DNA Sexing of the Philippine Eagle (Pithecophaga jefferyi Ogilvie-Grant) in Captivity at the Philippine Eagle Center, Davao City, Philippines

The Philippine eagle is a sexually monomorphic raptor which lacks the sex-linked morphology determining the gender especially in the juveniles. Thus, a PCR amplification technique was used to determine the sex of 24 eagles at different stages of development (2 to 37 years old) in captivity at the Philippine Eagle Center, Malagos Davao City. Fractions of the sex-linked genes, CHD-W and CHD-Z of each individual were amplified. Ka Brianne (female) and Jag (male) having 9 offspring conceived through artificial insemination were used as positive controls for sex identification of 22 other individuals. Two individuals of Gallus domesticus with confirmed genders were also included and run through PCR amplification together with the Philippine eagles using primers CHDFORNEW and CHDREVNEW to test the method. Females revealed two distinct bands (290 bp and 280 bp in size) while the males revealed only a single band of 280 bp. Eleven eagles were  found to be females while 13 were found to be  males. DNA sexing gave a 100% confirmation of the assigned sexes of the eagles, which were obtained through morphometric analysis done by personnel at the captive breeding center. DNA sexing could be a practical technique in sexing newly hatched eaglet and juveniles, naming of eagles, establishing life history characteristics, and pairing attempt or assignment of partners in the threatened avian species such as the Philippine eagles

Understanding the Antiproliferative Activity of Plant Extracts

Many plants possess medicinal properties. Some, such as the Pacific yew, have yielded chemotherapeutic drugs (taxanes). Scientists report that other extracts such as the leaves of Calendula officinalis (marigold), Vinca rosea (periwinkle), Viscum cruciatum (mistletoe), and Rosmarinus officinalis (rosemary) have anti-tumor activity. In most cases, the chemical components responsible for antiproliferative activity have not been identified and it is unclear if any individual components are as effective in isolation as they are in the context of the whole extract. Furthermore, in most cases, there are no data indicating whether these extracts have synergistic effects or cause negative reactions when used with other drugs. We are using HeLa (adenocarcinoma), RAW 264.7 (leukemia), HepG2 (hepatoma), MDA-MB-231 (adenocarcinoma), and human foreskin fibroblasts (HFF, non-tumorigenic) to test the antiproliferative activity of several plant extracts. We identified five extracts, grapeseed, guava, yew, juniper berry, and Vinca, that slow the growth of all five cell lines in a dose-dependent manner. We are using a variety of methods to understand the mechanism by which these extracts are blocking cell growth

Using a Genetic Screen to Discover Gene Functions in Mycobacteriophages Sbash and Island3

Sbash is a temperate bacteriophage that infects Mycobacterium smegmatis. It was assigned to cluster I2 based on gene-content similarity of 35% or higher to sequenced bacteriophages present in the Actinobacteriophage database, phagesDB. Its genome was annotated in 2014 and found to include 89 protein-coding genes, only 22 of which were assigned functions based on bioinformatic analysis. We are using a genetic screen to identify functions of phage genes for which no function is currently known. We cloned 40 of the genes in Sbash’s genome with sizes ranging from 90 bp to 3,666 bp. We screened each gene for cytotoxicity and identified six genes that reduced growth of the host cells when expressed. We also screened for defense, the ability of each gene product to protect the host cell from infection by another phage. We identified eight Sbash gene products that defend host cells from infection by other mycobacteriophages. We have also analyzed genes in Mycobacteriophage Island3, a cluster I1 phage, for cytotoxicity and defense to complete the screen of this phage started by students in previous research groups

Genomic Annotation of Bacteriophages Clayda5, GShelby23, Santhid, and Wrigley

We annotated the genomes of four recently discovered Actinobacteriophages. Clayda5 and GShelby23 were isolated on Microbacterium foliorum NRRL B-24224. Clayda5 is a lytic, cluster EB phage, one of only 47 discovered to date. It has 10 base pair 3’ sticky overhanging ends and a GC content is 67.2%. It has 70 protein-coding genes and two tRNA genes in its 39,894 bp genome. Clayda5 was purified from soil collected in Hull, IA. GShelby23 was isolated from soil collected in Storm Lake, IA. It is a cluster EM phage, one of only six discovered to date. Its genome is circularly permuted and 53,603 bp long. Its GC content is 64.8%. Santhid and Wrigley are phages that infect Gordonia terrae 3612. Santhid is a cluster DY phage, one of only five discovered to date. It was isolated from soil collected in Orange City, IA. Its genome is 39,295 bp long and includes 60 protein-coding genes. Its GC content is 67.7% and has 10 base pair 3’ sticky overhanging ends. Wrigley was isolated using an enrichment protocol from soil collected in Johnston, IA. It is a cluster CY phage, one of only 17 discovered to date. It is a temperate phage whose genome is 51,878 bp long and includes 81 protein-coding genes. It has 10 base pair 3’ sticky overhanging ends and a GC content of 66.3%.

The Surface Array planned for IceCube-Gen2

IceCube-Gen2, the extension of the IceCube Neutrino Observatory, will feature three main components: an optical array in the deep ice, a large-scale radio array in the shallow ice and firn, and a surface detector above the optical array. Thus, IceCube-Gen2 will not only be an excellent detector for PeV neutrinos, but also constitutes a unique setup for the measurement of cosmic-ray air showers, where the electromagnetic component and low-energy muons are measured at the surface and high-energy muons are measured in the ice. As for ongoing enhancement of IceCube’s current surface array, IceTop, we foresee a combination of elevated scintillation and radio detectors for the Gen2 surface array, aiming at high measurement accuracy for air showers. The science goals are manifold: The in-situ measurement of the cosmic-ray flux and mass composition, as well as more thorough tests of hadronic interaction models, will improve the understanding of muons and atmospheric neutrinos detected in the ice, in particular, regarding prompt muons. Moreover, the surface array provides a cosmic-ray veto for the in-ice detector and contributes to the calibration of the optical and radio arrays. Last but not least, the surface array will make major contributions to cosmic-ray science in the energy range of the transition from Galactic to extragalactic sources. The increased sensitivities for photons and for cosmic-ray anisotropies at multi-PeV energies provide a chance to solve the puzzle of the origin of the most energetic Galactic cosmic rays and will serve IceCube’s multimessenger mission