Comparative Genomics of Marine Bacteria from a Historically Defined Plastic Biodegradation Consortium with the Capacity to Biodegrade Polyhydroxyalkanoates

Biodegradable and compostable plastics are getting more attention as the environmental impacts of fossil-fuel-based plastics are revealed. Microbes can consume these plastics and biodegrade them within weeks to months under the proper conditions. The biobased polyhydroxyalkanoate (PHA) polymer family is an attractive alternative due to its physicochemical properties and biodegradability in soil, aquatic, and composting environments. Standard test methods are available for biodegradation that employ either natural inocula or defined communities, the latter being preferred for standardization and comparability. The original marine biodegradation standard test method ASTM D6691 employed such a defined consortium for testing PHA biodegradation. However, the taxonomic composition and metabolic potential of this consortium have never been confirmed using DNA sequencing technologies. To this end, we revived available members of this consortium and determined their phylogenetic placement, genomic sequence content, and metabolic potential. The revived members belonged to the Bacillaceae, Rhodobacteraceae, and Vibrionaceae families. Using a comparative genomics approach, we found all the necessary enzymes for both PHA production and utilization in most of the members. In a clearing-zone assay, three isolates also showed extracellular depolymerase activity. However, we did not find classical PHA depolymerases, but identified two potentially new extracellular depolymerases that resemble triacylglycerol lipases

Surrogate End Points and Patient-Reported Outcomes for Novel Oncology Drugs Approved between 2011 and 2017

The US Food and Drug Administration (FDA) may approve drugs based on surrogate end points that reasonably predict that a drug provides clinical benefit. If approved via the accelerated approval pathway, the FDA may require postmarketing studies to confirm the perceived clinical benefit. Assessment of patient-reported outcomes (PROs), defined as any report on a patient’s health that comes directly from the patient, can also play a key role in understanding benefits and tolerability of oncology drugs. We sought to examine the use of surrogate end points for overall survival (OS) in new oncology drug approvals, to evaluate the use of PROs in trials supporting approvals, and to determine whether oncology drugs initially approved without evidence of OS or PRO benefits demonstrated improvements in either measure postapproval

Ciliate diversity, community structure, and novel taxa in lakes of the McMurdo Dry Valleys, Antarctica

Author Posting. © Marine Biological Laboratory, 2014. This article is posted here by permission of Marine Biological Laboratory for personal use, not for redistribution. The definitive version was published in Biological Bulletin 227 (2014): 175-190.We report an in-depth survey of next-generation DNA sequencing of ciliate diversity and community structure in two permanently ice-covered McMurdo Dry Valley lakes during the austral summer and autumn (November 2007 and March 2008). We tested hypotheses on the relationship between species richness and environmental conditions including environmental extremes, nutrient status, and day length. On the basis of the unique environment that exists in these high-latitude lakes, we expected that novel taxa would be present. Alpha diversity analyses showed that extreme conditions—that is, high salinity, low oxygen, and extreme changes in day length—did not impact ciliate richness; however, ciliate richness was 30% higher in samples with higher dissolved organic matter. Beta diversity analyses revealed that ciliate communities clustered by dissolved oxygen, depth, and salinity, but not by season (i.e., day length). The permutational analysis of variance test indicated that depth, dissolved oxygen, and salinity had significant influences on the ciliate community for the abundance matrices of resampled data, while lake and season were not significant. This result suggests that the vertical trends in dissolved oxygen concentration and salinity may play a critical role in structuring ciliate communities. A PCR-based strategy capitalizing on divergent eukaryotic V9 hypervariable region ribosomal RNA gene targets unveiled two new genera in these lakes. A novel taxon belonging to an unknown class most closely related to Cryptocaryon irritans was also inferred from separate gene phylogenies.Funding was provided by NSF DEB-0717390 to Linda Amaral-Zettler (MIRADA-LTERS); OPP-1115245, OPP-0838933, OPP-1027284, and OPP-0839075 to John C. Priscu; and OPP-0631659 and OPP-1056396 to Rachael Morgan-Kiss. We would also like to acknowledge the China Scholarship Council (No. [2012] 3013) for fellowship support to Yuan Xu enabling her to study at the Marine Biological Laboratory. The Montana Space Grant Consortium provided additional funding for Trista Vick-Majors

Absence of quantum-confined Stark effect in GaN quantum disks embedded in (Al,Ga)N nanowires grown by molecular beam epitaxy

Several of the key issues of planar (Al,Ga)N-based deep-ultraviolet light emitting diodes could potentially be overcome by utilizing nanowire heterostructures, exhibiting high structural perfection and improved light extraction. Here, we study the spontaneous emission of GaN/(Al,Ga)N nanowire ensembles grown on Si(111) by plasma-assisted molecular beam epitaxy. The nanowires contain single GaN quantum disks embedded in long (Al,Ga)N nanowire segments essential for efficient light extraction. These quantum disks are found to exhibit intense emission at unexpectedly high energies, namely, significantly above the GaN bandgap, and almost independent of the disk thickness. An in-depth investigation of the actual structure and composition of the nanowires reveals a spontaneously formed Al gradient both along and across the nanowire, resulting in a complex core/shell structure with an Al deficient core and an Al rich shell with continuously varying Al content along the entire length of the (Al,Ga)N segment. This compositional change along the nanowire growth axis induces a polarization doping of the shell that results in a degenerate electron gas in the disk, thus screening the built-in electric fields. The high carrier density not only results in the unexpectedly high transition energies, but also in radiative lifetimes depending only weakly on temperature, leading to a comparatively high internal quantum efficiency of the GaN quantum disks up to room temperature.Comment: This document is the unedited Author's version of a Submitted Work that was subsequently accepted for publication in Nano Letters (2019), copyright (C) American Chemical Society after peer review. To access the final edited and published work see https://doi.org/10.1021/acs.nanolett.9b01521, the supporting information is available (free of charge) under the same lin