The paradoxical Giant Hummingbird: Comparison of Andean and coastal subspecies with respect to blood, migration, and genes

The Giant Hummingbird (Patagona gigas) is twice as large as the next largest hummingbird species and has long been considered paradoxical with respect to flight biomechanics. It is also an extreme outlier in other respects. For example, it is the only hummingbird species that breeds above 4,000 m elevation and also along the beaches of the Pacific Ocean. The high Andean populations of Giant Hummingbird (P. g. peruviana) that we have studied previously have a beta-hemoglobin genotype (serine at beta-hemoglobin A positions 13 and 83) that is characterized by high O2-affinity and is only shared with four unrelated hummingbird taxa that are also restricted to extreme high altitudes. Here we report that lowland-breeding populations of Giant Hummingbird (P. g. gigas) are genetically highly similar to their high-elevation counterparts; they even share the same beta-hemoglobin genotype, a unique characteristic among lowland hummingbirds. We found that hemoglobin concentration is lower and red blood cell volume is higher in the lowland P. g. gigas compared to their high Andean relatives. Complicating this comparison is the possibility that coastal P. g. gigas may be a seasonal elevational migrant, but neither the geographic range nor elevation of non-breeding P. g. gigas are known at present. We describe our efforts to describe its migratory behavior using geolocators

PREDATOR PLAYBACK, FORAGING HEIGHT, AND PHYLOGENY AFFECT GAP CROSSING BEHAVIOR IN TROPICAL FOREST BIRDS

Abstract ∙ The effects of fragmented landscapes on tropical bird movements remain poorly understood, partly due to a dearth of experimental tests of gap crossing behavior. To learn more about the factors involved in gap crossing behavior, we used predator‐playback experiments on four species of understory‐insectivore birds (Chestnut‐backed Antbird Poliocrania exsul, Black‐crowned Antshrike Thamnophilus atrinucha, White‐breasted Wood‐wren Henicorhina leucosticta, Stripe‐breasted Wren Cantorchilus thoracicus) at La Selva Biological Station, Costa Rica. We sought to understand species‐ and family‐level differences in gap crossing behavior, specifically: (1) the effect of forest‐opening (gap) width, and (2) the effect of perceived risk of predation. A total of 39 treatment (predator playback) and 39 control (silent playback) trials were conducted at gap sites ranging in width from 2.8 to 12.6 m. Predator playback decreased the number of times that birds crossed study gaps, increased latency time in all but one species, and increased the closest distance that birds approached the playback speaker. Gap width affected only latency time: as gap width increased, latency time increased. We observed strong differences in behavioral response between families and species of different foraging heights. In the statistical models, family (Thamnophilidae and Troglodytidae), foraging height (low or mid‐story), and trial type (silent control or predator treatment) consistently emerged as strongest predictors of bird behavior. Our results indicate that small linear gaps (< 12.6 m) do not impede movement for these four focal species, but that risk of predation may hinder bird movement even at small gaps. Resumen ∙ Playback de aves de presa, altura de forrajeo y filogenia afectan el comportamiento de aves insectívoras al cruzar claros de bosque en Costa Rica Se conoce poco sobre los efectos de los paisajes fragmentados sobre el movimiento de las aves tropicales, debido en parte a la escasez de experimentos sobre la renuencia de diferentes especies a cruzar los claros de bosque. Para aprender más sobre los factores involucrados en el comportamiento de aves al cruzar los claros de bosque, se utiliza‐ ron llamadas grabadas de un Gavilán Común (Leucopternis semiplumbeus) en experimentos de ‘playback’ sobre cuatro especies de aves insectívoras (Hormiguero Dorsicastaño Poliocrania exsul, Batará Pizarroso Occidental Thamnophilus atrinucha, Cucarachero Pechiblanco Henicorhina leucosticta, Cucarachero Pechirrayado Cantorchilus thoracicus) en la Estación Biológica La Selva, Costa Rica. Se trató de entender las diferencias en el comportamiento de cruzar claros de bosque a nivel de especie, específicamente: (1) el efecto de la anchura del claro y (2) el efecto del riesgo percibido de depredación. Se realizaron 39 experimentos con playback de gavilán (tratamiento) y 39 experimentos con playback de silencio (control) en sitios de claros de bosque con una anchura de 2,8 a 12,6 m. El playback del gavilán disminuyó el número de veces que las aves cruzaron los claros de bosque, aumentó el tiempo que tardaron en iniciar el cruce en tres de las cuatro especies estudiadas y aumentó la distancia más cercana que acercaron el altavoz. La anchura del claro de bosque afectó sólo el tiempo que las aves tardaron en iniciar el cruce: el tiempo que tardaron en iniciar el cruce aumentó con el aumento de la anchura del claro de bosque. Observamos diferencias fuertes en respuestas entre familias y especies de diferentes alturas de forrajeo. En los modelos, familia (Thamnophilidae y Troglodytidae), la altura de forrajeo (bajo o medio del dosel) y el tipo de playback (control de silencio o playback de gavilán) constantemente emergieron como predictores fuertes. Nuestros resultados indican que los claros de bosque pequeños y lineales (< 12,6 m) no impiden el movimiento de las cuatro especies estudiadas, pero que el riesgo de depredación tal vez dificulte el movimiento de aves aun en claros de bosque pequeños.

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016) : part two

Background The immunological escape of tumors represents one of the main ob- stacles to the treatment of malignancies. The blockade of PD-1 or CTLA-4 receptors represented a milestone in the history of immunotherapy. However, immune checkpoint inhibitors seem to be effective in specific cohorts of patients. It has been proposed that their efficacy relies on the presence of an immunological response. Thus, we hypothesized that disruption of the PD-L1/PD-1 axis would synergize with our oncolytic vaccine platform PeptiCRAd. Methods We used murine B16OVA in vivo tumor models and flow cytometry analysis to investigate the immunological background. Results First, we found that high-burden B16OVA tumors were refractory to combination immunotherapy. However, with a more aggressive schedule, tumors with a lower burden were more susceptible to the combination of PeptiCRAd and PD-L1 blockade. The therapy signifi- cantly increased the median survival of mice (Fig. 7). Interestingly, the reduced growth of contralaterally injected B16F10 cells sug- gested the presence of a long lasting immunological memory also against non-targeted antigens. Concerning the functional state of tumor infiltrating lymphocytes (TILs), we found that all the immune therapies would enhance the percentage of activated (PD-1pos TIM- 3neg) T lymphocytes and reduce the amount of exhausted (PD-1pos TIM-3pos) cells compared to placebo. As expected, we found that PeptiCRAd monotherapy could increase the number of antigen spe- cific CD8+ T cells compared to other treatments. However, only the combination with PD-L1 blockade could significantly increase the ra- tio between activated and exhausted pentamer positive cells (p= 0.0058), suggesting that by disrupting the PD-1/PD-L1 axis we could decrease the amount of dysfunctional antigen specific T cells. We ob- served that the anatomical location deeply influenced the state of CD4+ and CD8+ T lymphocytes. In fact, TIM-3 expression was in- creased by 2 fold on TILs compared to splenic and lymphoid T cells. In the CD8+ compartment, the expression of PD-1 on the surface seemed to be restricted to the tumor micro-environment, while CD4 + T cells had a high expression of PD-1 also in lymphoid organs. Interestingly, we found that the levels of PD-1 were significantly higher on CD8+ T cells than on CD4+ T cells into the tumor micro- environment (p < 0.0001). Conclusions In conclusion, we demonstrated that the efficacy of immune check- point inhibitors might be strongly enhanced by their combination with cancer vaccines. PeptiCRAd was able to increase the number of antigen-specific T cells and PD-L1 blockade prevented their exhaus- tion, resulting in long-lasting immunological memory and increased median survival

Diversity, abundance, and host relationships of avian malaria and related haemosporidians in New Mexico pine forests

Avian malaria and related haemosporidian parasites (genera Haemoproteus, Plasmodium, and Leucocytozoon) affect bird demography, species range limits, and community structure, yet they remain unsurveyed in most bird communities and populations. We conducted a community-level survey of these vector-transmitted parasites in New Mexico, USA, to describe their diversity, abundance, and host associations. We focused on the breeding-bird community in the transition zone between piñon-juniper woodland and ponderosa pine forests (elevational range: 2,150–2,460 m). We screened 186 birds representing 49 species using both standard PCR and microscopy techniques to detect infections of all three avian haemosporidian genera. We detected infections in 68 out of 186 birds (36.6%), the highest proportion of which were infected with Haemoproteus (20.9%), followed by Leucocytozoon (13.4%), then Plasmodium (8.0%). We sequenced mtDNA for 77 infections representing 43 haplotypes (25 Haemoproteus, 12 Leucocytozoon, 6 Plasmodium). When compared to all previously known haplotypes in the MalAvi and GenBank databases, 63% (27) of the haplotypes we recovered were novel. We found evidence for host specificity at the avian clade and species level, but this specificity was variable among parasite genera, in that Haemoproteus and Leucocytozoon were each restricted to three avian groups (out of six), while Plasmodium occurred in all groups except non-passerines. We found striking variation in infection rate among host species, with nearly universal infection among vireos and no infection among nuthatches. Using rarefaction and extrapolation, we estimated the total avian haemosporidian diversity to be 70 haplotypes (95% CI [43–98]); thus, we may have already sampled ∼60% of the diversity of avian haemosporidians in New Mexico pine forests. It is possible that future studies will find higher diversity in microhabitats or host species that are under-sampled or unsampled in the present study. Fortunately, this study is fully extendable via voucher specimens, frozen tissues, blood smears, parasite images, and documentation provided in open-access databases (MalAvi, GenBank, and ARCTOS)

Relational exchanges versus arm’s-length transactions during institutional transitions

Institutional transitions, Relational exchanges, Arm’s-length transactions,