Sequence variation at the major histocompatibility complex locus DQ beta in beluga whales (Delphinapterus leucas) [published erratum appears in Mol Biol Evol 1995 Nov;12(6):1174]

Genetic variation at the Major Histocompatibility Complex locus DQ beta was analyzed in 233 beluga whales (Delphinapterus leucas) from seven populations: St. Lawrence Estuary, eastern Beaufort Sea, eastern Chukchi Sea, western Hudson Bay, eastern Hudson Bay, southeastern Baffin Island, and High Arctic and in 12 narwhals (Monodon monoceros) sympatric with the High Arctic beluga population. Variation was assessed by amplification of the exon coding for the peptide binding region via the polymerase chain reaction, followed by either cloning and DNA sequencing or single-stranded conformation polymorphism analysis. Five alleles were found across the beluga populations and one in the narwhal. Pairwise comparisons of these alleles showed a 5:1 ratio of nonsynonymous to synonymous substitutions per site leading to eight amino acid differences, five of which were nonconservative substitutions, centered around positions previously shown to be important for peptide binding. Although the amount of allelic variation is low when compared with terrestrial mammals, the nature of the substitutions in the peptide binding sites indicates an important role for the DQ beta locus in the cellular immune response of beluga whales. Comparisons of allele frequencies among populations show the High Arctic population to be different (P < or = .005) from the other beluga populations surveyed. In these other populations an allele, Dele-DQ beta*0101-2, was found in 98% of the animals, while in the High Arctic it was found in only 52% of the animals. Two other alleles were found at high frequencies in the High Arctic population, one being very similar to the single allele found in narwhal.      

Conditional Survival in de novo Metastatic Urothelial Carcinoma

Background

Second-line therapy is frequently utilized for metastatic urothelial carcinoma, but there are limited data to guide this approach. While an assessment of overall survival based on registry data may not capture the impact of second- and third-line therapies on clinical outcome, this may be reflected in relative conditional survival (RCS).

Methods

Patients with stage IV urothelial carcinoma diagnosed from 1990–2010 were identified from the Surveillance, Epidemiology and End Results (SEER) dataset. The association of clinicopathologic variables with disease specific survival (DSS) was explored through univariate and multivariate analyses. DSS in subgroups divided by time period (1990–2000 v 2001–2010) was compared using the Kaplan-Meier method and log-rank test. One-year RCS at annual landmarks up to 5 years was compared in subgroups divided by time period.

Results

Of 261,987 patients diagnosed with urothelial carcinoma from 1990–2010, 3,110 patients met criteria for the current analysis. Characteristics of patients diagnosed between 1990 and 2000 (n = 810) and 2001 to 2010 (n = 2,300) were similar and there was no significant difference in DSS between the two groups. On multivariate analysis, older age (age ≥ 80) was associated with shorter DSS (HR 1.79, 95%CI 1.48–2.15), but no association was found between time period of diagnosis and outcome. One-year RCS improved substantially through successive annual landmarks up to 5 years, but no differences were seen in subgroups divided by time of diagnosis.

Conclusions

No difference in RCS was observed amongst patients with stage IV urothelial carcinoma diagnosed from 1990–2000 and 2001–2010. A lack of difference in RCS (more so than cumulative DSS) may reflect a lack of progress in salvage therapies for the disease.     

Ephemeroptera,Plecoptera, and Trichoptera on Isle Royale National Park,USA, compared to mainland species pool and size distribution

Extensive sampling for aquatic insects was conducted in the orders Ephemeroptera (mayflies), Plecoptera (stoneflies), and Trichoptera (caddisflies) (EPT) of Isle Royale National Park (ISRO), Michigan, United States of America, during summer 2013. The island was ice covered until 8,000 to 10,000 years ago and is isolated by 22–70 km distance from the mainland. Two hypotheses were examined: that ISRO EPT richness would be much reduced from the mainland, and that the species colonizing ISRO would be of smaller size than mainland, adults presumably using updrafts to bridge the distance from mainland sources. Data sets were developed for known mainland EPT species and size for those species. The first hypothesis was confirmed with the mainland species pool consisting of 417 EPT, while ISRO is known to support 73 species. Richness of EPT is directly related to the number of specimens examined. Small streams supported five EPT species, while 15–25 species were found in larger streams. Lakeshores had intermediate diversity. The second hypothesis was substantiated for stoneflies, but not for mayflies or caddisflies. Stoneflies apparently are poorer fliers than either of the other two orders.     

Population Dynamics and Potential for Biological Control of an Exotic Invasive Shrub in Hawaiian Rainforests

Introduction of biological control agents to reduce the abundance of exotic invasive plant species is often considered necessary but risky. I used matrix projection models to investigate the current population dynamics of Clidemia hirta (Melastomataceae), an invasive shrub, in two rainforest stands on the island of Hawaii and to predict the efficacy of hypothetical biological control agents in reducing population growth rates. Stage-structured matrix models were parameterized with field data collected over 3 years from 2906 C. hirta plants in a recently invaded forest with an open overstory (Laupahoehoe) and 600 plants in a less recently invaded forest with a closed canopy (Waiakea). Asymptotic population growth rates (λ) for both populations in all years were greater than one, demonstrating that both populations were growing. Composite elasticities were high for the seedling life-history stage and fecundity, and near-term demographic elasticities suggested that changes in seedling survival would have the largest effect on population size in the short term. However, simulations showed that almost 100% of seedlings or new recruits produced per reproductive adult would have to be destroyed to cause populations to go locally extinct under current environmental conditions. Herbivores or pathogens that decrease survival across all vegetative stages by 12% at Waiakea and 64% at Laupahoehoe were projected to cause the populations to decline. Thus, biocontrol agents that reduce survival of multiple life-history stages rather than seed production should be pursued to control C. hirta in Hawaiian rainforests.     

The effect of Chinese tallow tree (Sapium sebiferum) ecotype on soil–plant system carbon and nitrogen processes

The EICA hypothesis predicts that shifts in allocation of invasive plants give rise to higher growth rates and lower herbivore defense levels in their introduced range than conspecifics in their native range. These changes in traits of invasive plants may also affect ecosystem processes. We conducted an outdoor pot experiment with Chinese tallow tree (Sapium sebiferum, Euphorbiaceae) seedlings from its native (Jiangsu, China, native ecotype) and introduced ranges (Texas, USA, invasive ecotype) to compare their relative performances in its native range and to examine ecotype effects on soil processes with and without fertilization. Consistent with predictions, plant (shoot and root) mass was significantly greater and leaf defoliation tended to be higher, while the root:shoot ratio was lower for the invasive ecotype relative to the native ecotype. Seasonal amounts of soil–plant system CO₂ and N₂O emissions were higher for the invasive ecotype than for the native ecotype. Soil respiration rates and N₂O emission increases from fertilization were also greater for the invasive ecotype than for the native ecotype, while shoot-specific respiration rates (g CO₂–C g⁻¹ C day⁻¹) did not differ between ecotypes. Further, soil inorganic N (ammonium and nitrate) was higher, but soil total N was lower for soils with the invasive ecotype than soils with the native ecotype. Compared with native ecotypes, therefore, invasive ecotypes may have developed a competition advantage in accelerating soil processes and promoting more nitrogen uptake through soil–plant direct interaction. The results of this study suggest that soil and ecosystem processes accelerated by variation in traits of invasive plants may have implications for their invasiveness.     

CKD-EPI and Cockcroft-Gault Equations Identify Similar Candidates for Neoadjuvant Chemotherapy in Muscle-Invasive Bladder Cancer

Clinical guidelines suggest neoadjuvant cisplatin-based chemotherapy prior to cystectomy in the setting of muscle-invasive bladder cancer (MIBC). A creatinine clearance (CrCl) >60 mL/min is frequently used to characterize cisplatin-eligible patients, and use of the CKD-EPI equation to estimate CrCl has been advocated. From a prospectively maintained institutional database, patients with MIBC who received cystectomy were identified and clinicopathologic information was ascertained. CrCl prior to surgery was computed using three equations: (1) Cockcroft-Gault (CG), (2) CKD-EPI, and (3) MDRD. The primary objective was to determine if the CG and CKD-EPI equations identified a different proportion of patients who were cisplatin-eligible, based on an estimated CrCl of >60 mL/min. Cisplatin-eligibility was also assessed in subsets based on age, CCI score and race. Actuarial rates of neoadjuvant cisplatin-based chemotherapy use were also reported. Of 126 patients, 70% and 71% of patients were found to be cisplatin-eligible by the CKD-EPI and CG equations, respectively (P = 0.9). The MDRD did not result in significantly different characterization of cisplatin-eligibility as compared to the CKD-EPI and CG equations. In the subset of patients age >80, the CKD-EPI equation identified a much smaller proportion of cisplatin-eligible patients (25%) as compared to the CG equation (50%) or the MDRD equation (63%). Only 34 patients (27%) received neoadjuvant cisplatin-based chemotherapy. Of the 92 patients who did not receive neoadjuvant chemotherapy, 64% had a CrCl >60 mL/min by CG. In contrast to previous reports, the CKD-EPI equation does not appear to characterize a broader span of patients as cisplatin-eligible. Older patients (age >80) may less frequently be characterized as cisplatin-eligible by CKD-EPI. The discordance between actual rates of neoadjuvant chemotherapy use and rates of cisplatin eligibility suggest that other factors (e.g., patient and physician preference) may guide clinical decision-making.