Large scale patterns of genetic variation and differentiation in sugar maple from tropical Central America to temperate North America

© 2015 Vargas-Rodriguez et al. Background: Geological events in the latter Cenozoic have influenced the distribution, abundance and genetic structure of tree populations in temperate and tropical North America. The biogeographical history of temperate vegetation that spans large ranges of latitude is complex, involving multiple latitudinal shifts that might have occurred via different migration routes. We determined the regional structuring of genetic variation of sugar maple (Acer saccharum subsp. saccharum) and its only subspecies in tropical America (Acer saccharum subsp. skutchii) using nuclear and chloroplast data. The studied populations span a geographic range from Maine, USA (46°N), to El Progreso, Guatemala (15°N). We examined genetic subdivisions, explored the locations of ancestral haplotypes, analyzed genetic data to explore the presence of a single or multiple glacial refugia, and tested whether genetic lineages are temporally consistent with a Pleistocene or older divergence. Results: Nuclear and chloroplast data indicated that populations in midwestern USA and western Mexico were highly differentiated from populations in the rest of the sites. The time of the most recent common ancestor of the western Mexico haplotype lineage was dated to the Pliocene (5.9 Ma, 95 % HPD: 4.3-7.3 Ma). Splits during the Pleistocene separated the rest of the phylogroups. The most frequent and widespread haplotype occurred in half of the sites (Guatemala, eastern Mexico, southeastern USA, and Ohio). Our data also suggested that multiple Pleistocene refugia (tropics-southeastern USA, midwestern, and northeastern USA), but not western Mexico (Jalisco), contributed to post-glacial northward expansion of ranges. Current southern Mexican and Guatemalan populations have reduced population sizes, genetic bottlenecks and tend toward homozygosity, as indicated using nuclear and chloroplast markers. Conclusions: The divergence of western Mexican populations from the rest of the sugar maples likely resulted from orographic and volcanic barriers to gene flow. Past connectivity among populations in the southeastern USA and eastern Mexico and Guatemala possible occurred through gene flow during the Pleistocene. The time to the most common ancestor values revealed that populations from the Midwest and Northeast USA represented different haplotype lineages, indicating major divergence of haplotypes lineages before the Last Glacial Maximum and suggesting the existence of multiple glacial refugia

Blood and tissue biomarker analysis in dogs with osteosarcoma treated with palliative radiation and intra-tumoral autologous natural killer cell transfer.

We have previously reported radiation-induced sensitization of canine osteosarcoma (OSA) to natural killer (NK) therapy, including results from a first-in-dog clinical trial. Here, we report correlative analyses of blood and tissue specimens for signals of immune activation in trial subjects. Among 10 dogs treated with palliative radiotherapy (RT) and intra-tumoral adoptive NK transfer, we performed ELISA on serum cytokines, flow cytometry for immune phenotype of PBMCs, and PCR on tumor tissue for immune-related gene expression. We then queried The Cancer Genome Atlas (TCGA) to evaluate the association of cytotoxic/immune-related gene expression with human sarcoma survival. Updated survival analysis revealed five 6-month survivors, including one dog who lived 17.9 months. Using feeder line co-culture for NK expansion, we observed maximal activation of dog NK cells on day 17-19 post isolation with near 100% expression of granzyme B and NKp46 and high cytotoxic function in the injected NK product. Among dogs on trial, we observed a trend for higher baseline serum IL-6 to predict worse lung metastasis-free and overall survival (P = 0.08). PCR analysis revealed low absolute gene expression of CD3, CD8, and NKG2D in untreated OSA. Among treated dogs, there was marked heterogeneity in the expression of immune-related genes pre- and post-treatment, but increases in CD3 and CD8 gene expression were higher among dogs that lived > 6 months compared to those who did not. Analysis of the TCGA confirmed significant differences in survival among human sarcoma patients with high and low expression of genes associated with greater immune activation and cytotoxicity (CD3e, CD8a, IFN-γ, perforin, and CD122/IL-2 receptor beta). Updated results from a first-in-dog clinical trial of palliative RT and autologous NK cell immunotherapy for OSA illustrate the translational relevance of companion dogs for novel cancer therapies. Similar to human studies, analyses of immune markers from canine serum, PBMCs, and tumor tissue are feasible and provide insight into potential biomarkers of response and resistance

The FIRST Bright Quasar Survey. II. 60 Nights and 1200 Spectra Later

We have used the VLA FIRST survey and the APM catalog of the POSS-I plates as the basis for constructing a new radio-selected sample of optically bright quasars. This is the first radio-selected sample that is competitive in size with current optically selected quasar surveys. Using only two basic criteria, radio-optical positional coincidence and optical morphology, quasars and BL Lacs can be identified with 60% selection efficiency; the efficiency increases to 70% for objects fainter than magnitude 17. We show that a more sophisticated selection scheme can predict with better than 85% reliability which candidates will turn out to be quasars. This paper presents the second installment of the FIRST Bright Quasar Survey with a catalog of 636 quasars distributed over 2682 square degrees. The quasar sample is characterized and all spectra are displayed. The FBQS detects both radio-loud and radio-quiet quasars out to a redshift z>3. We find a large population of objects of intermediate radio-loudness; there is no evidence in our sample for a bimodal distribution of radio characteristics. The sample includes ~29 broad absorption line quasars, both high and low ionization, and a number of new objects with remarkable optical spectra.Comment: 41 pages plus 39 gifs which contain all quasar spectra. Accepted for publication in the Astrophysical Journal Supplement Serie

Direct Anterior Approach Utilizing a Bikini Incision has Less Wound Related Complications in Patients with High BMI

Introduction: Direct anterior approach (DAA) total hip arthroplasty (THA) can be performed through a traditional vertical skin incision, situating the proximal incision at the hip flexion crease, or a horizontal (bikini) skin incision, situating the incision slightly distal and parallel to the hip flexion crease. The dissection beyond the subcutaneous layer is identical for both methods. Objective: The purpose of this study was to compare these approaches, performed by an experienced single surgeon, in terms of overall wound complications and patient-reported esthetics 6-months post-operatively. It was hypothesized that the bikini incision would result in less wound complications and improved cosmesis due to decreased applied tension from the hip flexion crease. Methods: A case-control retrospective study was conducted and 86 bikini DAA patients were matched 3:1 to 230 conventional DAA patients for gender, age, body mass index (BMI), and American Society of Anesthesiologists score. The outcomes evaluated included wound complications, acute periprosthetic joint infection, transfusion, length of surgery, and dysesthesia with an additional subset analysis for obese patients (BMI \u3e30kg/m2). Patients rated incision cosmesis 6 months post-operatively using a Patient Scar Assessment Scale and the Vancouver scar assessment scale. Results: Bikini patients had lower rates of delayed wound healing compared to conventional incision (2.3% vs. 6.1%; p=0.087). This difference was statistically significant (0% vs. 16.6%; p\u3c0.05) in obese patients with no difference in incision cosmesis in either analysis. Discussion: The bikini incision could offer safety benefits in selected patients (BMI \u3e30kg/m2) undergoing DAA THA by decreasing wound complications while preserving cosmesis

High stakes and low bars: How international recognition shapes the conduct of civil wars

When rebel groups engage incumbent governments in war for control of the state, questions of international recognition arise. International recognition determines which combatants can draw on state assets, receive overt military aid, and borrow as sovereigns—all of which can have profound consequences for the military balance during civil war. How do third-party states and international organizations determine whom to treat as a state's official government during civil war? Data from the sixty-one center-seeking wars initiated from 1945 to 2014 indicate that military victory is not a prerequisite for recognition. Instead, states generally rely on a simple test: control of the capital city. Seizing the capital does not foreshadow military victory. Civil wars often continue for many years after rebels take control and receive recognition. While geopolitical and economic motives outweigh the capital control test in a small number of important cases, combatants appear to anticipate that holding the capital will be sufficient for recognition. This expectation generates perverse incentives. In effect, the international community rewards combatants for capturing or holding, by any means necessary, an area with high concentrations of critical infrastructure and civilians. In the majority of cases where rebels contest the capital, more than half of its infrastructure is damaged or the majority of civilians are displaced (or both), likely fueling long-term state weakness

DNA content of a functioning chicken kinetochore

© The Author(s) 2014. In order to understand the three-dimensional structure of the functional kinetochore in vertebrates, we require a complete list and stoichiometry for the protein components of the kinetochore, which can be provided by genetic and proteomic experiments. We also need to know how the chromatin-containing CENP-A, which makes up the structural foundation for the kinetochore, is folded, and how much of that DNA is involved in assembling the kinetochore. In this MS, we demonstrate that functioning metaphase kinetochores in chicken DT40 cells contain roughly 50 kb of DNA, an amount that corresponds extremely closely to the length of chromosomal DNA associated with CENP-A in ChIP-seq experiments. Thus, during kinetochore assembly, CENP-A chromatin is compacted into the inner kinetochore plate without including significant amounts of flanking pericentromeric heterochromatin. © 2014 The Author(s).Wellcome Trust [grant number 073915]; Wellcome Trust Centre for Cell Biology (core grant numbers 077707 and 092076); Darwin Trust of Edinburg

In situ measurements of atmospheric O2 and CO2 reveal an unexpected O2 signal over the tropical Atlantic Ocean

We present the first meridional transects of atmospheric O2 and CO2 over the Atlantic Ocean. We combine these measurements into the tracer atmospheric potential oxygen (APO), which is a measure of the oceanic contribution to atmospheric O2 variations. Our new in situ measurement system, deployed on board a commercial container ship during 2015, performs as well as or better than existing similar measurement systems. The data show small short-term variability (hours to days), a step-change corresponding to the position of the Intertropical Convergence Zone (ITCZ), and seasonal cycles that vary with latitude. In contrast to data from the Pacific Ocean and to previous modeling studies, our Atlantic Ocean APO data show no significant bulge in the tropics. This difference cannot be accounted for by interannual variability in the position of the ITCZ or the Atlantic Meridional Mode Index and appears to be a persistent feature of the Atlantic Ocean system. Modeled APO using the TM3 atmospheric transport model does exhibit a significant bulge over the Atlantic and overestimates the interhemispheric gradient in APO over the Atlantic Ocean. These results indicate that either there are inaccuracies in the oceanic flux data products in the equatorial Atlantic Ocean region, or that there are atmospheric transport inaccuracies in the model, or a combination of both. Our shipboard O2 and CO2 measurements are ongoing and will reveal the long-term nature of equatorial APO outgassing over the Atlantic as more data become available

The South Atlantic Anticyclone as a key player for the representation of the tropical Atlantic climate in coupled climate models

The key role of the South Atlantic Anticyclone (SAA) on the seasonal cycle of the tropical Atlantic is investigated with a regionally coupled atmosphere–ocean model for two different coupled domains. Both domains include the equatorial Atlantic and a large portion of the northern tropical Atlantic, but one extends southward, and the other northwestward. The SAA is simulated as internal model variability in the former, and is prescribed as external forcing in the latter. In the first case, the model shows significant warm biases in sea surface temperature (SST) in the Angola-Benguela front zone. If the SAA is externally prescribed, these biases are substantially reduced. The biases are both of oceanic and atmospheric origin, and are influenced by ocean–atmosphere interactions in coupled runs. The strong SST austral summer biases are associated with a weaker SAA, which weakens the winds over the southeastern tropical Atlantic, deepens the thermocline and prevents the local coastal upwelling of colder water. The biases in the basins interior in this season could be related to the advection and eddy transport of the coastal warm anomalies. In winter, the deeper thermocline and atmospheric fluxes are probably the main biases sources. Biases in incoming solar radiation and thus cloudiness seem to be a secondary effect only observed in austral winter. We conclude that the external prescription of the SAA south of 20°S improves the simulation of the seasonal cycle over the tropical Atlantic, revealing the fundamental role of this anticyclone in shaping the climate over this region