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American politics in the age of ignorance : why lawmakers choose belief over research
State and local governments are often trumpeted as laboratories of democracy, capable of significant policy innovation and expertise. Yet the reality is that states more often than not repeatedly reenact failed policies that past research shows do not work. American Politics in the Age of Ignorance contends that policy making is shrouded in many myths and that policy makers often ignore ample research and evidence when it comes to legislating on a range of issues. Examining such hot button issues as restricting immigration and welfare migration, seeking to lure businesses with tax breaks, and providing public subsidies for sports stadiums, this book catalogs a list of repeatedly enacted failed policies that public officials advocate, offering a critical and skeptical analysis of the policy process.
Book
Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database
Untargeted metabolomics provides a comprehensive platform for identifying metabolites whose levels are altered between two or more populations. By using liquid chromatography quadrupole time-of-flight mass spectrometry (LC-Q-TOF-MS), hundreds to thousands of peaks with a unique
m/z
ratio and retention time are routinely detected from most biological samples in an untargeted profiling experiment. Each peak, termed a metabolomic feature, can be characterized on the basis of its accurate mass, retention time and tandem mass spectral fragmentation pattern. Here a seven-step protocol is suggested for such a characterization by using the METLIN metabolite database. The protocol starts from untargeted metabolomic LC-Q-TOF-MS data that have been analyzed with the bioinformatics program XCMS, and it describes a strategy for selecting interesting features as well as performing subsequent targeted tandem MS. The seven steps described will require 2–4 h to complete per feature, depending on the compound.
Journal Article
Reproductive strategy of Delta Smelt Hypomesus transpacificus and impacts of drought on reproductive performance
Understanding reproductive biology and performance of fish is essential to formulate effective conservation and management programs. Here, we studied reproductive strategies of female Delta Smelt Hypomesus transpacificus , an endangered fish species in the State of California, the United States, focusing on (1) better understanding their distribution pattern during the winter and spring spawning season at very fine scale to predict their possible spawning grounds and (2) assessing impacts of a recent, severe drought on their reproductive performance. We formulated our hypotheses as follows; (1) female Delta Smelt migrate to particular locations for spawning so that mature females can be frequently found in those locations throughout the spawning season and (2) reproductive performance of individual female fish declined during the drought. To test the first hypotheses, we analyzed relationships between water quality parameters and maturity/distribution pattern of Delta Smelt. Salinity better explained the distribution pattern of Delta Smelt at subadult and adult stages compared with water temperature or turbidity. Although there are some freshwater locations where mature Delta Smelt can frequently be found during the spawning season, Delta Smelt at the final maturation stage (Stage 5: hydration) and post spawners appeared to be widespread in the area where salinity was below 1.0 during the spawning season. Therefore, Delta Smelt could theoretically spawn in any freshwater locations, with more specific spawning requirements in the wild (e.g., substrate type and depth) still unknown. Delta Smelt, which experienced dry and critically dry conditions (the 2013 and 2014 year-classes), showed smaller oocytes, and lower clutch size and gonadosomatic index compared with the fish caught in a wet year (2011 year-class) at the late vitellogenic stage (Stage 4 Late), suggesting reproductive performance was negatively affected by environmental conditions during the drought.
Journal Article
Lipid production in Nannochloropsis gaditana is doubled by decreasing expression of a single transcriptional regulator
Lipid production in the oleaginous microalga
Nannocholoropsis gaditana
is doubled by decreasing the expression of a transcriptional regulator identified through a CRISPR–Cas9 reverse-genetics approach.
Lipid production in the industrial microalga
Nannochloropsis gaditana
exceeds that of model algal species and can be maximized by nutrient starvation in batch culture. However, starvation halts growth, thereby decreasing productivity. Efforts to engineer
N. gaditana
strains that can accumulate biomass and overproduce lipids have previously met with little success. We identified 20 transcription factors as putative negative regulators of lipid production by using RNA-seq analysis of
N. gaditana
during nitrogen deprivation. Application of a CRISPR–Cas9 reverse-genetics pipeline enabled insertional mutagenesis of 18 of these 20 transcription factors. Knocking out a homolog of fungal Zn(
II
)
2
Cys
6
-encoding genes improved partitioning of total carbon to lipids from 20% (wild type) to 40–55% (mutant) in nutrient-replete conditions. Knockout mutants grew poorly, but attenuation of Zn(
II
)
2
Cys
6
expression yielded strains producing twice as much lipid (∼5.0 g m
−2
d
−1
) as that in the wild type (∼2.5 g m
−2
d
−1
) under semicontinuous growth conditions and had little effect on growth.
Journal Article
The health and condition responses of Delta Smelt to fasting: A time series experiment
There is an extensive literature establishing, validating, and quantifying a wide range of responses of fishes to fasting. Our study complements this work by comparing fed and unfed treatments of hatchery-raised Delta Smelt (Hypomesus transpacificus)-an imperiled fish that is endemic to the San Francisco Estuary and its tributaries in California, USA-across a diverse suite of endpoints over a two-month time series. The experiment was conducted at 15.9°C, and individuals were sampled at 12 time points as starvation became increasingly severe. We found that hepatosomatic index and condition factor were relatively sensitive to starvation, becoming significantly depressed at Day 4 and 7, respectively. Histological analysis of liver showed elevated cytoplasmic inclusion bodies at Day 7, followed by increased glycogen depletion, single cell necrosis, and hydropic vacuolar degeneration at Day 14, 21, and 28, respectively. Of four antioxidants measured, glutathione decreased at Day 4, superoxide dismutase increased at Day 14, catalase increased at Day 56, and glutathione peroxidase was not affected by starvation. The net result was a ~2-fold increase in lipid peroxidation (malondialdehyde) in fasted fish that was highly inconsistent through time. RNA to DNA ratio and triglycerides in muscle were relatively insensitive to starvation, only consistently decreasing with fasting after mortality began increasing in the 'No Feeding' treatment, at Day 21. Together, these results suggest that Delta Smelt mobilize hepatic energy stores far more rapidly than lipids in muscle when subjected to fasting, leading to rapid atrophy of liver and the development of cytoplasmic inclusion bodies-possibly autophagosomes-in hepatocytes.
Journal Article
Visual, spectral, and microchemical quantification of crystalline anomalies in otoliths of wild and cultured delta smelt
Developmental abnormalities in otoliths can impact growth and survival in teleost fishes. Here, we quantified the frequency and severity of developmental anomalies in otoliths of delta smelt (
Hypomesus transpacificus
), a critically endangered estuarine fish that is endemic to the San Francisco Estuary. Left–right asymmetry and anomalous crystalline polymorphs (i.e., vaterite) were quantified and compared between wild and cultured populations using digital image analysis. Visual estimates of vaterite were validated using X-ray diffraction, Raman spectroscopy, laser ablation ICPMS, and electron probe microanalysis. Results indicated that cultured delta smelt were 80 times more likely to contain a vateritic otolith and 18 times more likely to contain relatively large (≥ 15%) amounts of vaterite. Similarly, cultured fish exhibited 30% greater asymmetry than wild fish. These results indicate that cultured delta smelt exhibit a significantly higher frequency of vestibular abnormalities which are known to reduce fitness and survival. Such hatchery effects on otolith development could have important implications for captive culture practices and the supplementation of wild fish populations with cultured individuals.
Journal Article
No system-size anomalies in entropy of bcc iron at Earth’s inner-core conditions
New molecular modeling data show that the entropy of bcc iron exhibits no system-size anomalies, implying that it should be feasible to compute accurate free energies of this system using first-principles methods without requiring a prohibitively large number of atoms. Conclusions are based on rigorous calculations of size-dependent free energies for a Sutton-Chen model of iron previously fit to ab initio calculations, and refute statements recently appearing in the literature indicating that the size of the simulation cell is critical for stabilization of the bcc phase.
Journal Article
Freshwater Flow Affects Subsidies of a Copepod (Pseudodiaptomus forbesi) to Low-Salinity Food Webs in the Upper San Francisco Estuary
Productivity of the food web supporting small pelagic fishes in the upper San Francisco Estuary is chronically low, and some of the native fish species are in a long-term decline. The low-salinity (oligohaline) zone (LSZ) is particularly depauperate in phytoplankton and zooplankton. Based on prior empirical studies, it is hypothesized that freshwater flow increases the subsidy of a key copepod prey species (Pseudodiaptomus forbesi) from its freshwater population center into the LSZ. We combined hydrodynamic and particle-tracking modeling with Bayesian analysis in a box-model approach to estimate the magnitude of this subsidy and its dependence on freshwater flow rates. Net gains of P. forbesi into the LSZ came mostly from freshwater, landward regions of higher copepod abundance. The subsidy increased with freshwater flow, a finding that supports previous empirical analyses. However, in the context of persistent drought and ongoing climate change, the levels required to achieve a detectable net gain may be difficult and costly to achieve.
Journal Article