A Phase I Double Blind,Placebo-Controlled,Randomized Study of the Safety and Immunogenicity of Electroporated HIV DNA with or without Interleukin 12 in Prime-Boost Combinations with an Ad35 HIV Vaccine in Healthy HIV-Seronegative African Adults

Background

Strategies to enhance the immunogenicity of DNA vaccines in humans include i) co-administration of molecular adjuvants, ii) intramuscular administration followed by in vivo electroporation (IM/EP) and/or iii) boosting with a different vaccine. Combining these strategies provided protection of macaques challenged with SIV; this clinical trial was designed to mimic the vaccine regimen in the SIV study.

Methods

Seventy five healthy, HIV-seronegative adults were enrolled into a phase 1, randomized, double-blind, placebo-controlled trial. Multi-antigenic HIV (HIVMAG) plasmid DNA (pDNA) vaccine alone or co-administered with pDNA encoding human Interleukin 12 (IL-12) (GENEVAX IL-12) given by IM/EP using the TriGrid Delivery System was tested in different prime-boost regimens with recombinant Ad35 HIV vaccine given IM.

Results

All local reactions but one were mild or moderate. Systemic reactions and unsolicited adverse events including laboratory abnormalities did not differ between vaccine and placebo recipients. No serious adverse events (SAEs) were reported. T cell and antibody response rates after HIVMAG (x3) prime—Ad35 (x1) boost were independent of IL-12, while the magnitude of interferon gamma (IFN-γ) ELISPOT responses was highest after HIVMAG (x3) without IL-12. The quality and phenotype of T cell responses shown by intracellular cytokine staining (ICS) were similar between groups. Inhibition of HIV replication by autologous T cells was demonstrated after HIVMAG (x3) prime and was boosted after Ad35. HIV specific antibodies were detected only after Ad35 boost, although there was a priming effect with 3 doses of HIVMAG with or without IL-12. No anti-IL-12 antibodies were detected.

Conclusion

The vaccines were safe, well tolerated and moderately immunogenic. Repeated administration IM/EP was well accepted. An adjuvant effect of co-administered plasmid IL-12 was not detected.

Trial Registration

ClinicalTrials.gov NCT01496989     

Genome Wide Association Identifies Novel Loci Involved in Fungal Communication

Understanding how genomes encode complex cellular and organismal behaviors has become the outstanding challenge of modern genetics. Unlike classical screening methods, analysis of genetic variation that occurs naturally in wild populations can enable rapid, genome-scale mapping of genotype to phenotype with a medium-throughput experimental design. Here we describe the results of the first genome-wide association study (GWAS) used to identify novel loci underlying trait variation in a microbial eukaryote, harnessing wild isolates of the filamentous fungus Neurospora crassa. We genotyped each of a population of wild Louisiana strains at 1 million genetic loci genome-wide, and we used these genotypes to map genetic determinants of microbial communication. In N. crassa, germinated asexual spores (germlings) sense the presence of other germlings, grow toward them in a coordinated fashion, and fuse. We evaluated germlings of each strain for their ability to chemically sense, chemotropically seek, and undergo cell fusion, and we subjected these trait measurements to GWAS. This analysis identified one gene, NCU04379 (cse-1, encoding a homolog of a neuronal calcium sensor), at which inheritance was strongly associated with the efficiency of germling communication. Deletion of cse-1 significantly impaired germling communication and fusion, and two genes encoding predicted interaction partners of CSE1 were also required for the communication trait. Additionally, mining our association results for signaling and secretion genes with a potential role in germling communication, we validated six more previously unknown molecular players, including a secreted protease and two other genes whose deletion conferred a novel phenotype of increased communication and multi-germling fusion. Our results establish protein secretion as a linchpin of germling communication in N. crassa and shed light on the regulation of communication molecules in this fungus. Our study demonstrates the power of population-genetic analyses for the rapid identification of genes contributing to complex traits in microbial species.     

Genetic dissection of grain beta-glucan and amylose content in barley (Hordeum vulgare L.)

High beta-glucan (BG) barleys (Hordeum vulgare L.) have major potential as food ingredients due to their well-known health benefits. Quantitative trait loci (QTL) associated with BG have been reported in traditional barley varieties with intermediate levels of BG, but no QTL studies have been reported in hull-less barley varieties with high BG levels. In this study, QTL analysis was performed to identify markers linked to high BG and amylose in the hull-less barley varieties Falcon (4–5 % BG) and Azhul (8–9 % BG) using a newly developed recombinant inbred line (RIL) mapping population. The population was grown over 3 years (2007–2009) at sites in Yuma, AZ, USA; Leeston, New Zealand; Aberdeen, ID, USA; and Tetonia, ID, USA. We identified 17 QTL associated with either BG or amylose content. QTL contributing to high BG were located on chromosomes 3H, 4H, 5H, 6H and 7H, while QTL contributing to amylose were located on chromosomes 1H, 5H and 7H. Additionally, we identified QTL affecting both BG and amylose content located on chromosomes 1H and 7H. Transgressive segregation was observed in some of the RILs and exceptions were discovered contradicting an inverse relationship between BG and amylose. This work will provide the basis for gene cloning and marker-assisted selection in combination with traditional field selection to improve barley breeding for high BG content.     

Sequential dynein effectors regulate axonal autophagosome motility in a maturation-dependent pathway

Autophagy is a degradative pathway required to maintain homeostasis. Neuronal autophagosomes form constitutively at the axon terminal and mature via lysosomal fusion during dynein-mediated transport to the soma. How the dynein–autophagosome interaction is regulated is unknown. Here, we identify multiple dynein effectors on autophagosomes as they transit along the axons of primary neurons. In the distal axon, JIP1 initiates autophagosomal transport. Autophagosomes in the mid-axon require HAP1 and Huntingtin. We find that HAP1 is a dynein activator, binding the dynein–dynactin complex via canonical and noncanonical interactions. JIP3 is on most axonal autophagosomes, but specifically regulates the transport of mature autolysosomes. Inhibiting autophagosomal transport disrupts maturation, and inhibiting autophagosomal maturation perturbs the association and function of dynein effectors; thus, maturation and transport are tightly linked. These results reveal a novel maturation-based dynein effector handoff on neuronal autophagosomes that is key to motility, cargo degradation, and the maintenance of axonal health.     

The effects of dexpramipexole (KNS-760704) in individuals with amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is characterized by upper and lower motor neuron dysfunction and loss, rapidly progressive muscle weakness, wasting and death. Many factors, including mitochondrial dysfunction, may contribute to ALS pathogenesis. Riluzole, which has shown only modest benefits in a measure of survival time without demonstrated effects on muscle strength or function, is the only approved treatment for ALS. We tested the putative mitochondrial modulator dexpramipexole (KNS-760704; (6R)-4,5,6,7-tetrahydro-N6-propyl-2,6-benzothiazole-diamine) in subjects with ALS in a two-part, double-blind safety and tolerability study, with a preliminary assessment of its effects on functional decline and mortality. In part 1, the effects of dexpramipexole (50, 150 or 300 mg d(-1)) versus placebo were assessed over 12 weeks. In part 2, after a 4-week, single-blind placebo washout, continuing subjects were re-randomized to dexpramipexole at 50 mg d(-1) or 300 mg d(-1) as double-blind active treatment for 24 weeks. Dexpramipexole was safe and well tolerated. Trends showing a dose-dependent attenuation of the slope of decline of the ALS Functional Rating Scale-Revised (ALSFRS-R) in part 1 and a statistically significant (P = 0.046) difference between groups in a joint rank test of change from baseline in ALSFRS-R and mortality in part 2 strongly support further testing of dexpramipexole in ALS.     

National and regional patterns of habitat association with foraging Barn Swallows Hirundo rustica in the UK

Capsule Barn Swallows showed a consistent association with cattle across the UK, but certain landscape features, particularly mixed field types and tall trees, were also important.

Aim To provide nationally representative data on habitat selection in foraging Barn Swallows.

Method Observers carried out four timed point counts within an allocated 2-km square(s). Point counts were at least 500 m apart and considered as independent sample points. Each point count covered 100 m radius and was visited twice during the summer. An index of foraging activity was derived from the number of foraging passes made by Barn Swallows within ten minutes. The maximum count of Swallows present was also recorded. Habitat data included the presence or absence of landscape features and buildings and the proportion of area covered by particular crop and boundary types within the 100 m count radius.

Results Cattle were the single most important and most consistent variable associated with foraging Barn Swallows, in every UK region. Horses were also important in the southeast. Grassland was only important if livestock were present. Foraging pass rates were higher where count circles contained a mixture of grass and arable fields rather than just one or the other. There was a general positive relationship between foraging pass rates and the presence of tall trees in boundaries, and this was significant in the arable eastern region of the UK, where their relative importance of concentrating prey may be more acute.

Conclusion Historical changes in the distribution and availability of habitat features associated with foraging Barn Swallows are consistent with regional differences in population change for this species in the UK. These patterns of association are discussed in terms of changes in land use, the widespread loss of mixed farming and simplifications to landscape complexity.     

The effect of different nutrient concentrations on the growth rate and nitrogen storage of watercress (Nasturtium officinale R. Br.)

The mechanisms that allow broadly distributed aquatic plants to inhabit variable resource environments are unclear, yet understanding these mechanisms is important because broad environmental tolerance is often linked to invasiveness in terrestrial and aquatic plants. In an experimental stream, we examined the effects of different nutrient concentrations on the growth rate, biomass, and foliar nutrient concentrations of a cosmopolitan and potentially invasive aquatic plant, Nasturtium officinale (R. Br.). Nasturtium seedlings were grown under six nutrient treatment levels ranging from 0.64 μm N:0.09 μm P to 1531 μm N:204.13 μm P, for 8 weeks. Absolute and relative growth rates, and biomass of seedlings increased along a gradient of increasing nutrient concentrations but the effect of nutrient concentration was dependent on growing time. Seedling biomass varied among nutrient treatments in weeks 4 through 8 of the experiment, but did not differ in week 2. By week 8, the two highest nutrient treatments had greater biomass than the two lowest nutrient treatments. Foliar nitrogen concentration increased, whereas carbon concentration and C:N ratios decreased in response to increasing nutrients. Nasturtium grows slowly in nutrient-poor conditions but rapidly increases its growth, biomass accrual, and nitrogen storage as conditions become nutrient-rich. The response of Nasturtium to enhanced nutrient conditions may indicate how aquatic nuisance species successfully invade and dominate plant communities in streams, where resources often vary both temporally and spatially.     

Peppy: A virtual reality environment for exploring the principles of polypeptide structure

A key learning outcome for undergraduate biochemistry classes is a thorough understanding of the principles of protein structure. Traditional approaches to teaching this material, which include two‐dimensional (2D) images on paper, physical molecular modeling kits, and projections of 3D structures into 2D, are unable to fully capture the dynamic 3D nature of proteins. We have built a virtual reality application, Peppy, aimed at facilitating teaching of the principles of protein secondary structure. Rather than attempt to model molecules with the same fidelity to the underlying physical chemistry as existing, research‐oriented molecular modelling approaches, we took the more straightforward approach of harnessing the Unity video game physics engine. Indeed, the simplicity and limitations of our model are strengths in a teaching context, provoking questions and thus deeper understanding. Peppy allows exploration of the relative effects of hydrogen bonding (and electrostatic interactions more generally), backbone φ/ψ angles, basic chemical structure, and steric effects on a polypeptide structure in an accessible format that is novel, dynamic, and fun to use. Apart from describing the implementation and use of Peppy, we discuss the outcomes of deploying Peppy in undergraduate biochemistry courses.