Evidence for a founder effect for pseudoxanthoma elasticum in the Afrikaner population of South Africa

Pseudoxanthoma elasticum (PXE) is a heritable elastic tissue disorder recently shown to be attributable to mutations in the ABCC6 ( MRP6) gene. Whereas PXE has been identified in all ethnic groups studied to date, the prevalence of this disease in various populations is uncertain, although often assumed to be similar. A notable exception however is the prevalence of PXE among South African Afrikaners. A previous report has suggested that a founder effect may explain the higher prevalence of PXE in Afrikaners, a European-derived population that first settled in South Africa in the 17th century. To investigate this hypothesis, we performed haplotype and mutational analysis of DNA from 24 South African families of Afrikaner, British and Indian descent. Among the 17 Afrikaner families studied, three common haplotypes and six different disease-causing variants were identified. Three of these mutant alleles were missense variants, two were nonsense mutations and one was a single base-pair insertion. The most common variant accounted for 53% of the PXE alleles, whereas other mutant alleles appeared at lower frequencies ranging from 3% to 12%. Haplotype analysis of the Afrikaner families showed that the three most frequent mutations were identical-by-descent, indicating a founder origin of PXE in this population.     

CD1d-restricted NKT cells express a chemokine receptor profile indicative of Th1-type inflammatory homing cells

CD1d-restricted T cells (NKT cells) are innate memory cells activated by lipid Ags and play important roles in the initiation and regulation of the immune response. However, little is known about the trafficking patterns of these cells or the tissue compartment in which they exert their regulatory activity. In this study, we determined the chemokine receptor profile expressed by CD1d-restricted T cells found in the peripheral blood of healthy volunteers as well as CD1d-restricted T cell clones. CD1d-restricted T cells were identified by Abs recognizing the invariant Valpha24 TCR rearrangement or by binding to CD1d-Fc fusion tetramers loaded with alpha-GalCer. CD1d-restricted T cells in the peripheral blood and CD1d-restricted T cell clones expressed high levels of CXCR3, CCR5, and CCR6; intermediate levels of CXCR4 and CXCR6; and low levels of CXCR1, CCR1, CCR2, and CX(3)CR1, a receptor pattern often associated with tissue-infiltrating effector Th1 cells and CD8+ T cells. Very few of these cells expressed the lymphoid-homing receptors CCR7 or CXCR5. CCR4 was expressed predominantly on CD4+, but not on double-negative CD1d-restricted T cells, which may indicate differential trafficking patterns for these two functionally distinct subsets. CD1d-restricted T cell clones responded to chemokine ligands for CXCR1/2, CXCR3, CXCR4, CXCR6, CCR4, and CCR5 in calcium flux and/or chemotaxis assays. These data indicate that CD1d-restricted T cells express a chemokine receptor profile most similar to Th1 inflammatory homing cells and suggest that these cells perform their function in peripheral tissue sites rather than in secondary lymphoid organs.     

Genetic variants associated with breast cancer risk for Ashkenazi Jewish women with strong family histories but no identifiable BRCA1/2 mutation

The ability to establish genetic risk models is critical for early identification and optimal treatment of breast cancer. For such a model to gain clinical utility, more variants must be identified beyond those discovered in previous genome-wide association studies (GWAS). This is especially true for women at high risk because of family history, but without BRCA1/2 mutations. This study incorporates three datasets in a GWAS analysis of women with Ashkenazi Jewish (AJ) homogeneous ancestry. Two independent discovery cohorts comprised 239 and 238 AJ women with invasive breast cancer or preinvasive ductal carcinoma in situ and strong family histories of breast cancer, but lacking the three BRCA1/2 founder mutations, along with 294 and 230 AJ controls, respectively. An independent, third cohort of 203 AJ cases with familial breast cancer history and 263 healthy controls of AJ women was used for validation. A total of 19 SNPs were identified as associated with familial breast cancer risk in AJ women. Among these SNPs, 13 were identified from a panel of 109 discovery SNPs, including an FGFR2 haplotype. In addition, six previously identified breast cancer GWAS SNPs were confirmed in this population. Seven of the 19 markers were significant in a multivariate predictive model of familial breast cancer in AJ women, three novel SNPs [rs17663555(5q13.2), rs566164(6q21), and rs11075884(16q22.2)], the FGFR2 haplotype, and three previously published SNPs [rs13387042(2q35), rs2046210(ESR1), and rs3112612(TOX3)], yielding moderate predictive power with an area under the curve (AUC) of the ROC (receiver-operator characteristic curve) of 0.74. Population-specific genetic variants in addition to variants shared with populations of European ancestry may improve breast cancer risk prediction among AJ women from high-risk families without founder BRCA1/2 mutations.     

The effect of concentrated smoke products on the restoration of highly disturbed mineral sands in southeast Victoria

Summary Recent studies have recognized the potential of broad‐scale surface application of smoke compounds for enhancing germination from the soil seed‐bank in fire‐prone vegetation communities. Results suggest that smoke technology may play, in the future, a significant role in the restoration and management of areas supporting indigenous vegetation. An important step in the development of smoke‐based restoration tools is the conduct of in situ field trials in a range of geographical locations and environmental conditions. However, most of the published work on the effectiveness of smoke products in promoting seedbank germination has been conducted at sites in southwestern Australia. The present study examines the effect of commercially available smoke‐water products on the regeneration of a highly disturbed former mine‐site at the Royal Botanic Gardens Cranbourne, in southeastern Victoria. Various combinations of concentrated smoke products and topsoil harvested from a nearby heathy woodland community were applied to exposed, uniform mineral sands to test their effect on seedling density and species richness of regrowth. The trials showed that after 12 months a number of common, herbaceous species including Austrodanthonia setacea, Opercularia varia and Platysace heterophylla were recorded in significantly higher numbers in areas treated with a commercial smoke‐water. However, there was no overall improvement in the density of seedlings or the richness of species as a result of the application of the smoke products. Similarly, total seedling density and species richness were not affected by the addition of topsoil, either alone or in combination with smoke products.     

Light-, nitrogen-, and phosphorus-limited growth of Phaeodactylum tricornutum Bohlin strain TFX-1: Chemical composition,carbon partitioning,and the diel periodicity of physiological processes

Phaeodactylum tricomutum Bohlin (strain TFX-1) was grown under light-, nitrogen-, and phosphorus-limited conditions in continuous or semicontinuous cultures under a 12L-12D light regime. The C, N, and P contents were determined at each steady state, as was the partitioning of cellular organic carbon into protein, lipids, polysaccharides, and metabolic intermediates. All determinations were made at the beginning and again at the end of the light period. The rates of nutrient assimilation and of synthesis of biochemical constituents during the light and dark periods were calculated from the above data, and the periodicities of these processes characterized. The elemental composition of the cells was different under each limitation. In particular, phosphorus limitation severely restricted the ability of the cell to store nitrogen in non-protein forms. Biochemical composition and the diel periodicity of cellular processes also differed between limitations. Nutrient uptake was most strongly periodic under light limitation. Protein synthesis showed increased periodicity under nitrogen limitation, relative to the other limitations, while the periodicity of lipid synthesis was reduced under phosphate limitation. Polysaccharide was synthesized at high rates during the light period and consumed in the dark under all limitations.     

Restricted gene flow and incipient speciation in disjunct Pacific Ocean and Sea of Cortez populations of a reef fish species, Girella nigricans

Abstract.— Population disjunctions have been proposed to play an important role in speciation processes. In this study, we have examined the possible role of the Pacific Ocean-Sea of Cortez disjunction as a contributing factor to cryptic speciation in a reef fish, the opaleye, Girella nigricans . Mitochondrial control region (D-loop) sequences (380 bp) of 117 individuals completely separated opaleye populations from the Pacific Ocean and the Sea of Cortez. Although opaleye exhibit pelagic larval stages that remain in the water column for several months, gene flow between the Pacific Ocean and the Sea of Cortez was found to be extremely limited ( F_ST = 0.84, Nm = 0.10). Whereas limited gene flow and reciprocal monophyly suggest that the observed physical and genetic disjunction are potentially contributing to the incipient speciation of Pacific and Sea of Cortez opaleye, moderate levels of D-loop sequence divergence (3.3%) and the absence of fixed allozyme markers challenge this idea. Pacific Coast populations also exhibited restricted gene flow levels ( F_ST = 0.25, Nm = 1.49) across Punta Eugenia, a recognized oceanographic boundary along the Baja California coast. Thus, opaleye individuals grouped into three clades: one clade in the Sea of Cortez, one Pacific clade south of Punta Eugenia, and one Pacific clade north of Punta Eugenia. Future work in this region will determine if our results can be generalized to other disjunct populations.     

Transient transfection of purified Babesia bovis merozoites

Transient transfection of intraerythrocytic Babesia bovis parasites has been previously reported. In this study, we describe the development and optimization of methods for transfection of purified B. bovis merozoites using either nucleofection (Amaxa) or conventional electroporation (Gene Pulser II, BioRad). Initially, the optimal buffer ("Plasmodium 88A6") and program (v-24) for nucleofection of free merozoites with a plasmid containing the luciferase gene as a reporter were determined. Using the same reporter plasmid, optimal voltage, capacitance and resistance for transfecting free merozoites by electroporation were defined to be 1.2 kV/25 microF/200 Omega. Using these optimal parameters, analysis of the time course of luciferase expression using either system to transfect free B. bovis merozoites showed high enzyme activity at 24h, with a rapid decline thereafter. Nucleofection was approximately five times more effective than electroporation when using a small quantity (2 microg) of DNA, while electroporation was twice as effective as nucleofection when a larger quantity of plasmid DNA (100 microg) was used. Parasite viability was significantly higher when using nucleofection when compared to electroporation regardless of the amount of DNA used. Comparison of luciferase expression after transfection of merozoites with circular, linearized, or double digested plasmid indicated that intact, circular plasmid was necessary for optimal luciferase expression. Overall, the results provide a basis for optimal transfection of purified B. bovis merozoites using either nucleofection or conventional electroporation. However, nucleofection is significantly more efficient when transfecting either circular or restriction digested DNA in the 2-10 microg range.     

Effects of a Single Histoplasmin Skin Test on the Serological Diagnosis of Histoplasmosis

Numerous reports have indicated that a single histoplasmin skin test may stimulate humoral antibodies to Histoplasma capsulatum antigens in histoplasmin-hypersensitive individuals. Although these investigations concur that antibody elevations are evoked, they vary in the reported degree of incidence and response induced, and they cast doubt on the interpretation of serological tests in the diagnosis of histoplasmosis. Histoplasmin-hypersensitive subjects (114) were bled prior to administration of the skin test, 2 days later, at the time this test was read, and 15 and 30 days after testing. No significant antibody titers were observed at 2 days. At 15- and 30-day intervals, only 17 (15%) of the subjects demonstrated circulating antibodies. All 17 showed agar gel bands; 5 demonstrated no complement-fixation (CF) titers, 10 produced CF antibodies ranging from 1:8 to 1:16, and 2 demonstrated titers of 1:32. The data suggest that skin testing does not interfere significantly with antibody levels in sera drawn approximately 2 days after administration of antigen. However, since titers as high as 1:32 were obtained at later intervals, such reactions should be evaluated cautiously and only after consideration of clinical findings.     

Detection of PrPsc in Blood from Sheep Infected with the Scrapie and Bovine Spongiform Encephalopathy Agents

The role of blood in the iatrogenic transmission of transmissible spongiform encephalopathy (TSE) or prion disease has become an increasing concern since the reports of variant Creutzfeldt-Jakob disease (vCJD) transmission through blood transfusion from humans with subclinical infection. The development of highly sensitive rapid assays to screen for prion infection in blood is of high priority in order to facilitate the prevention of transmission via blood and blood products. In the present study we show that PrP^sc, a surrogate marker for TSE infection, can be detected in cells isolated from the blood from naturally and experimentally infected sheep by using a rapid ligand-based immunoassay. In sheep with clinical disease, PrP^sc was detected in the blood of 55% of scrapie agent-infected animals (n = 80) and 71% of animals with bovine spongiform encephalopathy (n = 7). PrP^sc was also detected several months before the onset of clinical signs in a subset of scrapie agent-infected sheep, followed from 3 months of age to clinical disease. This study confirms that PrP^sc is associated with the cellular component of blood and can be detected in preclinical sheep by an immunoassay in the absence of in vitro or in vivo amplification.Transmission of variant Creutzfeldt-Jakob disease (vCJD) has been linked with blood transfusion in four reported cases in Great Britain (19, 24, 26, 32), indicating that this is likely to be an efficient route of transmission. Such findings highlight a significant risk to recipients of vCJD-contaminated blood components, and blood services in the United Kingdom have responded by putting in place precautionary measures, including leucodepletion. However, it remains uncertain whether such a procedure is able to remove all prion infectivity. For example, in two studies by Gregori et al. (13, 14) only 42 and 72% of infectivity was removed by leucodepletion from blood from hamsters with scrapie. Therefore, a rapid blood test for vCJD that is able to screen for likely infected blood is critical given that the presymptomatic stages of vCJD are long and that the prevalence of infection in the human population is unknown (6, 9). This knowledge has given rise to concerns that a large-scale vCJD epidemic could occur by human-to-human transmission (16, 21).Infectivity in human blood is consistent with the demonstration of transmission of disease by blood transfusion in sheep incubating both scrapie and experimental BSE infection (17, 18, 20). Transmission was demonstrated from both whole blood and buffy coat fractions from sheep blood, indicating a cellular source of prions although, from studies done in rodent models, it is likely that the plasma fraction also contains infectivity (4, 13, 14). Furthermore, transmission was possible from sheep showing clinical signs and from sheep that were infected but still in the preclinical phase. However, identification of the abnormal prion protein (PrP^sc) in blood as a surrogate marker for infection has proved more elusive (3). Recently, PrP^sc has been amplified from the blood of experimentally infected rodents (5, 25, 28) and from sheep naturally infected with scrapie agent (29) using protein misfolded cyclic amplification (PMCA), but often these studies take days or weeks to complete. Here, we demonstrate, using a ligand-based immunoassay, that PrP^sc is associated with blood leukocytes from sheep with terminal scrapie or bovine spongiform encephalopathy (BSE) and in sheep incubating scrapie prior to the onset of clinical signs. This assay is a modification of a test that has been validated for use as a postmortem test for BSE, scrapie, and chronic wasting disease (CWD) in Europe and the United States (7).     

Enzyme activities of aerobic lignocellulolytic bacteria isolated from wet tropical forest soils

Lignocellulolytic bacteria have promised to be a fruitful source of new enzymes for next-generation lignocellulosic biofuel production. Puerto Rican tropical forest soils were targeted because the resident microbes decompose biomass quickly and to near-completion. Isolates were initially screened based on growth on cellulose or lignin in minimal media. 75 Isolates were further tested for the following lignocellulolytic enzyme activities: phenol oxidase, peroxidase, β-d-glucosidase, cellobiohydrolase, β-xylopyranosidase, chitinase, CMCase, and xylanase. Cellulose-derived isolates possessed elevated β-d-glucosidase, CMCase, and cellobiohydrolase activity but depressed phenol oxidase and peroxidase activity, while the contrary was true of lignin isolates, suggesting that these bacteria are specialized to subsist on cellulose or lignin. Cellobiohydrolase and phenol oxidase activity rates could classify lignin and cellulose isolates with 61% accuracy, which demonstrates the utility of model degradation assays. Based on 16S rRNA gene sequencing, all isolates belonged to phyla dominant in the Puerto Rican soils, Proteobacteria, Firmicutes, and Actinobacteria, suggesting that many dominant taxa are capable of the rapid lignocellulose degradation characteristic of these soils. The isolated genera Aquitalea, Bacillus, Burkholderia, Cupriavidus, Gordonia, and Paenibacillus represent rarely or never before studied lignolytic or cellulolytic species and were undetected by metagenomic analysis of the soils. The study revealed a relationship between phylogeny and lignocellulose-degrading potential, supported by Kruskal–Wallis statistics which showed that enzyme activities of cultivated phyla and genera were different enough to be considered representatives of distinct populations. This can better inform future experiments and enzyme discovery efforts.