TbTRF suppresses the TERRA level and regulates the cell cycle-dependent TERRA foci number with a TERRA binding activity in its C-terminal Myb domain

Telomere repeat-containing RNA (TERRA) has been identified in multiple organisms including Trypanosoma brucei, a protozoan parasite that causes human African trypanosomiasis. T. brucei regularly switches its major surface antigen, VSG, to evade the host immune response. VSG is expressed exclusively from subtelomeric expression sites, and we have shown that telomere proteins play important roles in the regulation of VSG silencing and switching. In this study, we identify several unique features of TERRA and telomere biology in T. brucei. First, the number of TERRA foci is cell cycle-regulated and influenced by TbTRF, the duplex telomere DNA binding factor in T. brucei. Second, TERRA is transcribed by RNA polymerase I mainly from a single telomere downstream of the active VSG. Third, TbTRF binds TERRA through its C-terminal Myb domain, which also has the duplex DNA binding activity, in a sequence-specific manner and suppresses the TERRA level without affecting its half-life. Finally, levels of the telomeric R-loop and telomere DNA damage were increased upon TbTRF depletion. Overexpression of an ectopic allele of RNase H1 that resolves the R-loop structure in TbTRF RNAi cells can partially suppress these phenotypes, revealing an underlying mechanism of how TbTRF helps maintain telomere integrity.     

Partial deletions of a sequence family ("DXS278") and its physical linkage to steroid sulfatase as detected by pulsed-field gel electrophoresis

pCRI-S232 (DXS278) is a 7-kb genomic sequence that hybridizes to multiple polymorphic X-linked restriction fragments on standard Southern analysis. Physical mapping of pCRI-S232 by pulsed-field gel electrophoresis (PFGE) suggests that a sequence in S232 is repeated in multiple X-chromosomal regions in normal individuals. Steroid sulfatase (STS) and DXS237 each hybridize to two of six X-linked SfiI fragments detected by S232. Two independent familial STS deletions, one of which is associated with a phenotype of ichthyosis plus ocular albinism (XI/OA1) and the other with nystagmus plus Rud syndrome, lack some but not all of the normal S232 PFGE fragments. We isolated a DNA fragment, E25B1.8, from a cosmid that contains S232. E25B1.8 detects a subset of the S232 polymorphic fragments on standard Southern blots plus new constant fragments; some, but not all, of the E25B1.8-hybridizing fragments are deleted in the XI/OA1 and Rud syndrome/nystagmus males. The simpler, but highly informative, polymorphism detected by E25B1.8 (DXS452) also eliminates an "intralocus" recombination seen with S232. We conclude that (1) males with STS deletions and complex phenotypes are partially deleted for DXS278, (2) DXS237 and part of DXS278 lie within 800 kb of STS, and (3) a repeat sequence within or around pCRI-S232 is probably located in multiple X-chromosomal locations spanning at least 2-3 Mb.     

Intragenic TaqI restriction fragment length polymorphism (RFLP) in CICN4, between the loci for X linked ocular albinism (OA1) and microphthalmia with linear skin defects syndrome (MLS)

A TaqI RFLP was detected within the C1CN4 gene, which lies between the loci for OA1 and MLS. There were no observed recombinations between this RFLP and the OA1 mutation in three informative families. Thus, the marker will be useful for genetic counseling in OA1.     

Fluorescence from low-energy chlorophylls in Photosystem I of Synechocystis sp. PCC 6803 at physiological temperatures

Fluorescence spectra from Photosystem I (PS I) are measured from 25 to –5 °C on a PS II-less mutant of the cyanobacterium Synechocystis sp. PCC 6803. Emission from antenna chlorophylls (Chls) with energy levels below that of the reaction center, or low-energy Chls (LE Chls), is resolved verifying their presence at physiological temperatures. The 25°C spectrum is characterized by peaks at 688 and 715 nm. As temperature decreases, fluorescence at 688 nm decreases while at 715 nm it increases. The total fluorescence yield does not change. The temperature dependent spectra are fit to a sum of two basis spectra. At 25°C, the first basis spectrum has a major peak at 686 nm and a minor peak at 740 nm. This is attributed to fluorescence from the majority or bulk antenna Chls. The second basis spectrum has a major peak at 712 nm, with shoulders at 722 and 770 nm. It characterizes fluorescence from a small number of LE Chls. A progressive shift to the red in the fluorescence spectra occurs as the temperature is decreased. The temperature dependence in the relative amount of fluorescence from the bulk and LE Chls is fit using a two-component energy transfer model at thermal equilibrium.     

Exploring variation in fitness surfaces over time or space

As the number of studies estimating selection on multiple traits has increased in recent years, fitness surfaces have become a fundamental tool for understanding multivariate selection and evolution. However, rigorous statistical comparisons of multivariate selection surfaces over time or space have been limited to parametric analyses of selection coefficients estimated using a quadratic regression model. Although parametric comparisons are useful when selection is approximately linear or quadratic in nature, they are limited when confronting the complex nature of rugged fitness surfaces. Here, I present a novel solution to comparing nonparametric fitness surfaces over time or space. Using a Tucker3 tensor decomposition, which is essentially a higher order principal components analysis, I show how major features of fitness surfaces can be compared statistically. Combined with a bootstrap algorithm, I develop three statistical tests that identify (1) differences in the shape of nonparametric fitness surfaces, (2) differences in the contribution of each surface to variation in fitness across time or space, and (3) specific areas of the surfaces (trait combinations) that vary significantly over time or space. I illustrate the tensor decomposition and statistical analyses using idealized fitness surfaces.     

Automated identification of multiple micro-organisms from resequencing DNA microarrays

There is an increasing recognition that detailed nucleic acid sequence information will be useful and even required in the diagnosis, treatment and surveillance of many significant pathogens. Because generating detailed information about pathogens leads to significantly larger amounts of data, it is necessary to develop automated analysis methods to reduce analysis time and to standardize identification criteria. This is especially important for multiple pathogen assays designed to reduce assay time and costs. In this paper, we present a successful algorithm for detecting pathogens and reporting the maximum level of detail possible using multi-pathogen resequencing microarrays. The algorithm filters the sequence of base calls from the microarray and finds entries in genetic databases that most closely match. Taxonomic databases are then used to relate these entries to each other so that the microorganism can be identified. Although developed using a resequencing microarray, the approach is applicable to any assay method that produces base call sequence information. The success and continued development of this approach means that a non-expert can now perform unassisted analysis of the results obtained from partial sequence data.     

Leishmania spp.: cellular levels and synthesis of polyamines during growth cycles

Polyamines were extracted from five different leishmanial strains (Leishmania sp., L. tropica major, L. mexicana, and two L. donovani isolates) and identified as pulrescine, spermidine, and spermine by thin-layer chromatography and mass spectrometry. These sensitive methods were also used to demonstrate the conversion of radioactive putrescine into spermidine and spermine. As in other types of cells, polyamine levels fluctuated during the growth cycle, maximal levels being attained during the logarithmic growth phase. In the five leishmanial strains, which were members of four different serotypes, the spermidine—putrescine ratios also varied, and in two strains of the same serotype, polyamine ratios were practically identical, suggesting that polyamine characteristics might serve as a further criterion for strain identification and classification.