Mauritian Cynomolgus Macaques Share Two Exceptionally Common Major Histocompatibility Complex Class I Alleles That Restrict Simian Immunodeficiency Virus-Specific CD8+ T Cells

Vaccines that elicit CD8⁺ T-cell responses are routinely tested for immunogenicity in nonhuman primates before advancement to clinical trials. Unfortunately, the magnitude and specificity of vaccine-elicited T-cell responses are variable in currently utilized nonhuman primate populations, owing to heterogeneity in major histocompatibility (MHC) class I genetics. We recently showed that Mauritian cynomolgus macaques (MCM) have unusually simple MHC genetics, with three common haplotypes encoding a shared pair of MHC class IA alleles, Mafa-A*25 and Mafa-A*29. Based on haplotype frequency, we hypothesized that CD8⁺ T-cell responses restricted by these MHC class I alleles would be detected in nearly all MCM. We examine here the frequency and functionality of these two alleles, showing that 88% of MCM express Mafa-A*25 and Mafa-A*29 and that animals carrying these alleles mount three newly defined simian immunodeficiency virus-specific CD8⁺ T-cell responses. The epitopes recognized by each of these responses accumulated substitutions consistent with immunologic escape, suggesting these responses exert antiviral selective pressure. The demonstration that Mafa-A*25 and Mafa-A*29 restrict CD8⁺ T-cell responses that are shared among nearly all MCM indicates that these animals are an advantageous nonhuman primate model for comparing the immunogenicity of vaccines that elicit CD8⁺ T-cell responses.The immunogenicity and efficacy of vaccines intended for human use are commonly evaluated in rhesus and cynomolgus macaques. Indeed, researchers studied an estimated one million macaques in the search for a polio vaccine (5). More recently, these animals have become the dominant preclinical model for human immunodeficiency virus (HIV) vaccine evaluation. Rhesus and cynomolgus macaques are susceptible to infection with pathogenic strains of simian immunodeficiency virus (SIV), lentiviruses that share close genetic homology to HIV and cause AIDS-defining illnesses (11, 14). Vaccines designed to provide sterilizing immunity or control immunodeficiency virus replication can therefore be evaluated in macaques. In addition, the immune systems of humans and macaques are highly similar, providing hope that promising vaccines in macaques can be readily adapted for use in humans.CD8⁺ T cells are particularly attractive candidates for vaccine development. Several lines of evidence indicate that CD8⁺ T cells are important to the control of HIV/SIV viral replication. Expansion of HIV/SIV-specific CD8⁺ T cells during acute viremia is associated with a sharp decline in viral load (6, 21, 50), while the depletion of CD8⁺ cells in SIV-infected macaques results in increased viral loads (13, 27) and abrogates the protection elicited by live, attenuated vaccination (30, 38). Furthermore, major histocompatibility complex (MHC) genotyping studies have identified multiple MHC class I alleles enriched in human and macaque elite controllers (17, 19, 26, 31, 49).Recently, Merck and the HIV Vaccine Trials Network cancelled a phase IIb clinical trial evaluating an HIV vaccine designed to elicit CD8⁺ T-cell immunity. An interim analysis revealed the vaccine was ineffective and that participants with prior immunity to the vaccine vector actually had a higher incidence of HIV infection (7, 28, 39, 43). Dozens of additional vaccines that aim to elicit CD8⁺ T cells are in various stages of preclinical and early-stage clinical development, and testing these vaccines in macaques will provide the proof-of-concept necessary to predict their success.Unfortunately, it has been impossible to definitively associate the breadth, magnitude, or phenotype of SIV-specific CD8⁺ T-cell responses, elicited by competing vaccine modalities, to viral control. Indian rhesus macaques are the most commonly used model for HIV vaccine testing but have extremely diverse MHC class I genetics, giving rise to heterogeneous CD8⁺ T-cell responses. SIV derived CD8⁺ T-cell epitopes have been defined for eight Indian rhesus macaque MHC class I alleles (24). However, more than 400 classical MHC class I alleles have been identified in rhesus macaques, leaving an enormous gap in our understanding of the overall CD8⁺ T-cell repertoire following SIV infection (37). Identifying large cohorts of Indian rhesus macaques matched for one or more MHC class I alleles, and thus predicted to mount CD8⁺ T-cell responses against the same epitopes, is both difficult and expensive. An abundant nonhuman primate model with limited MHC diversity could standardize testing of each new vaccine entering preclinical development. Indeed, head-to-head testing of CD8⁺ T-cell vaccines is essential to maximize the efficiency of the global vaccine enterprise and prioritize rapid advancement of promising candidates.In contrast to Indian rhesus macaques, Mauritian cynomolgus macaques (MCM) are an insular population that expanded from a small number of founder animals (23) over the last 500 years. The unique natural history of these animals is manifest by exceptionally low genetic diversity. We have characterized the MHC genetics of this population and found only seven common haplotypes containing fewer than 30 MHC class I alleles (12, 48). The three most common MHC haplotypes each express Mafa-A*25 and Mafa-A*29. We examine here the frequency and functionality of these two alleles, showing that 88% of MCM express Mafa-A*25 and Mafa-A*29 and that animals carrying these alleles mount three newly defined SIV-specific CD8⁺ T-cell responses that drive SIV variation. These results suggest that MCM will provide an exceptionally valuable resource for head-to-head evaluations of competing vaccine modalities.     

Atmospheric culturable bacteria associated with meteorological conditions at a summer-time site in the mid-Willamette Valley,Oregon

A set of simultaneously collected quantitative measurements of 12 meteorological and 6 culturable atmospheric bacterial (CAB) variables was made over a grass seed field during several early, mid, and late summer days. The observation site was located between the Cascade and Coastal Mountain Ranges near Corvallis in the Willamette Valley, Oregon. Principal component analysis identified those meteorological variables that had the highest loadings in six eigenvectors that account for 95.9% of variation in the data factors, i.e., temperature @ 6.3 m above ground level (AGL), wind velocity @ 10.0 m AGL, wind velocity difference @ 1.7–10.0 m, barometric pressure, wind direction standard deviation, and wind direction. When these variables were used in a cluster analysis, they formed three statistically distinct meteorological variable clusters with means at ca. “midnight”, ca. “midday”, and ca. “evening.” The highest mean density of CAB (i.e., 153.4 ± 162.5 CFU/m³) was associated with the “midday” meteorological Cluster-1 that had warm, dry “gentle breezes” from the southeast, in the relatively bacteria loaded Willamette Valley air. The lowest mean density of CAB (i.e., 35.5 ± 24.1 CFU/m³) was associated with meteorological Cluster-3 in the late afternoon and “evening” occurring during the hottest and driest part of the day with “fresh breezes” coming from the north northwest in air off the Pacific Ocean. Finally, the last cluster, Cluster-2 occurred about midnight and had an intermediate density of CAB (74.2 ± 76.2 CFU/m³) in “light air” coming from the northwest, perhaps off the Pacific Ocean. The CAB associated with each of the three meteorological clusters was only partially statistically distinct. Partially because the CAB in both the Pacific Ocean derived air masses of the “evening” Cluster-3 and “midnight” Cluster-2 were not statically separable, though both were statistically separable from the midday, Willamette Valley derived Cluster-1. Further indicating their common source, both Pacific Ocean derived air masses had very similar percentages of pigmented bacteria, which were dissimilar to the pigmented bacterial population density in the Willamette Valley air masses. In short, it is speculated that “midnight” atmosphere may simply contain the settling concentrated residual bacterial particles in the abated fresh Pacific Ocean breezes after sundown. It is clearly shown that with the methods employed, it is possible to associate the uniqueness of the quantity, and to a lesser extent the quality, of the CAB population with the atmospheric conditions reported herein. From this project comes speculation that the strategies relating the quasi-conservative bacterial populations associated with distinct but nonconservative air mass properties can help to better understand more of the bacterial dynamics found in such situations. And to a further extent, molecular biological methods could be applied to identify bacterial taxa in specific air masses.     

Developmental response of <Emphasis Type="Italic">Euplectrus comstockii</Emphasis> to ascorbic acid in the diet of the larval host, <Emphasis Type="Italic">Heliothis virescens</Emphasis>

Recent developments in genetic engineering have paved the way for researchers to produce crops of high nutritional and yield value, in addition to being resistant to diseases and pests. Ascorbic acid content is one of the parameters researchers are trying to enhance in plants. This study investigated the effect of different levels of dietary ascorbic acid of a beneficial wasp, Euplectrus comstockii Howard (Hymenoptera: Eulophidae), by measuring life history parameters of the wasp when reared on lepidopteran larvae fed a basal diet containing low and high levels of ascorbic acid. Odds and odds ratio analyses showed that the probability of egg hatch and adult emergence for the wasp increased with the amount of ascorbic acid in the diet of the host, and that the rate of development and probability of female or male progeny was similar for most levels of ascorbic acid tested. This would indicate that as the ascorbic acid concentration increases in the pest insect the effectiveness of the wasp is likely to increase and when, by comparison with other published findings, the effectiveness of microbial pathogens is likely to decrease.     

Occasional intraguild predation structuring small mammal assemblages: the marsupial Didelphis aurita in the Atlantic Forest of Brazil

The didelphid marsupial, Didelphis aurita, is suggested as an intraguild predator and as key‐species in small mammal assemblages of the Atlantic Forest of Brazil. The field experiments required to test this hypothesis are complex to implement, but the recent revival of regression methods offers a viable alternative. Here we use the dynamic and static regression methods to determine the importance of D. aurita as a competitor and intraguild predator. Capture–recapture data from two localities in the Rio de Janeiro State were used, Garrafão (municipality of Guapimirim), a coastal forest of the Serra do Mar, and Barra de Maricá, a costal sand dune vegetation. Population and microhabitat variables were monitored from April 1997 to April 2003 in Garrafão, and from January 1986 to July 1990 in Barra de Maricá. Microhabitat variables were related to Canopy, Plant, Litter and Rock covers, Obstruction from 0 to 1.5 m, and Number of logs. Exploitation competition was tested by the dynamic method, which models the effects of D. aurita on the per capita growth rate of a species. Interference by predation or competition was tested by the static method, where the abundance of D. aurita at trap stations was regressed against the abundance of other small mammals, after removal of any variation associated with microhabitat factors. Exploitation competition was not detected, but the interference of D. aurita was pervasive, affecting all small mammals studied in the two localities. The clear avoidance of D. aurita by all small mammals tested in two localities of different physiognomies indicates that it functions as an intraguild predator, even if actual predation by D. aurita is an occasional event.     

Malignant Transformation of Non-Neoplastic Barrett's Epithelial Cells through Well-Defined Genetic Manipulations

Background

Human Barrett''s cancer cell lines have numerous, poorly-characterized genetic abnormalities and, consequently, those lines have limited utility as models for studying the early molecular events in carcinogenesis. Cell lines with well-defined genetic lesions that recapitulate various stages of neoplastic progression in Barrett''s esophagus would be most useful for such studies.

Methodology/Principal Findings

To develop such model cell lines, we started with telomerase-immortalized, non-neoplastic Barrett''s epithelial (BAR-T) cells, which are spontaneously deficient in p16, and proceeded to knock down p53 using RNAi, to activate Ras by introducing oncogenic H-Ras^G12V, or both. BAR-T cells infected with either p53 RNAi or oncogenic H-Ras^G12V alone maintained cell-to-cell contact inhibition and did not exhibit anchorage-independent growth in soft agar. In contrast, the combination of p53 RNAi knockdown with expression of oncogenic H-Ras^G12V transformed the p16-deficient BAR-T cells, as evidenced by their loss of contact inhibition, by their formation of colonies in soft agar, and by their generation of tumors in immunodeficient mice.

Conclusions/Significance

Through these experiments, we have generated a number of transformed and non-transformed cell lines with well-characterized genetic abnormalities recapitulating various stages of carcinogenesis in Barrett''s esophagus. These lines should be useful models for the study of carcinogenesis in Barrett''s esophagus, and for testing the efficacy of chemopreventive and chemotherapeutic agents.     

toxin-mediated insect resistance in plants

We are currently in an interesting phase of plant biotechnology releases, both for the scientists responsible for these innovations who are beginning to see their ideas realized, and for the biotechnology companies that are starting to see a return on their investment. One of the most notable examples, is the introduction of transgenic crops that are engineered to express a Bacillus thuringiensis toxin that confers resistance to insect predation. However, the picture is not altogether positive - there is concern that the introduction of this technology was premature or should not have happened at all, and that the valuable insecticidal properties of Bacillus thuringiensis will be lost.     

Polydnavirus-mediated suppression of insect immunity

Polydnaviruses are symbiotic proviruses of some ichneumonid and braconid wasps that modify the physiology, growth and development of host lepidopteran larvae. Polydnavirus infection targets neuroendocrine and immune systems, altering behavior, stunting growth, and immobilizing immune responses to wasp eggs and larvae. Polydnavirus-mediated disruption of cellular and humoral immunity renders parasitized lepidopteran larvae suitable for development of wasp larvae as well as more susceptible to opportunistic infections. Evidence from the Campoletis sonorensis polydnavirus system indicates that the unique genomic organization of polydnaviruses may have evolved to amplify the synthesis of immunosuppressive viral proteins. Immunosuppressive viruses have been essential to elucidating vertebrate immunity. Polydnaviruses have similar potential to clarify insect immune responses and may also provide novel insights into the role of insect immunity in shaping polydnavirus genomes.     

A new sperm-specific Na+/H+ exchanger required for sperm motility and fertility

It has long been speculated that intracellular pH is a critical regulator of both invertebrate and vertebrate sperm motility, and sodium-hydrogen exchange has been suggested as a mediator of such pH(i) regulation in various instances. Two sodium-hydrogen exchangers (NHE1 and NHE5) are expressed in spermatozoa. However, elimination of the NHE1 gene fails to cause infertility, suggesting that normal sperm function is maintained in NHE1-null animals. Here, we used a functionally unbiased signal peptide trap screen to identify a novel sperm-specific NHE. The NHE contains 14 predicted transmembrane segments, including a potential voltage sensor and a consensus cyclic nucleotide-binding motif. Testis histology, sperm numbers and morphology were normal, but NHE-null males were completely infertile with severely diminished sperm motility. The addition of ammonium chloride, which elevates intracellular pH, partially rescued the motility and fertility defects. Surprisingly, cyclic AMP analogues almost completely rescued the motility and infertility phenotypes. The existence of this new sperm NHE provides an attractive contraceptive target, given its cell-specific expression and absolute requirement for fertility.     

A Newly Discovered Bacteroides Conjugative Transposon, CTnGERM1, Contains Genes Also Found in Gram-Positive Bacteria

Results of a recent study of antibiotic resistance genes in human colonic Bacteroides strains suggested that gene transfer events between members of this genus are fairly common. The identification of Bacteroides isolates that carried an erythromycin resistance gene, ermG, whose DNA sequence was 99% identical to that of an ermG gene found previously only in gram-positive bacteria raised the further possibility that conjugal elements were moving into Bacteroides species from other genera. Six of seven ermG-containing Bacteroides strains tested were able to transfer ermG by conjugation. One of these strains was chosen for further investigation. Results of pulsed-field gel electrophoresis experiments showed that the conjugal element carrying ermG in this strain is an integrated element about 75 kb in size. Thus, the element appears to be a conjugative transposon (CTn) and was designated CTnGERM1. CTnGERM1 proved to be unrelated to the predominant type of CTn found in Bacteroides isolates—CTns of the CTnERL/CTnDOT family—which sometimes carry another type of erm gene, ermF. A 19-kbp segment of DNA from CTnGERM1 was cloned and sequenced. A 10-kbp portion of this segment hybridized not only to DNA from all the ermG-containing strains but also to DNA from strains that did not carry ermG. Thus, CTnGERM1 seems to be part of a family of CTns, some of which have acquired ermG. The percentage of G+C content of the ermG region was significantly lower than that of the chromosome of Bacteroides species—an indication that CTnGERM1 may have entered Bacteroides strains from some other bacterial genus. A survey of strains isolated before 1970 and after 1990 suggests that the CTnGERM1 type of CTn entered Bacteroides species relatively recently. One of the genes located upstream of ermG encoded a protein that had 85% amino acid sequence identity with a macrolide efflux pump, MefA, from Streptococcus pyogenes. Our having found >90% sequence identity of two upstream genes, including mefA, and the remnants of two transposon-carried genes downstream of ermG with genes found previously only in gram-positive bacteria raises the possibility that gram-positive bacteria could have been the origin of CTnGERM1.