Validation Between Gene Expression Measurement Platforms

https://openworks.mdanderson.org/sumexp22/1088/thumbnail.jp

Evaluation of laser-based spectrometers for greenhouse gas flux measurements in coastal marshes

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Limnology and Oceanography: Methods 14 (2016): 466–476, doi:10.1002/lom3.10105.Precise and rapid analyses of greenhouse gases (GHGs) will advance understanding of the net climatic forcing of coastal marsh ecosystems. We examined the ability of a cavity ring down spectroscopy (CRDS) analyzer (Model G2508, Picarro) to measure carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) fluxes in real-time from coastal marshes through comparisons with a Shimadzu GC-2014 (GC) in a marsh mesocosm experiment and with a similar laser-based N2O analyzer (Model N2O/CO, Los Gatos Research) in both mesocosm and field experiments. Minimum (analytical) detectable fluxes for all gases were more than one order of magnitude lower for the Picarro than the GC. In mesocosms, the Picarro analyzer detected several CO2, CH4, and N2O fluxes that the GC could not, but larger N2O fluxes (218–409 μmol m−2 h−1) were similar between analyzers. Minimum detectable fluxes for the Picarro were 1 order of magnitude higher than the Los Gatos analyzer for N2O. The Picarro and Los Gatos N2O fluxes (3–132 μmol m−2 h−1) differed in two mesocosm nitrogen addition experiments, but were similar in a mesocosm with larger N2O fluxes (326–491 μmol m−2 h−1). In a field comparison, Picarro and Los Gatos N2O fluxes (13 ± 2 μmol m−2 h−1) differed in plots receiving low nitrogen loads but were similar in plots with higher nitrogen loads and fluxes roughly double in magnitude. Both the Picarro and Los Gatos analyzers offer efficient and precise alternatives to GC-based methods, but the former uniquely enables simultaneous measurements of three major GHGs in coastal marshes.This study was funded by the USDA National Institute of Food and Agriculture (Hatch project # 229286, grant to Moseman-Valtierra) and a Woods Hole Sea Grant award to Moseman-Valtierra and Tang

The Role of Apparent Competition in Facilitating Ecological Release of a Range-expanding Insect

Due to anthropogenic climate change, species are expanding their historical natural ranges. However, interacting species will not shift synchronously and range-expanding species are likely to lose interactions and pick up novel ones in their expanded range. If antagonistic interactions, such as with competitors or enemies are lost, range-expanding species may experience “ecological release” and have impacts in their expanded range. Of the parasitoid wasps that attack phytophagous insects, some are specialists and some are generalists attacking alternative hosts (competitors). Range-expanding species may lose enemies if their specialists fail to follow from their native range and if generalist enemies fail to switch from competitors in the expanded range (“release from apparent competition”). We study a poleward range-expansion of a phytophagous gall-forming insect Neuroterus saltatorius that expanded its range from mainland western North America to Vancouver Island, BC, where it is outbreaking on its plant Querucs garryana. N. saltatorius co-occurs with several other gall-formers on its host, including Andricus opertus, throughout its native and expanded range. Here, we ask if A. opertus acts as an apparent competitor (shares enemies) with N. saltatorius, and if apparent competition is weaker in the expanded range. These two host species were collected from 18 sites that span the range of Q. garryana. We reared parasitoid wasps from them and identified parasitoids to morphospecies using taxonomic keys. We identified 16 parasitoids from N. saltatorius and 39 from A. opertus. Of these, 13 species of parasitoids are shared between the two host species in all regions, and we will calculate the rate of shared overlap to see if there are fewer shared species in the expanded range. This result would suggest that release from apparent competition contributes to ecological release. Understanding how biotic interactions change under range expansions is important to predict species responses to climate change.https://orb.binghamton.edu/research_days_posters_2021/1095/thumbnail.jp

Archaea and Fungi of the Human Gut Microbiome: Correlations with Diet and Bacterial Residents

Diet influences health as a source of nutrients and toxins, and by shaping the composition of resident microbial populations. Previous studies have begun to map out associations between diet and the bacteria and viruses of the human gut microbiome. Here we investigate associations of diet with fungal and archaeal populations, taking advantage of samples from 98 well-characterized individuals. Diet was quantified using inventories scoring both long-term and recent diet, and archaea and fungi were characterized by deep sequencing of marker genes in DNA purified from stool. For fungi, we found 66 genera, with generally mutually exclusive presence of either the phyla Ascomycota or Basiodiomycota. For archaea, Methanobrevibacter was the most prevalent genus, present in 30% of samples. Several other archaeal genera were detected in lower abundance and frequency. Myriad associations were detected for fungi and archaea with diet, with each other, and with bacterial lineages. Methanobrevibacter and Candida were positively associated with diets high in carbohydrates, but negatively with diets high in amino acids, protein, and fatty acids. A previous study emphasized that bacterial population structure was associated primarily with long-term diet, but high Candida abundance was most strongly associated with the recent consumption of carbohydrates. Methobrevibacter abundance was associated with both long term and recent consumption of carbohydrates. These results confirm earlier targeted studies and provide a host of new associations to consider in modeling the effects of diet on the gut microbiome and human health

Predictive modeling of die filling of the pharmaceutical granules using the flexible neural tree

In this work, a computational intelligence (CI) technique named flexible neural tree (FNT) was developed to predict die filling performance of pharmaceutical granules and to identify significant die filling process variables. FNT resembles feedforward neural network, which creates a tree-like structure by using genetic programming. To improve accuracy, FNT parameters were optimized by using differential evolution algorithm. The performance of the FNT-based CI model was evaluated and compared with other CI techniques: multilayer perceptron, Gaussian process regression, and reduced error pruning tree. The accuracy of the CI model was evaluated experimentally using die filling as a case study. The die filling experiments were performed using a model shoe system and three different grades of microcrystalline cellulose (MCC) powders (MCC PH 101, MCC PH 102, and MCC DG). The feed powders were roll-compacted and milled into granules. The granules were then sieved into samples of various size classes. The mass of granules deposited into the die at different shoe speeds was measured. From these experiments, a dataset consisting true density, mean diameter (d50), granule size, and shoe speed as the inputs and the deposited mass as the output was generated. Cross-validation (CV) methods such as 10FCV and 5x2FCV were applied to develop and to validate the predictive models. It was found that the FNT-based CI model (for both CV methods) performed much better than other CI models. Additionally, it was observed that process variables such as the granule size and the shoe speed had a higher impact on the predictability than that of the powder property such as d50. Furthermore, validation of model prediction with experimental data showed that the die filling behavior of coarse granules could be better predicted than that of fine granules

Crystal structure and phase transitions across the metal-superconductor boundary in the SmFeAsO1-xFx (0 < x < 0.20) family

The fluorine-doped rare-earth iron oxyarsenides, REFeAsO1-xFx (RE =rare earth) have recently emerged as a new family of high-temperature superconductors with transition temperatures (Tc) as high as 55 K (refs 1-4). Early work has provided compelling evidence that the undoped parent materials exhibit spin-density-wave (SDW) antiferromagnetic order and undergo a structural phase transition from tetragonal to orthorhombic crystal symmetry upon cooling.5 Both the magnetic and structural instabilities are suppressed upon doping with fluoride ions before the appearance of superconductivity.6,7 Here we use high-resolution synchrotron X-ray diffraction to study the structural properties of SmFeAsO1-xFx (0 < x < 0.20) in which superconductivity emerges near x ~ 0.07 and Tc increases monotonically with doping up to x ~ 0.20.8 We find that orthorhombic symmetry survives through the metal-superconductor boundary well into the superconducting regime 2 and the structural distortion is only suppressed at doping levels, x > 0.15 when the superconducting phase becomes metrically tetragonal. Remarkably this crystal symmetry crossover coincides with reported drastic anomalies in the resistivity and the Hall coefficient8 and a switch of the pressure coefficient of Tc from positive to negative,9 thereby implying that the low-temperature structure plays a key role in defining the electronic properties of these superconductors