Placental tissue metabolome analysis by GC-MS: Oven-drying is a viable sample preparation method

Abstract

Analysis of the human placenta metabolome has great potential to advance the understanding of complicated pregnancies and deleterious fetal outcomes in remote populations, but samples preparation can present unique challenges. Herein, we introduce oven-drying as a simple and widely available method of sample preparation that will facilitate investigations of the placental metabolome from remote and under-studied populations. Placentae from complicated and uncomplicated pregnancies were prepared in three ways (oven-dried at 60?°C, fresh, lyophilized) for metabolome analysis via gas chromatography-mass spectrometry (GC-MS). Multiple computer models (e.g. PLS-DA, ANN) were employed to classify and determine if there was a difference in placentae metabolome and a group of metabolites with high variable importance in projection scores across the three preparations and by complicated vs. control groups. The analyses used herein were shown to be thorough and sensitive. Indeed, significant differences were detected in metabolomes of complicated vs. uncomplicated pregnancies; however, there were no statistical differences in the metabolome of placentae prepared by oven-drying vs. lyophilization vs. fresh placentae. Oven-drying is a viable sample preparation method for placentae intended for use in metabolite analysis via GC-MS. These results open many possibilities for researching metabolome patterns associated with fetal outcomes in remote and resource-poor communities worldwide.     

High throughput preparation of fly genomic DNA in 96-well format using a paint-shaker

Sample homogenization is an essential step for genomic DNA extraction, with multiple downstream applications in Molecular Biology. Genotyping hundreds or thousands of samples requires an automation of this homogenization step, and high throughput homogenizer equipment currently costs 7000 euros or more. We present an apparatus for homogenization of individual Drosophila adult flies in 96-well micro-titer dishes, which was built from a small portable paint-shaker (F5 portable paint-shaker, Ushake). Single flies are disrupted in each well that contains extraction buffer and a 4-mm metal ball. Our apparatus can hold up to five 96-well micro-titer plates. Construction of the homogenizer apparatus takes about 3–4 days, and all equipment can be obtained from a home improvement store. The total material cost is approximately 700 euros including the paint-shaker. We tested the performance of our apparatus using the ZR-96 Quick-gDNA? kit (Zymo Research) homogenization buffer and achieved nearly complete tissue homogenization after 15 minutes of shaking. PCR tests did not detect any cross contamination between samples of neighboring wells. We obtained on average 138 ng of genomic DNA per fly, and DNA quality was adequate for standard PCR applications. In principle, our tissue homogenizer can be used for isolation of DNA suitable for library production and high throughput genotyping by Multiplexed Shotgun Genotyping (MSG), as well as RNA isolation from single flies. The sample adapter can also hold and shake other items, such as centrifuge tubes (15–50 mL) or small bottles.     

Detection of Architectural Distortion in Prior Mammograms via Analysis of Oriented Patterns

We demonstrate methods for the detection of architectural distortion in prior mammograms of interval-cancer cases based on analysis of the orientation of breast tissue patterns in mammograms. We hypothesize that architectural distortion modifies the normal orientation of breast tissue patterns in mammographic images before the formation of masses or tumors. In the initial steps of our methods, the oriented structures in a given mammogram are analyzed using Gabor filters and phase portraits to detect node-like sites of radiating or intersecting tissue patterns. Each detected site is then characterized using the node value, fractal dimension, and a measure of angular dispersion specifically designed to represent spiculating patterns associated with architectural distortion.Our methods were tested with a database of 106 prior mammograms of 56 interval-cancer cases and 52 mammograms of 13 normal cases using the features developed for the characterization of architectural distortion, pattern classification via quadratic discriminant analysis, and validation with the leave-one-patient out procedure. According to the results of free-response receiver operating characteristic analysis, our methods have demonstrated the capability to detect architectural distortion in prior mammograms, taken 15 months (on the average) before clinical diagnosis of breast cancer, with a sensitivity of 80% at about five false positives per patient.     

Deep body and surface temperature responses to hot and cold environments in the zebra finch

Global warming increasingly challenges thermoregulation in endothermic animals, particularly in hot and dry environments where low water availability and high temperature increase the risk of hyperthermia. In birds, un-feathered body parts such as the head and bill work as ‘thermal windows’, because heat flux is higher compared to more insulated body regions. We studied how such structures were used in different thermal environments, and if heat flux properties change with time in a given temperature. We acclimated zebra finches (Taeniopygia guttata) to two different ambient temperatures, ‘cold’ (5 °C) and ‘hot’ (35 °C), and measured the response in core body temperature using a thermometer, and head surface temperature using thermal imaging. Birds in the hot treatment had 10.3 °C higher head temperature than those in the cold treatment. Thermal acclimation also resulted in heat storage in the hot group: core body temperature was 1.1 °C higher in the 35 °C group compared to the 5 °C group. Hence, the thermal gradient from core to shell was 9.03 °C smaller in the hot treatment. Dry heat transfer rate from the head was significantly lower in the hot compared to the cold treatment after four weeks of thermal acclimation. This reflects constraints on changes to peripheral circulation and maximum body temperature. Heat dissipation capacity from the head region increased with acclimation time in the hot treatment, perhaps because angiogenesis was required to reach peak heat transfer rate. We have shown that zebra finches meet high environmental temperature by heat storage, which saves water and energy, and by peripheral vasodilation in the head, which facilitates dry heat loss. These responses will not exclude the need for evaporative cooling, but will lessen the amount of energy expend on body temperature reduction in hot environments.     

Ultrafast molecular dynamics of biofuel extraction for microalgae and bacteria milking: blocking membrane folding pathways to damaged lipid-bilayer conformations with nanomicelles

Cell milking is a 100% renewable green energy for CO₂ by extraction of biofuels inside the cytosol of photosynthetic micro-organisms as microalgae and bacteria. The cells are exposed to a hydrophobic solvent forming holes and cracks through their membranes from which the biofuels can leak out. In protein folding, the goal would be to find pathways to the unique functional protein conformer. However, in the lipid-bilayer interaction with the solvent for milking, the objective is to block the pathways for damaged membrane conformations of low free energy with undesired nanostructures, using the solvent properties, as shown with an ab initio structural bioinformatic model. Statistical thermodynamics is used to compute the free energy (including entropy) from the molecular dynamics trajectory of the biomolecular system with many conformational changes. This model can be extended to the general problem of biomolecules folding as for proteins and nucleic acids. Using an adaptation of the Einstein diffusion law, the conformational change dynamics of the lipid bilayer depends on the two diffusion coefficients of the solvent: D₁ before the irreversible folding transition time and the much smaller D₂ thereafter. In contrast to the n-hexane and n-heptane hydrocarbons of smaller size, the residual D₂?=?4.7?×?10^?7?cm²/s of the n-decane solvent, with the highest partition coefficient among the three extractors, is the only to present a D₂ value that is significantly below the critical threshold of 10^?6?cm²/s. Therefore, the membrane would resist to long hydrocarbons and the exposed cells would remain viable for milking.     

Early-life exposure to a herbicide has enduring effects on pathogen-induced mortality

Exposure to stressors at formative stages in the development of wildlife and humans can have enduring effects on health. Understanding which, when and how stressors cause enduring health effects is crucial because these stressors might then be avoided or mitigated during formative stages to prevent lasting increases in disease susceptibility. Nevertheless, the impact of early-life exposure to stressors on the ability of hosts to resist and tolerate infections has yet to be thoroughly investigated. Here, we show that early-life, 6-day exposure to the herbicide atrazine (mean ± s.e.: 65.9±3.48 µg l⁻¹) increased frog mortality 46 days after atrazine exposure (post-metamorphosis), but only when frogs were challenged with a chytrid fungus implicated in global amphibian declines. Previous atrazine exposure did not affect resistance of infection (fungal load). Rather, early-life exposure to atrazine altered growth and development, which resulted in exposure to chytrid at more susceptible developmental stages and sizes, and reduced tolerance of infection, elevating mortality risk at an equivalent fungal burden to frogs unexposed to atrazine. Moreover, there was no evidence of recovery from atrazine exposure. Hence, reducing early-life exposure of amphibians to atrazine could reduce lasting increases in the risk of mortality from a disease associated with worldwide amphibian declines. More generally, these findings highlight that a better understanding of how stressors cause enduring effects on disease susceptibility could facilitate disease prevention in wildlife and humans, an approach that is often more cost-effective and efficient than reactive medicine.     

从能量角度粗谈人体的几个定量问题

本文构思源于线粒体的功能研究,从能量角度,分析了静息状态下裸露的人体散热及功耗,其中辐射散热占1／2以上,对流散热约1／3,排泄散热约1／8;进而讨论了人体所需食物、氧和水;同时探讨人体生理温度的维持,粗略计算了人体理想最低功耗及负熵量,提供了满足个体需求的简便算法,为越来越流行的节食减肥或节食长寿留下可供参考的红线。     

Monitoring vegetation change caused by trampling: a study in the Cairngorms,Scotland

Summary

A study was made in the Cairngorms, Scotland to make recommendations for a monitoring scheme capable of detecting changes in the vegetation caused by recreational pressure following the development of a funicular railway. Four methods were used in field trials to assess percentage cover of plant species and gravel, rock and bare ground, where appropriate, in two vegetation types (open and closed). The methods used were visual estimates in 50 × 40 cm quadrats (Q), the mean of visual estimates in twenty 10 × 10 cm sub-quadrats of the 50 × 40 cm quadrats (Q₂₀), a modified point intercept method (RL) and photography. Variances between observers and between-quadrats were estimated for the different methods. The sampling design for detecting change was based on a model of variance, constructed from field trial data.

Between-observer and between-quadrat variances were related to mean percentage cover and approximated to a binomial distribution. The between-quadrat variance was larger than observer variance. The Q₂₀ method achieved appreciably better precision than the other methods. Analysis of half of the 10 × 10 cmsub-quadrats (1/2Q₂₀) selected in a checker board design achieved a relative efficiency of 78% compared with the Q₂₀. This result suggests that comparable precision to the Q₂₀ method could be achieved by choosing about 14 sub-quadrats in a larger quadrat, thus saving some time. Variation between quadrats also suggested that the Q₂₀ method was the one of choice for maximising precision. The precision of the photographic method was based on fewer data points, so is less accurate than other estimates.

Minimum sample sizes were estimated for detecting a 10% relative change of a species in open vegetation with 30% cover (i.e. a change from 30% to <27 or to >33% cover). With a 10 % Type II error rate and 5 % Type I error rate the minimum sample sizes were 47 quadrats for Q, 18 for Q ₂₀, 43 for RL, and 23 for the means of ten 10 × 10 cm sub-quadrats in open vegetation.

The most time-efficient field recording appeared to be the use of Q despite the required sample size being 2.6 times higher than that of Q₂₀. The far lower time requirement per quadrat, however, compensated for the higher numbers. The number of quadrats would depend on the specified change in percentage cover and on the statistical significance level used. For example, to detect a 10% absolute change in cover (i.e. from 30% to either <20 % or >40 % cover) at 95 % probability the net effective recording time is estimated at 5 h per vegetation type while to detect a 5 % change at 99 % probability would require c. 25 h. Larger samples may be required for other species or for species with a low initial cover.     

The effect of harvest date and harvest method on the combustion characteristics of Miscanthus × giganteus

Miscanthus × giganteus is an energy crop with many attributes that make it a potential biofuel feedstock. This study examined the chemical composition of M. × giganteus stems cut at different dates throughout the spring harvest window (January, February and March) and either left in a swath or left flat in a thin layer on the ground and compared the composition to that of the standing crop collected on the same date in April (control). The research then examined the effect of cutting date on the chemical composition of whole plant M. × giganteus biomass (leaf and stem). The parameters examined in both parts of this experiment were lower heating value on a wet basis (LHV_WB), ash, chlorine, potassium, nitrogen, sulphur, carbon and hydrogen content. The range of values recorded for the parameters from both aspects of this trial were LHV_WB 4.84–11.87 MJ kg^?1; ash 1.44–1.97%; Cl 0.07–0.23%; K 0.15–0.32%; N 0.28–0.39%; S 0.13–0.19%; C 46.75–50.00%; H 5.76–6.09%. The length of time that the M. × giganteus remained in the field after cutting affected the LHV_WB (increased with time) of the stem biomass material. Cutting the biomass and leaving it in the field lowered the ash, Cl and C content of the stem material compared to that of the control which was cut and collected on the same date. No differences were observed for the other parameters. Date of harvest affected the LHV_WB, Cl and C content which all improved with later cutting dates. Thus, combustion quality can be improved by delaying the harvest date or by cutting the crop and leaving it in the field for a period prior to collection. Choosing the correct combination of time and harvest method can therefore improve biomass fuel quality.