outcomes are often unsatisfactory. Much of the existing literature has focused on the continuing concerns of appropriate use of bisphosphonates and other antiresorptive medications, the incomplete or underdeveloped research on ONJ, and the use of drugs with anabolic potential for treatment of osteoporosis. While recognizing that ONJ is a rare occurrence and ONJ-associated medications play an important role in fracture risk reduction in osteoporotic patients, evidence to date suggests that health care providers can lower the risk further by dental evaluations and care prior to initiating antiresorptive therapies and by monitoring dental health during and after treatment. This review describes the current clinical management guidelines for ONJ, the critical role of dental-medical management in mitigating risks, and the current understanding of the effects of predominantly osteoclast-modulating drugs on bone homeostasis.

A spontaneous complex structural variant in rcan-1 increases exploratory behavior and laboratory fitness of Caenorhabditis elegans.

Over long evolutionary timescales, major changes to the copy number, function, and genomic organization of genes occur, however, our understanding of the individual mutational events responsible for these changes is lacking. In this report, we study the genetic basis of adaptation of two strains of C. elegans to laboratory food sources using competition experiments on a panel of 89 recombinant inbred lines (RIL). Unexpectedly, we identified a single RIL with higher relative fitness than either of the parental strains. This strain also displayed a novel behavioral phenotype, resulting in higher propensity to explore bacterial lawns. Using bulk-segregant analysis and short-read resequencing of this RIL, we mapped the change in exploration behavior to a spontaneous, complex rearrangement of the rcan-1 gene that occurred during construction of the RIL panel. We resolved this rearrangement into five unique tandem inversion/duplications using Oxford Nanopore long-read sequencing. rcan-1 encodes an ortholog to human RCAN1/DSCR1 calcipressin gene, which has been implicated as a causal gene for Down syndrome. The genomic rearrangement in rcan-1 creates two complete and two truncated versions of the rcan-1 coding region, with a variety of modified 5' and 3' non-coding regions. While most copy-number variations (CNVs) are thought to act by increasing expression of duplicated genes, these changes to rcan-1 ultimately result in the reduction of its whole-body expression due to changes in the upstream regions. By backcrossing this rearrangement into a common genetic background to create a near isogenic line (NIL), we demonstrate that both the competitive advantage and exploration behavioral changes are linked to this complex genetic variant. This NIL strain does not phenocopy a strain containing an rcan-1 loss-of-function allele, which suggests that the residual expression of rcan-1 is necessary for its fitness effects. Our results demonstrate how colonization of new environments, such as those encountered in the laboratory, can create evolutionary pressure to modify gene function. This evolutionary mismatch can be resolved by an unexpectedly complex genetic change that simultaneously duplicates and diversifies a gene into two uniquely regulated genes. Our work shows how complex rearrangements can act to modify gene expression in ways besides increased gene dosage.

smFISH in chips: a microfluidic-based pipeline to quantify in situ gene expression in whole organisms.

Gene expression and genetic regulatory networks in multi-cellular organisms control complex physiological processes ranging from cellular differentiation to development to aging. Traditional methods to investigate gene expression relationships rely on using bulk, pooled-population assays (e.g. RNA-sequencing and RT-PCR) to compare gene expression levels in hypo- or hyper-morphic mutant animals (e.g. gain-of-function or knockout). This approach is limited, especially in complex gene networks, as these genetic mutations may affect the expressions of related genes in unforseen ways. In contrast, we developed a microfluidic-based pipeline to discover gene relationships in a single genetic background. The microfluidic device provides efficient reagent exchange and the ability to track individual animals. By automating a robust microfluidic reagent exchange strategy, we adapted and validated single molecule fluorescent in situ hybridization (smFISH) on-chip and combined this technology with live-imaging of fluorescent transcriptional reporters. Together, this multi-level information enabled us to quantify a gene expression relationship with single-animal resolution. While this microfluidic-based pipeline is optimized for live-imaging and smFISH C. elegans studies, the strategy is highly-adaptable to other biological models as well as combining other live and end-point biological assays, such as behavior-based toxicology screening and immunohistochemistry.

Rapid and multi-cycle smFISH enabled by microfluidic ion concentration polarization for in-situ profiling of tissue-specific gene expression in whole C. elegans.

Understanding gene regulation networks in multicellular organisms is crucial to decipher many complex physiological processes ranging from development to aging. One technique to characterize gene expression with tissue-specificity in whole organisms is single-molecule fluorescence in situ hybridization (smFISH). However, this protocol requires lengthy incubation times, and it is challenging to achieve multiplexed smFISH in a whole organism. Multiplexing techniques can yield transcriptome-level information, but they require sequential probing of different genes. The inefficient macromolecule exchange through diffusion-dominant transport across dense tissues is the major bottleneck. In this work, we address this challenge by developing a microfluidic/electrokinetic hybrid platform to enable multicycle smFISH in an intact model organism, Caenorhabditis elegans. We integrate an ion concentration polarization based ion pump with a microfluidic array to rapidly deliver and remove gene-specific probes and stripping reagents on demand in individual animals. Using our platform, we can achieve rapid smFISH, an order of magnitude faster than traditional smFISH protocols. We also demonstrate the capability to perform multicycle smFISH on the same individual samples, which is impossible to do off-chip. Our method hence provides a powerful tool to study individual-specific, spatially resolvable, and large-scale gene expression in whole organisms.

Determination of Multiresidue Pesticides in Botanical Dietary Supplements Using Gas Chromatography-Triple-Quadrupole Mass Spectrometry (GC-MS/MS).

A simplified sample preparation method in combination with gas chromatography-triple-quadrupole mass spectrometry (GC-MS/MS) analysis was developed and validated for the simultaneous determination of 227 pesticides in green tea, ginseng, gingko leaves, saw palmetto, spearmint, and black pepper samples. The botanical samples were hydrated with water and extracted with acetonitrile, magnesium sulfate, and sodium chloride. The acetonitrile extract was cleaned up using solid phase extraction with carbon-coated alumina/primary-secondary amine with or without C18. Recovery studies using matrix blanks fortified with pesticides at concentrations of 10, 25, 100, and 500 µg/kg resulted in average recoveries of 70-99% and relative standard deviation of 5-13% for all tested botanicals except for black pepper, for which lower recoveries of fortified pesticides were observed. Matrix-matched standard calibration curves revealed good linearity (r(2) > 0.99) across a wide concentration range (1-1000 µg/L). Nine commercially available tea and 23 ginseng samples were analyzed using this method. Results revealed 36 pesticides were detected in the 9 tea samples at concentrations of 2-3500 µg/kg and 61 pesticides were detected in the 23 ginseng samples at concentrations of 1-12500 µg/kg.

Numerical evaluation of lactoperoxidase inactivation during continuous pulsed electric field processing.

A computational fluid dynamics (CFD) model describing the flow, electric field and temperature distribution of a laboratory-scale pulsed electric field (PEF) treatment chamber with co-field electrode configuration was developed. The predicted temperature increase was validated by means of integral temperature studies using thermocouples at the outlet of each flow cell for grape juice and salt solutions. Simulations of PEF treatments revealed intensity peaks of the electric field and laminar flow conditions in the treatment chamber causing local temperature hot spots near the chamber walls. Furthermore, thermal inactivation kinetics of lactoperoxidase (LPO) dissolved in simulated milk ultrafiltrate were determined with a glass capillary method at temperatures ranging from 65 to 80 °C. Temperature dependence of first order inactivation rate constants was accurately described by the Arrhenius equation yielding an activation energy of 597.1 kJ mol(-1). The thermal impact of different PEF processes on LPO activity was estimated by coupling the derived Arrhenius model with the CFD model and the predicted enzyme inactivation was compared to experimental measurements. Results indicated that LPO inactivation during combined PEF/thermal treatments was largely due to thermal effects, but 5-12% enzyme inactivation may be related to other electro-chemical effects occurring during PEF treatments.

Effect of the ionic strength of pulsed electric field treatment medium on the physicochemical and structural characteristics of lactoferrin.

Pulsed electric field (PEF) treatment (35 kV cm(-1) for 19.2 µs using bipolar 2 µs pulses) was conducted on bovine lactoferrin (LF; 0.4 mg mL(-1)) prepared in simulated milk ultrafiltrate (SMUF), at concentrations between 0.2× and 2× normal strength, with electrical conductivities ranging from 0.17 to 1.04 S m(-1). The physicochemical and structural characteristics (LF content by a spectrophotometric and an ELISA method, surface hydrophobicity, electrophoretic mobility, far-UV circular dichroism spectra, and tryptophan fluorescence) of LF dissolved in SMUF of all strengths tested were not changed after PEF treatment. The PEF treatment of LF in 0.2 strength SMUF did not cause the release of LF-bound ferric ion into the aqueous phase, with a concentration of LF-bound iron being the same as that of the untreated LF control (174 µg L(-1)). However, in treatment media with higher ionic strengths, ferric ion was released from the LF molecule into the aqueous phase. The concentration of LF-bound iron decreased from 174 µg L(-1) for the LF treated in 0.2 strength SMUF to 80 µg L(-1) for that treated in double-strength SMUF. The results suggest that the PEF-induced iron depletion of LF does not appear to cause an appreciable conformational change in LF molecules. PEF treatment could be developed as a novel physical way to produce iron-depleted LF, as an alternative to the existing chemical method.

Alternative disinfection techniques to extend the shelf life of minimally processed iceberg lettuce.

Chlorination continues to be widely used by the fresh-cut industry for washing and disinfecting minimally processed fruits and vegetables. However, as chlorination has been reported to produce unhealthy by-products such as, chloramines and trihalomethanes, many alternative methods have been reported in the literature. This study examined the use of silver and hydrogen peroxide as possible alternative to chlorination. The results revealed an obvious bactericidal effect of hydrogen peroxide, silver and their combination on spoilage organisms. Combination of electrochemically generated silver (5 ppm) and hydrogen peroxide (0.4 ppm) caused significant (P < 0.05) reduction in the total plate count (0.87 log), Pseudomonas (2.66 logs), Enterobactericeae (1.61 logs) and yeast and mould (1.60 logs) immediately after washing in comparison to water washed shredded lettuce. However, washing with chlorinated water (5 ppm) under same conditions revealed insignificant reduction in TPC (0.17 log), Pseudomonas (0.60 log), Enterobactericeae (0.15 log) or yeast and mould (0.81 log) counts. Results revealed also that both sources of silver (electrochemical silver and silver nitrate) have similar disinfecting effects, however, electrochemical silver maintained the quality of washed lettuce.

Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme.

The crystal structure of biotin synthase from Escherichia coli in complex with S-adenosyl-L-methionine and dethiobiotin has been determined to 3.4 angstrom resolution. This structure addresses how "AdoMet radical" or "radical SAM" enzymes use Fe4S4 clusters and S-adenosyl-L-methionine to generate organic radicals. Biotin synthase catalyzes the radical-mediated insertion of sulfur into dethiobiotin to form biotin. The structure places the substrates between the Fe4S4 cluster, essential for radical generation, and the Fe2S2 cluster, postulated to be the source of sulfur, with both clusters in unprecedented coordination environments.

Detection of Listeria monocytogenes in salmon using the Probelia polymerase chain reaction system.

A validation was conducted on the performance of a commercially available polymerase chain reaction (PCR) kit (Probelia) in comparison with International Organization for Standardization (ISO) method 11290-1 (adopted as an Australian New Zealand Standard Method, AS/NZS 1766.2.16.1:1998) for the detection of Listeria monocytogenes in salmon samples. The validation was conducted following the guidelines of an Australian New Zealand Standard (Guide to Determining the Equivalence of Food Microbiology Test Methods, Part 1, Qualitative Tests, AS/NZS 4659.1:1999), which adopts an approach similar to that recommended by the Association of Analytical Communities Microbiology Method Validation Program for Performance Tested and Peer Verified Methods. The validation study involved the use of five cultures of L. monocytogenes, each challenged at a single level of inoculation into five different types of salmon samples. A total of 60 salmon samples (30 unchallenged and 30 challenged) were tested using both the PCR method and the ISO method. Results from this study indicated that the Probelia PCR method is equivalent to the ISO method. In addition, the detection sensitivity of the Probelia PCR system was determined as approximately 0.5 CFU per PCR assay (equivalent to 20 CFU/ml broth culture) for a pure culture of L. monocytogenes. The Probelia PCR method offers the advantage of detecting L. monocytogenes to genetic specificity within 48 to 50 h, whereas the ISO method requires 5 days for negative results with additional days for confirmed positive results by the use of other biochemical and cultural tests.

Thermal inactivation of reduced ferredoxin (flavodoxin):NADP+ oxidoreductase from Escherichia coli.

Ferredoxin (flavodoxin):NADP+ oxidoreductase (FNR) is an essential enzyme that supplies electrons from NADPH to support flavodoxin-dependent enzyme radical generation and enzyme activation. FNR is a monomeric enzyme that contains a non-covalently bound FAD cofactor. We report that reduced FNR from Escherichia coli is subject to inactivation due to unfolding of the protein and dissociation of the FADH(2) cofactor at 37 degrees C. The inactivation rate is temperature-dependent in a manner that parallels the thermal unfolding of the protein and is slowed by binding of ferredoxin or flavodoxin. Understanding factors that minimize inactivation is critical for utilizing FNR as an accessory protein for S-adenosyl-L-methionine-dependent radical enzymes and manipulating FNR as an electron source for biotechnology applications.

Electron acceptor specificity of ferredoxin (flavodoxin):NADP+ oxidoreductase from Escherichia coli.

Reduced flavodoxin I (Fld1) is required in Escherichia coli for reductive radical generation in AdoMet-dependent radical enzymes and reductive activation of cobalamin-dependent methionine synthase. Ferredoxin (Fd) and flavodoxin II (Fld2) are also present, although their precise roles have not been ascertained. Ferredoxin (flavodoxin):NADP+ oxidoreductase (FNR) was discovered in E. coli as an NADPH-dependent reductant of Fld1 that facilitated generation of active methionine synthase in vitro; FNR and Fld1 will also supply electrons for the reductive cleavage of AdoMet essential for generating protein or substrate radicals in pyruvate formate-lyase, class III ribonucleotide reductase, biotin synthase, and, potentially, lipoyl synthase. As part of ongoing efforts to understand the various redox pathways that will support AdoMet-dependent radical enzymes in E. coli, we have examined the relative specificity of E. coli FNR for Fd, Fld1, and Fld2. While FNR will reduce all three proteins, Fd is the kinetically and thermodynamically preferred partner. Fd binds to FNR with high affinity (K(d)