Evaluation of the Efficacy of a Recombinant Simian Varicella Virus Vaccine Expressing Simian Immunodeficiency Virus Envelope and Capsid Proteins

Human Immunodeficiency Virus (HIV) is a retrovirus that infects CD4+ T-lymphocytes, which when left untreated, later develops into Acquired Immunodeficiency Syndrome (AIDS). Up to 25,000 people die every week from AIDS infection, making HIV and AIDS research a very high priority for virologists. While highly researched by scholars around the world, no person has been able to develop a successful vaccine, as the retroviral nature of the virus and its high mutation rate make vaccine development incredibly difficult. However, recombinant genetic technology will hopefully allow the revolutionization of vaccines which have already proven effective in immunization. The already developed varicella-zoster virus (VZV) vaccine’s safety, effectiveness, and infection range limited to humans make it a great vector for the creation of a recombinant HIV Vaccine. In this study, simian varicella virus (SVV) and simian immunodeficiency virus (SIV) act as a model to evaluate a recombinant vaccine’s effectiveness on non-human primates’ humoral responses. The wide-scale goal of HIV and concurrent AIDS and SIV research is to both cure and prevent these diseases; in the research this thesis follows, the aim is to create a recombinant SVV vaccine which can manifest immunity in non-human primates, with hopes to parallel that research for a similar vaccine for human use. The specific aims of this thesis include: the development of an optimal protocol for antibody response analysis, and the evaluation of the efficacy of a recombinant SVV vaccine expressing SIV gag and env proteins, either with a protein boost or a DNA boost. After the protocol was modified and optimized, sera from rhesus macaques at different points throughout their immunization schedules were analyzed via western blot. Results showed that the prime-boost schedule is effective in inducing an antibody-mediated response, specifically after boosting, and that a protein vaccine boost rather than DNA vaccine boost is the most effective. This model will continue to be researched further in hopes of developing a successful SIV, and subsequently, HIV vaccine

Comparing Electronic Monitoring and human observer collected fishery data in the tropical purse seine operating in the Western and Central Pacific Ocean

Electronic Monitory (EM) systems have been proven a valid tool for collecting fishery dependent data. They are being widely used in many fisheries as a complement or alternative to human observers to increase the monitoring coverage of fisheries. However, considering its wide application, following agreed minimum standard, it is important to compare the congruence between the information collected by EM and observers. We compared EM and two sets of different observer data collected on 6 trips of tuna purse seiners in the Eastern and Western and Central Pacific Ocean to analyze the similarity of fishing set type identification, estimation of tuna and bycatch catches between both monitoring systems. Overall EM was a valid tool to estimate the type of fishing set. Retained total catch of tunas by set was estimated by EM as reliable as that by both observer programs and logbook. When comparing the information by set, EM estimation of the main species, such as skipjack and bigeye and the combination of bigeye/yellowfin, was proven to be less accurate but statistically similar to the estimates made by both observers’ programs. EM tended to underestimate the retained catch of skipjack in comparison to both observers estimates and slightly overestimate bigeye and yellowfin, the overestimation being less pronounced for bigeye than for yellowfin. For bycatch species, EM is able to identify main bycatch species as observers do. However, the capability of EM to estimate the same number of bycatch items in comparison to IATTC and WCPFC observers varies greatly by species group. For sharks, which are the main bycatch issue in the FAD purse seine fishery, the overall congruence between EM and observers was high. EM and IATTC observer identified a similar overall number of individual sharks, however, WCPFC observers estimated lower number of shark individuals than the other two monitoring systems when considering all trips together.Versión del edito

Creep and Creep-Fatigue Crack Growth at Structural Discontinuities and Welds

The subsection ASME NH high temperature design procedure does not admit crack-like defects into the structural components. The US NRC identified the lack of treatment of crack growth within NH as a limitation of the code and thus this effort was undertaken. This effort is broken into two parts. Part 1, summarized here, involved examining all high temperature creep-fatigue crack growth codes being used today and from these, the task objective was to choose a methodology that is appropriate for possible implementation within NH. The second part of this task, which has just started, is to develop design rules for possible implementation within NH. This second part is a challenge since all codes require step-by-step analysis procedures to be undertaken in order to assess the crack growth and life of the component. Simple rules for design do not exist in any code at present. The codes examined in this effort included R5, RCC-MR (A16), BS 7910, API 579, and ATK (and some lesser known codes). There are several reasons that the capability for assessing cracks in high temperature nuclear components is desirable. These include: (1) Some components that are part of GEN IV reactors may have geometries that have sharp corners - which are essentially cracks. Design of these components within the traditional ASME NH procedure is quite challenging. It is natural to ensure adequate life design by modeling these features as cracks within a creep-fatigue crack growth procedure. (2) Workmanship flaws in welds sometimes occur and are accepted in some ASME code sections. It can be convenient to consider these as flaws when making a design life assessment. (3) Non-destructive Evaluation (NDE) and inspection methods after fabrication are limited in the size of the crack or flaw that can be detected. It is often convenient to perform a life assessment using a flaw of a size that represents the maximum size that can elude detection. (4) Flaws that are observed using in-service detection methods often need to be addressed as plants age. Shutdown inspection intervals can only be designed using creep and creep-fatigue crack growth techniques. (5) The use of crack growth procedures can aid in examining the seriousness of creep damage in structural components. How cracks grow can be used to assess margins on components and lead to further safe operation. After examining the pros and cons of all these methods, the R5 code was chosen as the most up-to-date and validated high temperature creep and creep fatigue code currently used in the world at present. R5 is considered the leader because the code: (1) has well established and validated rules, (2) has a team of experts continually improving and updating it, (3) has software that can be used by designers, (4) extensive validation in many parts with available data from BE resources as well as input from Imperial college's database, and (5) was specifically developed for use in nuclear plants. R5 was specifically developed for use in gas cooled nuclear reactors which operate in the UK and much of the experience is based on materials and temperatures which are experienced in these reactors. If the next generation advanced reactors to be built in the US used these same materials within the same temperature ranges as these reactors, then R5 may be appropriate for consideration of direct implementation within ASME code NH or Section XI. However, until more verification and validation of these creep/fatigue crack growth rules for the specific materials and temperatures to be used in the GEN IV reactors is complete, ASME should consider delaying this implementation. With this in mind, it is this authors opinion that R5 methods are the best available for code use today. The focus of this work was to examine the literature for creep and creep-fatigue crack growth procedures that are well established in codes in other countries and choose a procedure to consider implementation into ASME NH. It is very important to recognize that all creep and creep fatigue crack growth procedures that are part of high temperature design codes are related and very similar. This effort made no attempt to develop a new creep-fatigue crack growth predictive methodology. Rather examination of current procedures was the only goal. The uncertainties in the R5 crack growth methods and recommendations for more work are summarized here also

Uncoupling of Satellite DNA and Centromeric Function in the Genus Equus

In a previous study, we showed that centromere repositioning, that is the shift along the chromosome of the centromeric function without DNA sequence rearrangement, has occurred frequently during the evolution of the genus Equus. In this work, the analysis of the chromosomal distribution of satellite tandem repeats in Equus caballus, E. asinus, E. grevyi, and E. burchelli highlighted two atypical features: 1) several centromeres, including the previously described evolutionary new centromeres (ENCs), seem to be devoid of satellite DNA, and 2) satellite repeats are often present at non-centromeric termini, probably corresponding to relics of ancestral now inactive centromeres. Immuno-FISH experiments using satellite DNA and antibodies against the kinetochore protein CENP-A demonstrated that satellite-less primary constrictions are actually endowed with centromeric function. The phylogenetic reconstruction of centromere repositioning events demonstrates that the acquisition of satellite DNA occurs after the formation of the centromere during evolution and that centromeres can function over millions of years and many generations without detectable satellite DNA. The rapidly evolving Equus species gave us the opportunity to identify different intermediate steps along the full maturation of ENCs

The role of LINEs and CpG islands in dosage compensation on the chicken Z chromosome

Most avian Z genes are expressed more highly in ZZ males than ZW females, suggesting that chromosome-wide mechanisms of dosage compensation have not evolved. Nevertheless, a small percentage of Z genes are expressed at similar levels in males and females, an indication that a yet unidentified mechanism compensates for the sex difference in copy number. Primary DNA sequences are thought to have a role in determining chromosome gene inactivation status on the mammalian X chromosome. However, it is currently unknown whether primary DNA sequences also mediate chicken Z gene compensation status. Using a combination of chicken DNA sequences and Z gene compensation profiles of 310 genes, we explored the relationship between Z gene compensation status and primary DNA sequence features. Statistical analysis of different Z chromosomal features revealed that long interspersed nuclear elements (LINEs) and CpG islands are enriched on the Z chromosome compared with 329 other DNA features. Linear support vector machine (SVM) classifiers, using primary DNA sequences, correctly predict the Z compensation status for >60% of all Z-linked genes. CpG islands appear to be the most accurate classifier and alone can correctly predict compensation of 63% of Z genes. We also show that LINE CR1 elements are enriched 2.7-fold on the chicken Z chromosome compared with autosomes and that chicken chromosomal length is highly correlated with percentage LINE content. However, the position of LINE elements is not significantly associated with dosage compensation status of Z genes. We also find a trend for a higher proportion of CpG islands in the region of the Z chromosome with the fewest dosage-compensated genes compared with the region containing the greatest concentration of compensated genes. Comparison between chicken and platypus genomes shows that LINE elements are not enriched on sex chromosomes in platypus, indicating that LINE accumulation is not a feature of all sex chromosomes. Our results suggest that CpG islands are not randomly distributed on the Z chromosome and may influence Z gene dosage compensation status

Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition

In birds, as in mammals, one pair of chromosomes differs between the sexes. In birds, males are ZZ and females ZW. In mammals, males are XY and females XX. Like the mammalian XY pair, the avian ZW pair is believed to have evolved from autosomes, with most change occurring in the chromosomes found in only one sex—the W and Y chromosomes1, 2, 3, 4, 5. By contrast, the sex chromosomes found in both sexes—the Z and X chromosomes—are assumed to have diverged little from their autosomal progenitors2. Here we report findings that challenge this assumption for both the chicken Z chromosome and the human X chromosome. The chicken Z chromosome, which we sequenced essentially to completion, is less gene-dense than chicken autosomes but contains a massive tandem array containing hundreds of duplicated genes expressed in testes. A comprehensive comparison of the chicken Z chromosome with the finished sequence of the human X chromosome demonstrates that each evolved independently from different portions of the ancestral genome. Despite this independence, the chicken Z and human X chromosomes share features that distinguish them from autosomes: the acquisition and amplification of testis-expressed genes, and a low gene density resulting from an expansion of intergenic regions. These features were not present on the autosomes from which the Z and X chromosomes originated but were instead acquired during the evolution of Z and X as sex chromosomes. We conclude that the avian Z and mammalian X chromosomes followed convergent evolutionary trajectories, despite their evolving with opposite (female versus male) systems of heterogamety. More broadly, in birds and mammals, sex chromosome evolution involved not only gene loss in sex-specific chromosomes, but also marked expansion and gene acquisition in sex chromosomes common to males and females.National Science Foundation (U.S.)Howard Hughes Medical Institut

Investigating variation in replicability

Although replication is a central tenet of science, direct replications are rare in psychology. This research tested variation in the replicability of 13 classic and contemporary effects across 36 independent samples totaling 6,344 participants. In the aggregate, 10 effects replicated consistently. One effect – imagined contact reducing prejudice – showed weak support for replicability. And two effects – flag priming influencing conservatism and currency priming influencing system justification – did not replicate. We compared whether the conditions such as lab versus online or US versus international sample predicted effect magnitudes. By and large they did not. The results of this small sample of effects suggest that replicability is more dependent on the effect itself than on the sample and setting used to investigate the effect

The Properties of Adaptive Walks in Evolving Populations of Fungus

A novel method to infer the number and fitness effect of beneficial mutations reveals that the bulk of adaptive evolution is attributable to a few mutations with variable effects on fitness

Initial Mutations Direct Alternative Pathways of Protein Evolution

Whether evolution is erratic due to random historical details, or is repeatedly directed along similar paths by certain constraints, remains unclear. Epistasis (i.e. non-additive interaction between mutations that affect fitness) is a mechanism that can contribute to both scenarios. Epistasis can constrain the type and order of selected mutations, but it can also make adaptive trajectories contingent upon the first random substitution. This effect is particularly strong under sign epistasis, when the sign of the fitness effects of a mutation depends on its genetic background. In the current study, we examine how epistatic interactions between mutations determine alternative evolutionary pathways, using in vitro evolution of the antibiotic resistance enzyme TEM-1 β-lactamase. First, we describe the diversity of adaptive pathways among replicate lines during evolution for resistance to a novel antibiotic (cefotaxime). Consistent with the prediction of epistatic constraints, most lines increased resistance by acquiring three mutations in a fixed order. However, a few lines deviated from this pattern. Next, to test whether negative interactions between alternative initial substitutions drive this divergence, alleles containing initial substitutions from the deviating lines were evolved under identical conditions. Indeed, these alternative initial substitutions consistently led to lower adaptive peaks, involving more and other substitutions than those observed in the common pathway. We found that a combination of decreased enzymatic activity and lower folding cooperativity underlies negative sign epistasis in the clash between key mutations in the common and deviating lines (Gly238Ser and Arg164Ser, respectively). Our results demonstrate that epistasis contributes to contingency in protein evolution by amplifying the selective consequences of random mutations

Population-Based Resequencing of Experimentally Evolved Populations Reveals the Genetic Basis of Body Size Variation in Drosophila melanogaster

Body size is a classic quantitative trait with evolutionarily significant variation within many species. Locating the alleles responsible for this variation would help understand the maintenance of variation in body size in particular, as well as quantitative traits in general. However, successful genome-wide association of genotype and phenotype may require very large sample sizes if alleles have low population frequencies or modest effects. As a complementary approach, we propose that population-based resequencing of experimentally evolved populations allows for considerable power to map functional variation. Here, we use this technique to investigate the genetic basis of natural variation in body size in Drosophila melanogaster. Significant differentiation of hundreds of loci in replicate selection populations supports the hypothesis that the genetic basis of body size variation is very polygenic in D. melanogaster. Significantly differentiated variants are limited to single genes at some loci, allowing precise hypotheses to be formed regarding causal polymorphisms, while other significant regions are large and contain many genes. By using significantly associated polymorphisms as a priori candidates in follow-up studies, these data are expected to provide considerable power to determine the genetic basis of natural variation in body size