Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals

To understand the evolutionary dynamics between transcription factor (TF) binding and gene expression in mammals, we compared transcriptional output and the binding intensities for three tissue-specific TFs in livers from four closely related mouse species. For each transcription factor, TF-dependent genes and the TF binding sites most likely to influence mRNA expression were identified by comparing mRNA expression levels between wild-type and TF knockout mice. Independent evolution was observed genome-wide between the rate of change in TF binding and the rate of change in mRNA expression across taxa, with the exception of a small number of TF-dependent genes. We also found that binding intensities are preferentially conserved near genes whose expression is dependent on the TF, and the conservation is shared among binding peaks in close proximity to each other near the TSS. Expression of TF-dependent genes typically showed an increased sensitivity to changes in binding levels as measured by mRNA abundance. Taken together, these results highlight a significant tolerance to evolutionary changes in TF binding intensity in mammalian transcriptional networks and suggest that some TF-dependent genes may be largely regulated by a single TF across evolution

Refining the model of barrier island formation along a paraglacial coast in the Gulf of Maine

Author Posting. © The Author(s), 2012. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Marine Geology 307-310 (2012):40-57, doi:10.1016/j.margeo.2012.03.001.Details of the internal architecture and local geochronology of Plum Island, the longest barrier in the Gulf of Maine, has refined our understanding of barrier island formation in paraglacial settings. Ground-penetrating radar and shallow-seismic profiles coupled with sediment cores and radiocarbon dates provide an 8000-year evolutionary history of this barrier system in response to changes in sediment sources and supply rates as well as variability in the rate of sea-level change. The barrier sequence overlies tills of Wisconsinan and Illinoian glaciations as well as late Pleistocene glaciomarine clay deposited during the post-glacial sea-level highstand at approximately 17 ka. Holocene sediment began accumulating at the site of Plum Island at 7–8 ka, in the form of coarse fluvial channel-lag deposits related to the 50-m wide erosional channel of the Parker River that carved into underlying glaciomarine deposits during a lower stand of sea level. Plum Island had first developed in its modern location by ca. 3.6 ka through onshore migration and vertical accretion of reworked regressive and lowstand deposits. The prevalence of southerly, seaward-dipping layers indicates that greater than 60% of the barrier lithosome developed in its modern location through southerly spit progradation, consistent with a dominantly longshore transport system driven by northeast storms. Thinner sequences of northerly, landward-dipping clinoforms represent the northern recurve of the prograding spit. A 5–6-m thick inlet-fill sequence was identified overlying the lower stand fluvial deposit; its stratigraphy captures events of channel migration, ebb-delta breaching, onshore bar migration, channel shoaling and inlet infilling associated with the migration and eventual closing of the inlet. This inlet had a maximum cross-sectional area of 2800 m2 and was active around 3.5–3.6 ka. Discovery of this inlet suggests that the tidal prism was once larger than at present. Bay infilling, driven by the import of sediment into the backbarrier environment through tidal inlets, as well as minor sediment contribution from local rivers, led to a vast reduction in the bay tidal prism. This study demonstrates that, prior to about 3 ka, Plum Island and its associated marshes, tidal flats, and inlets were in a paraglacial environment; that is, their main source of sediment was derived from the erosion and reworking of glaciogenic deposits. Since that time, Plum Island has been in a state of dynamic equilibrium with its non-glacial sediment sources and therefore can be largely considered to be in a stable, “post-paraglacial” state. This study is furthermore the first in the Gulf of Maine to show that spit accretion and inlet processes were the dominant mechanisms in barrier island formation and thus serves as a foundation for future investigations of barrier development in response to backbarrier infilling.This study was funded by the Minerals Management Service (now the “Bureau of Ocean Energy Manegement, Regulation and Enforcement”), the USGS Eastern Geology and Paleoclimate Science Center, the USGS National Cooperative Geologic Mapping Program (State Map), a Geological Society of America (GSA) Student Research Grant, the American Association of Petroleum Geologists (AAPG) Grants-in-Aid program, and the Boston University Undergraduate Research Opportunities Program (UROP). Additionally, E. Carruthers was funded in part by the Clare Booth Luce Summer Research Fellowship and C. Hein was funded by the National Science Foundation (NSF) Graduate Research Fellowship

Molecular insights into RBR E3 ligase ubiquitin transfer mechanisms

National Institute of General Medical Sciences R01 GM0880555T32 GM007270, Francis Crick Institute FCI01, Cancer Research UK, Medical Research Council U117565398, Wellcome Trus

Attitudes of small animal practitioners toward participation in veterinary clinical trials

To determine attitudes of small animal practitioners toward veterinary clinical trials and variables influencing their likelihood of participating in such trials

Beryllium and Alpha-Element Abundances in a Large Sample of Metal-Poor Stars

The light elements, Li, Be, and B, provide tracers for many aspects of astronomy including stellar structure, Galactic evolution, and cosmology. We have taken spectra of Be in 117 metal-poor stars ranging in metallicity from [Fe/H] = -0.5 to -3.5 with Keck I + HIRES at a resolution of 42,000 and signal-to-noise ratios of near 100. We have determined the stellar parameters spectroscopically from lines of Fe I, Fe II, Ti I and Ti II. The abundances of Be and O were derived by spectrum synthesis techniques, while abundances of Fe, Ti, and Mg were found from many spectral line measurements. There is a linear relationship between [Fe/H] and A(Be) with a slope of +0.88 +-0.03 over three orders of magnitude in [Fe/H]. We fit the relationship between A(Be) and [O/H] with both a single slope and with two slopes. The relationship between [Fe/H] and [O/H] seems robustly linear and we conclude that the slope change in Be vs. O is due to the Be abundance. Although Be is a by-product of CNO, we have used Ti and Mg abundances as alpha-element surrogates for O in part because O abundances are rather sensitive to both stellar temperature and surface gravity. We find that A(Be) tracks [Ti/H] very well with a slope of 1.00 +-0.04. It also tracks [Mg/H] very well with a slope of 0.88 +-0.03. We find that there are distinct differences in the relationships of A(Be) and [Fe/H] and of A(Be) and [O/H] for our dissipative stars and our accretive stars. We suggest that the Be in the dissipative stars was primarily formed by GCR spallation and Be in the accretive stars was formed in the vicinity of SN II.Comment: Accepted for Ap.J. Nov. 10, 2011, v. 741 70 pages, 27 figures, 5 table

Examination of Reticulocytosis among Chronically Transfused Children with Sickle Cell Anemia.

Sickle cell anemia (SCA) is an inherited hemolytic anemia with compensatory reticulocytosis. Recent studies have shown that increased levels of reticulocytosis during infancy are associated with increased hospitalizations for SCA sequelae as well as cerebrovascular pathologies. In this study, absolute reticulocyte counts (ARC) measured prior to transfusion were analysed among a cohort of 29 pediatric SCA patients receiving chronic transfusion therapy (CTT) for primary and secondary stroke prevention. A cross-sectional flow cytometric analysis of the reticulocyte phenotype was also performed. Mean duration of CTT was 3.1 ± 2.6 years. Fifteen subjects with magnetic resonance angiography (MRA) -vasculopathy had significantly higher mean ARC prior to initiating CTT compared to 14 subjects without MRA-vasculopathy (427.6 ± 109.0 K/μl vs. 324.8 ± 109.2 K/μl,

A “How-To” Guide for Designing Judgment Bias Studies to Assess Captive Animal Welfare

Robust methods to assess nonhuman animal emotion are essential for ensuring good welfare in captivity. Cognitive bias measures such as the judgment bias task have recently emerged as promising tools to assess animal emotion. The simple design and objective response measures make judgment bias tasks suitable for use across species and contexts. In reviewing 64 studies published to date, it emerged that (a) judgment biases have been measured in a number of mammals and birds and an invertebrate; (b) no study has tested judgment bias in any species of fish, amphibian, or reptile; and (c) no study has yet investigated judgment bias in a zoo or aquarium. This article proposes that judgment bias measures are highly suitable for use with these understudied taxa and can provide new insight into welfare in endangered species housed in zoos and aquariums, where poor welfare impacts breeding success and, ultimately, species survival. The article includes a “how-to” guide to designing judgment bias tests with recommendations for working with currently neglected “exotics” including fishes, amphibians, and reptiles

Screening for in vitro systematic reviews: a comparison of screening methods and training of a machine learning classifier

Objective: Existing strategies to identify relevant studies for systematic review may not perform equally well across research domains. We compare four approaches based on either human or automated screening of either title and abstract or full text, and report the training of a machine learning algorithm to identify in vitro studies from bibliographic records. Methods: We used a systematic review of oxygen-glucose deprivation (OGD) in PC-12 cells to compare approaches. For human screening, two reviewers independently screened studies based on title and abstract or full text, with disagreements reconciled by a third. For automated screening, we applied text mining to either title and abstract or full text. We trained a machine learning algorithm with decisions from 2000 randomly selected PubMed Central records enriched with a dataset of known in vitro studies. Results: Full-text approaches performed best, with human (sensitivity: 0.990, specificity: 1.000 and precision: 0.994) outperforming text mining (sensitivity: 0.972, specificity: 0.980 and precision: 0.764). For title and abstract, text mining (sensitivity: 0.890, specificity: 0.995 and precision: 0.922) outperformed human screening (sensitivity: 0.862, specificity: 0.998 and precision: 0.975). At our target sensitivity of 95% the algorithm performed with specificity of 0.850 and precision of 0.700. Conclusion: In this in vitro systematic review, human screening based on title and abstract erroneously excluded 14% of relevant studies, perhaps because title and abstract provide an incomplete description of methods used. Our algorithm might be used as a first selection phase in in vitro systematic reviews to limit the extent of full text screening required.</p

Episodic population fragmentation and gene flow reveal a trade-off between heterozygosity and allelic richness

In episodic environments like deserts, populations of some animal species exhibit irregular fluctuations such that populations are alternately large and connected or small and isolated. Such dynamics are typically driven by periodic resource pulses due, for example, to large but infrequent rainfall events. The repeated population bottlenecks resulting from fragmentation should lower genetic diversity over time, yet species undergoing these fluctuations appear to maintain high levels of genetic diversity. To resolve this apparent paradox, we simulated a metapopulation of constant size undergoing repeat episodes of fragmentation and change in gene flow to mimic outcomes experienced by mammals in an Australian desert. We show that episodic fragmentation and gene flow have contrasting effects on two measures of genetic diversity: heterozygosity and allelic richness. Specifically, fragmentation into many, small subpopulations, coupled with periods of infrequent gene flow, preserves allelic richness at the expense of heterozygosity. In contrast, fragmentation into a few, large subpopulations maintains heterozygosity at the expense of allelic richness. The strength of the trade-off between heterozygosity and allelic richness depends on the amount of gene flow and the frequency of gene flow events. Our results imply that the type of genetic diversity maintained among species living in strongly fluctuating environments will depend on the way populations fragment, with our results highlighting different mechanisms for maintaining allelic richness and heterozygosity in small, fragmented populations

Plastic and marine turtles: a review and call for research

Plastic debris is now ubiquitous in the marine environment affecting a wide range of taxa, from microscopic zooplankton to large vertebrates. Its persistence and dispersal throughout marine ecosystems has meant that sensitivity toward the scale of threat is growing, particularly for species of conservation concern, such as marine turtles. Their use of a variety of habitats, migratory behaviour, and complex life histories leave them subject to a host of anthropogenic stressors, including exposure to marine plastic pollution. Here, we review the evidence for the effects of plastic debris on turtles and their habitats, highlight knowledge gaps, and make recommendations for future research. We found that, of the seven species, all are known to ingest or become entangled in marine debris. Ingestion can cause intestinal blockage and internal injury, dietary dilution, malnutrition, and increased buoyancy which in turn can result in poor health, reduced growth rates and reproductive output, or death. Entanglement in plastic debris (including ghost fishing gear) is known to cause lacerations, increased drag—which reduces the ability to forage effectively or escape threats—and may lead to drowning or death by starvation. In addition, plastic pollution may impact key turtle habitats. In particular, its presence on nesting beaches may alter nest properties by affecting temperature and sediment permeability. This could influence hatchling sex ratios and reproductive success, resulting in population level implications. Additionally, beach litter may entangle nesting females or emerging hatchlings. Lastly, as an omnipresent and widespread pollutant, plastic debris may cause wider ecosystem effects which result in loss of productivity and implications for trophic interactions. By compiling and presenting this evidence, we demonstrate that urgent action is required to better understand this issue and its effects on marine turtles, so that appropriate and effective mitigation policies can be developed