SIGNIFICANCE AND CONTROL OF FUNGAL DISEASES RELATED TO BIRD ROOSTS

Certain fungi have been found frequently as saprophytes in areas containing large amounts of bird excreta. These fungi have the ability to survive, multiply, and cause disease once they have entered a host. Two of these are Crypto-coccus neoformans and Histoplasma capsulatum. Both may easily become airborne and be disseminated throughout an area by the prevailing winds. C. neo-formans is commonly isolated from the excreta of pigeon habitats, and in turn has been associated with clinical cases of cryptococcosis, while blackbird roosts, harboring H. capsulatum, have been responsible for several outbreaks of histoplasmosis. When either of these fungi have become established in nature, the sites may become foci for infection and epidemics may occur if the sites are disturbed. This has led to investigation of these organisms with respect to: 1) the frequency of isolation of H. capsulatum from the soil beneath blackbird roosts in a histoplasmosis endemic area; 2) the infectivity of undisturbed roosts positive for H. capsulatum; and 3) the effectiveness of chemical decontamination of areas containing C. neoformans or H. capsulatum

Bostonia: The Boston University Alumni Magazine. Volume 29

Founded in 1900, Bostonia magazine is Boston University's main alumni publication, which covers alumni and student life, as well as university activities, events, and programs

Silencing of TESTIN by dense biallelic promoter methylation is the most common molecular event in childhood acute lymphoblastic leukaemia

<p>Abstract</p> <p>Background</p> <p>Aberrant promoter DNA methylation has been reported in childhood acute lymphoblastic leukaemia (ALL) and has the potential to contribute to its onset and outcome. However, few reports demonstrate consistent, prevalent and dense promoter methylation, associated with tumour-specific gene silencing. By screening candidate genes, we have detected frequent and dense methylation of the <it>TESTIN </it>(<it>TES</it>) promoter.</p> <p>Results</p> <p>Bisulfite sequencing showed that 100% of the ALL samples (n = 20) were methylated at the <it>TES </it>promoter, whereas the matched remission (n = 5), normal bone marrow (n = 6) and normal PBL (n = 5) samples were unmethylated. Expression of <it>TES </it>in hyperdiploid, TEL-AML⁺, BCR-ABL⁺, and E2A-PBX⁺subtypes of B lineage ALL was markedly reduced compared to that in normal bone marrow progenitor cells and in B cells. In addition <it>TES </it>methylation and silencing was demonstrated in nine out of ten independent B ALL propagated as xenografts in NOD/SCID mice.</p> <p>Conclusion</p> <p>In total, 93% of B ALL samples (93 of 100) demonstrated methylation with silencing or reduced expression of the <it>TES </it>gene. Thus, <it>TES </it>is the most frequently methylated and silenced gene yet reported in ALL. <it>TES</it>, a LIM domain-containing tumour suppressor gene and component of the focal adhesion complex, is involved in adhesion, motility, cell-to-cell interactions and cell signalling. Our data implicate <it>TES </it>methylation in ALL and provide additional evidence for the involvement of LIM domain proteins in leukaemogenesis.</p

Analysis of the paleomagnetism and rock magnetism of the Surco Intrusion, Peru: an attempt to obtain a Southern Hemisphere reversal record

Investigation of the Surco pluton, a granodioritic body approximately 12 km in diameter and age 20 Ma, located near Lima, Peru, was initiated in order to obtain a geomagnetic reversal record. More than 300 samples provide a complete section through the intrusion. Preliminary results obtained using conventional paleomagnetic techniques indicate that the western part of the pluton records the ambient field behavior well; a consistent reversed direction is followed by a partial reversed to normal transition as one progresses into the core of the intrusion. Plots of NRM vs. IRM(S) demagnetization indicate a steady decrease in the geomagnetic field intensity prior to the reversal. The intrusion does not appear to have recorded the recovery of the normal intensity after the reversal. The existence of a complete section through the intrusion permitted, in principle, the observation of a symmetrical record of the reversal from each side of the pluton. However, the results from the eastern Surco section present a confusing picture and reveal significant variations in rock magnetic and remanence properties along section. Magnetic properties of mineral separates were studied in an attempt to understand variability in the rock as a paleomagnetic recorder. In general, the feldspars contain an unstable magnetization, while the mafic minerals hold a more stable magentization. In the eastern Surco, there are considerable variations in their magnetic properties

Shuttle Ground Support Equipment (GSE) T-0 Umbilical to Space Shuttle Program (SSP) Flight Elements Consultation

The NASA Engineering and Safety Center (NESC) was tasked with assessing the validity of an alternate opinion that surfaced during the investigation of recurrent failures at the Space Shuttle T-0 umbilical interface. The most visible problem occurred during the Space Transportation System (STS)-112 launch when pyrotechnics used to separate Solid Rocket Booster (SRB) Hold-Down Post (HDP) frangible nuts failed to fire. Subsequent investigations recommended several improvements to the Ground Support Equipment (GSE) and processing changes were implemented, including replacement of ground-half cables and connectors between flights, along with wiring modifications to make critical circuits quad-redundant across the interface. The alternate opinions maintained that insufficient data existed to exonerate the design, that additional data needed to be gathered under launch conditions, and that the interface should be further modified to ensure additional margin existed to preclude failure. The results of the assessment are contained in this report

Effects of Smoking and Genotype on the PSR Index of Periodontal Disease in Adults Aged 18–49

Studies have found both genetic and environmental influences on chronic periodontitis. The purpose of this study was to examine the relationships among previously identified genetic variants, smoking status, and two periodontal disease-related phenotypes (PSR1 and PSR2) in 625 Caucasian adults (aged 18–49 years). The PSR Index was used to classify participants as affected or unaffected under the PSR1 and PSR2 phenotype definitions. Using logistic regression, we found that the form of the relationship varied by single nucleotide polymorphism (SNP): For rs10457525 and rs12630931, the effects of smoking and genotype on risk were additive; whereas for rs10457526 and rs733048, smoking was not independently associated with affected status once genotype was taken into consideration. In contrast, smoking moderated the relationships of rs3870371 and rs733048 with affected status such that former and never smokers with select genotypes were at increased genetic risk. Thus, for several groups, knowledge of genotype may refine the risk prediction over that which can be determined by knowledge of smoking status alone. Future studies should replicate these findings. These findings provide the foundation for the exploration of novel pathways by which periodontitis may occur

Technical Considerations for Reduced Representation Bisulfite Sequencing with Multiplexed Libraries

Reduced representation bisulfite sequencing (RRBS), which couples bisulfite conversion and next generation sequencing, is an innovative method that specifically enriches genomic regions with a high density of potential methylation sites and enables investigation of DNA methylation at single-nucleotide resolution. Recent advances in the Illumina DNA sample preparation protocol and sequencing technology have vastly improved sequencing throughput capacity. Although the new Illumina technology is now widely used, the unique challenges associated with multiplexed RRBS libraries on this platform have not been previously described. We have made modifications to the RRBS library preparation protocol to sequence multiplexed libraries on a single flow cell lane of the Illumina HiSeq 2000. Furthermore, our analysis incorporates a bioinformatics pipeline specifically designed to process bisulfite-converted sequencing reads and evaluate the output and quality of the sequencing data generated from the multiplexed libraries. We obtained an average of 42 million paired-end reads per sample for each flow-cell lane, with a high unique mapping efficiency to the reference human genome. Here we provide a roadmap of modifications, strategies, and trouble shooting approaches we implemented to optimize sequencing of multiplexed libraries on an a RRBS background

Methodology Report Technical Considerations for Reduced Representation Bisulfite Sequencing with Multiplexed Libraries

Reduced representation bisulfite sequencing (RRBS), which couples bisulfite conversion and next generation sequencing, is an innovative method that specifically enriches genomic regions with a high density of potential methylation sites and enables investigation of DNA methylation at single-nucleotide resolution. Recent advances in the Illumina DNA sample preparation protocol and sequencing technology have vastly improved sequencing throughput capacity. Although the new Illumina technology is now widely used, the unique challenges associated with multiplexed RRBS libraries on this platform have not been previously described. We have made modifications to the RRBS library preparation protocol to sequence multiplexed libraries on a single flow cell lane of the Illumina HiSeq 2000. Furthermore, our analysis incorporates a bioinformatics pipeline specifically designed to process bisulfite-converted sequencing reads and evaluate the output and quality of the sequencing data generated from the multiplexed libraries. We obtained an average of 42 million paired-end reads per sample for each flow-cell lane, with a high unique mapping efficiency to the reference human genome. Here we provide a roadmap of modifications, strategies, and trouble shooting approaches we implemented to optimize sequencing of multiplexed libraries on an a RRBS background

High-Throughput SHAPE Analysis Reveals Structures in HIV-1 Genomic RNA Strongly Conserved across Distinct Biological States

Replication and pathogenesis of the human immunodeficiency virus (HIV) is tightly linked to the structure of its RNA genome, but genome structure in infectious virions is poorly understood. We invent high-throughput SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) technology, which uses many of the same tools as DNA sequencing, to quantify RNA backbone flexibility at single-nucleotide resolution and from which robust structural information can be immediately derived. We analyze the structure of HIV-1 genomic RNA in four biologically instructive states, including the authentic viral genome inside native particles. Remarkably, given the large number of plausible local structures, the first 10% of the HIV-1 genome exists in a single, predominant conformation in all four states. We also discover that noncoding regions functioning in a regulatory role have significantly lower (p-value < 0.0001) SHAPE reactivities, and hence more structure, than do viral coding regions that function as the template for protein synthesis. By directly monitoring protein binding inside virions, we identify the RNA recognition motif for the viral nucleocapsid protein. Seven structurally homologous binding sites occur in a well-defined domain in the genome, consistent with a role in directing specific packaging of genomic RNA into nascent virions. In addition, we identify two distinct motifs that are targets for the duplex destabilizing activity of this same protein. The nucleocapsid protein destabilizes local HIV-1 RNA structure in ways likely to facilitate initial movement both of the retroviral reverse transcriptase from its tRNA primer and of the ribosome in coding regions. Each of the three nucleocapsid interaction motifs falls in a specific genome domain, indicating that local protein interactions can be organized by the long-range architecture of an RNA. High-throughput SHAPE reveals a comprehensive view of HIV-1 RNA genome structure, and further application of this technology will make possible newly informative analysis of any RNA in a cellular transcriptome

Femtomole SHAPE Reveals Regulatory Structures in the Authentic XMRV RNA Genome

Higher-order structure influences critical functions in nearly all non-coding and coding RNAs. Most single-nucleotide resolution RNA structure determination technologies cannot be used to analyze RNA from scarce biological samples, like viral genomes. To make quantitative RNA structure analysis applicable to a much wider array of RNA structure-function problems, we developed and applied high-sensitivity selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) to structural analysis of authentic genomic RNA of the xenotropic murine leukemia virus-related virus (XMRV). For analysis of fluorescently labeled cDNAs generated in high-sensitivity SHAPE experiments, we developed a two-color capillary electrophoresis approach with zeptomole molecular detection limits and sub-femtomole sensitivity for complete SHAPE experiments involving hundreds of individual RNA structure measurements. High-sensitivity SHAPE data correlated closely (R = 0.89) with data obtained by conventional capillary electrophoresis. Using high-sensitivity SHAPE, we determined the dimeric structure of the XMRV packaging domain, examined dynamic interactions between a packaging domain RNA and viral nucleocapsid protein inside virion particles, and identified the packaging signal for this virus. Despite extensive sequence differences between XMRV and the intensively studied Moloney murine leukemia virus, architectures of the regulatory domains are similar and reveal common principles of gammaretrovirus RNA genome packaging