Abnormal Dosage of Ultraconserved Elements Is Highly Disfavored in Healthy Cells but Not Cancer Cells

Ultraconserved elements (UCEs) are strongly depleted from segmental duplications and copy number variations (CNVs) in the human genome, suggesting that deletion or duplication of a UCE can be deleterious to the mammalian cell. Here we address the process by which CNVs become depleted of UCEs. We begin by showing that depletion for UCEs characterizes the most recent large-scale human CNV datasets and then find that even newly formed de novo CNVs, which have passed through meiosis at most once, are significantly depleted for UCEs. In striking contrast, CNVs arising specifically in cancer cells are, as a rule, not depleted for UCEs and can even become significantly enriched. This observation raises the possibility that CNVs that arise somatically and are relatively newly formed are less likely to have established a CNV profile that is depleted for UCEs. Alternatively, lack of depletion for UCEs from cancer CNVs may reflect the diseased state. In support of this latter explanation, somatic CNVs that are not associated with disease are depleted for UCEs. Finally, we show that it is possible to observe the CNVs of induced pluripotent stem (iPS) cells become depleted of UCEs over time, suggesting that depletion may be established through selection against UCE-disrupting CNVs without the requirement for meiotic divisions

Algae removal by roughing filter

Algae removal by roughing filte

Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes

Fluorescence in situ hybridization (FISH) is a powerful single-cell technique for studying nuclear structure and organization. Here we report two advances in FISH-based imaging. We first describe the in situ visualization of single-copy regions of the genome using two single-molecule super-resolution methodologies. We then introduce a robust and reliable system that harnesses single-nucleotide polymorphisms (SNPs) to visually distinguish the maternal and paternal homologous chromosomes in mammalian and insect systems. Both of these new technologies are enabled by renewable, bioinformatically designed, oligonucleotide-based Oligopaint probes, which we augment with a strategy that uses secondary oligonucleotides (oligos) to produce and enhance fluorescent signals. These advances should substantially expand the capability to query parent-of-origin-specific chromosome positioning and gene expression on a cell-by-cell basis

Frequency of natural out-crossing in partially cleistogamous pigeonpea lines in diverse environments

Natural out-crossing is the major cause of loss of varietal purity in pegeonpea [Cajanus cajan (L.) Millsp.]. The frequency of natural out-crossing of partially cleistogamous mutant lines, characterized by a modified keel and filamentous anthers, was studied at two locations in Sri Lanka and three locations in India. Indeterminate growth habit and normal floral morphology were used as dominant markers and the frequency of anural out-crossing was estimated as percentage of the observed hybrid plants. Natural out-crossing in the mutant lines in Sri Lanka ranged from 0.14 to 1.33% in comparison to 6.34 to 19.64% in the controls. In the Indian environments, natural outcrossing ranged from 0.16 to 2.67%. The mutant was higly stable over diverse environments, and may be of considerable economic importance in pigeonpea improvement and seed-production programs

Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor

Background The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype and relied almost exclusively on comparative molecular cytogenetics of only the largest chromosomes. Here, novel whole genome sequence information from 21 avian genome sequences (most newly assembled) made available on an interactive browser (Evolution Highway) was analyzed. Results Focusing on the six best-assembled genomes allowed us to assemble a putative karyotype of the dinosaur ancestor for each chromosome. Reconstructing evolutionary events that led to each species' genome organization, we determined that the fastest rate of change occurred in the zebra finch and budgerigar, consistent with rapid speciation events in the Passeriformes and Psittaciformes. Intra- and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace. Analyzing chicken and zebra finch, we found little evidence to support the hypothesis of an association of evolutionary breakpoint regions with recombination hotspots but some evidence to support the hypothesis that microchromosomes largely represent conserved blocks of synteny in the majority of the 21 species analyzed. All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count. Ostrich, however, appeared to retain an overall karyotype structure of 2n = 80 despite undergoing a large number (26) of hitherto un-described interchromosomal changes. Conclusions Results suggest that mechanisms exist to preserve a static overall avian karyotype/genomic structure, including the microchromosomes, with widespread interchromosomal change occurring rarely (e.g. in ostrich and budgerigar lineages). Of the species analyzed, the chicken lineage appeared to have undergone the fewest changes compared to the dinosaur ancestor

Evaluation of pigeonpea accessions and selected lines for reaction to Maruca

Maruca vitrata (Geyer) is a serious insect pest of tropical legumes. In Sri Lanka, yield losses due to Maruca damage in pigeonpea [Cajanus cajan (L.) Millsp.] range up to 100%. The development of resistant cultivars and germplasm is one of the best means of control. The objectives of this study were to screen 271 accessions for resistance to M. vitrata and evaluate reaction of lines selected from the promising accessions. The high level of natural incidence of Maruca in Sri Lanka provided an opportunity for evaluation of germplasm at Field Crops Research and Development Institute, Maha Illuppallama. Screening of the germplasm accessions revealed large variation in Maruca damage to flowers and pods. On average, the Maruca damage in determinate accessions (66–75%) was higher than that of nondeterminate accessions (41–50%). Resistant plants from four determinate and 12 nondeterminate accessions were selected. Further selection for resistance to Maruca damage among and within lines derived from the resistant plants was exercised for six generations under nonsprayed field conditions. Under insecticide-free conditions, the selections from two accessions showed significant yield advantages over controls. Data on pod damage and larval counts indicated that the resistance was conditioned through yield compensation mechanisms. In pigeonpea, this is the first report of the selection of Maruca resistant lines. Further studies showed that by using the resistant genotypes it is possible to reduce the number of insecticide sprays for economic yields

Preliminary survey of knowledge, attitudes and practices among nurses regarding seasonal influenza and influenza vaccination

Health care workers are  at risk of influenza through occupational exposure. Uptake of influenza vaccine is poor even in countries where it is provided free. We sought to determine the knowledge, attitudes and practices regarding seasonal influenza and barriers for vaccination among nurses in Colombo. A cross sectional survey was carried out from February to March 2020 on 97 randomly selected nurses. Level of knowledge was measured using a scoring system. Only a few (n=7; 7.2%) nurses had been immunized against influenza. Overall knowledge regarding influenza and vaccines was average in most nurses (n=53; 55%). The majority (n=62; 63.9%) believed the vaccine was safe and 79.4% (n=77) were willing to be vaccinated if vaccine is provided free. However, 15 of these 77 (19.5%) were reluctant to be vaccinated annually. Identified barriers for vaccination were the perception that the vaccine was not essential, doubt about its efficacy, fear of vaccines and side effects. Knowledge should be improved, and misconceptions and fears need to be addressed through health education and promotion.</p

Locating Photography

The specter of global dissemination haunted photography from its very beginning. This chapter explains two aspects of photography's “globalization”: its use as a “western” technique to document an increasingly colonized world and its dissemination around the world and its adoption by local practitioners. In rural and small‐town central India, the studio retains a central place in most people's encounters with photography. Martín Chambi would retain a lifelong adherence to the purity of the photographic image but other indigenista photographers, such as Juan Manuel Figueroa Aznar, would increasingly use paint alongside photography. A World System Photography, seen in networks that fold locally articulated practices into trajectories that fuse technics, history, and culture, can help people think in new ways about the “location” of photography. Locations have to be re‐imagined as “Terra Infirma”, unstable and complex positions which may have more of the quality of linking sections of a network than of territories

Learner autonomy in developing countries

Learner autonomy may have special relevance now in developing countries, where a dissonance often exists between what formal education offers and what many learners want or need. Globalization and its technologies are providing new means of accessing knowledge, but school language lessons remain largely unchanged. Almost by default, successful language learners in developing country contexts are autonomous learners who can exploit out-of-school resources, while some of the most effective pedagogy involves promoting autonomy as a means of confronting low-resource challenges. This chapter argues for more research into both these phenomena, in order to increase understanding of them and to enable identification of principles for practice. It also emphasizes the need for such research to be conducted with and by local teachers and learners

Prospective validation of the RAPID clinical risk prediction score in adult patients with pleural infection: the PILOT study

BACKGROUND: Over 30% of adult patients with pleural infection either die and/or require surgery. There is no robust means of predicting at baseline presentation which patients will suffer a poor clinical outcome. A validated risk prediction score would allow early identification of high-risk patients, potentially directing more aggressive treatment thereafter. OBJECTIVES: To prospectively assess a previously described risk score (RAPID - Renal (urea), Age, fluid Purulence, Infection source, Dietary (albumin)) in adults with pleural infection. METHODS: Prospective observational cohort study recruiting patients undergoing treatment for pleural infection. RAPID score and risk category were calculated at baseline presentation. The primary outcome was mortality at 3 months; secondary outcomes were mortality at 12 months, length of hospital stay, need for thoracic surgery, failure of medical treatment, and lung function at 3 months. RESULTS: Mortality data were available in 542 of 546 (99.3%) patients recruited. Overall mortality was 10% (54/542) at 3 months and 19% (102/542) at 12 months. The RAPID risk category predicted mortality at 3 months; low-risk (RAPID score 0-2) mortality 5/222 (2.3%, 95%CI 0.9 to 5.7), medium-risk (RAPID score 3-4) mortality 21/228 (9.2%, 95%CI 6.0 to 13.7), and high-risk (RAPID score 5-7) mortality 27/92 (29.3%, 95%CI 21.0 to 39.2). C-statistics for the score at 3 and 12 months were 0.78 (95%CI 0.71 to 0.83) and 0.77 (95%CI 0.72 to 0.82) respectively. CONCLUSIONS: The RAPID score stratifies adults with pleural infection according to increasing risk of mortality and should inform future research directed at improving outcomes in this patient population