Ubiquitous antisense transcription in eukaryotes: novel regulatory mechanism or byproduct of opportunistic RNA polymerase?

One of the more notable observations made in the last few years in gene regulation is that eukaryotic genomes appear to be pervasively transcribed. Recent transcriptome mapping studies have shown that much of the genome is transcribed, and in some instances transcripts from both strands of specific genomic loci are detectable. While some of these transcripts map to known RNA polymerase II transcription units [that is, protein encoding open reading frames (ORFs)], many are derived from regions of DNA thought to be non-genic. Parallel chromatin immunoprecipitation studies of template-bound RNA polymerase II have shown that it is indeed resident on those regions found to be transcribed, both ORF and non-ORF. However, the strandedness of these pervasive transcripts has never been measured on a genome-wide basis. Four recent reports have addressed this question and, in the process, have made the startling discovery that many loci of mRNA sense gene transcription are associated with very active antisense or divergent transcription that begins at mapped transcription start sites and proceeds in an upstream direction

Crystal structure and thermal behavior of Bi ₆ Te ₂ O ₁₅:Investigation of synthetic and natural pingguite

The previously unknown crystal structure of pingguite was determined and refined from laboratory X-ray powder diffraction data using a synthetic sample. Additional single crystal diffraction of natural pingguite confirms that the crystal structure of the synthetic sample is identical to the natural mineral. This new crystal structure calls for a revised chemistry of the rare mineral pingguite to Bi6Te2O15 instead of the previously reported formula Bi6Te2O13. Pingguite contains TeVI only and not TeIV as previously reported. Pingguite undergoes an irreversible phase transition around 840 ∘C which is characterized by a loss of oxygen and a reduction from TeVI to TeIV resulting in a δ-Bi2O3 like type structure. In addition, we report the Raman spectroscopic data on the natural pingguite

Retinal Optical Coherence Tomography Features Associated With Incident and Prevalent Parkinson Disease

Background and objectives: Cadaveric studies have shown disease-related neurodegeneration and other morphological abnormalities in the retina of individuals with Parkinson disease (PD), however it remains unclear whether this can be reliably detected with in vivo imaging. We investigated inner retinal anatomy, measured using optical coherence tomography (OCT), in prevalent PD and subsequently assessed the association of these markers with the development of PD using a prospective research cohort.// Methods: This cross-sectional analysis used data from two studies. For the detection of retinal markers in prevalent PD, we used data from AlzEye, a retrospective cohort of 154,830 patients aged 40 years and over attending secondary care ophthalmic hospitals in London, UK between 2008 and 2018. For the evaluation of retinal markers in incident PD, we used data from UK Biobank, a prospective population-based cohort where 67,311 volunteers aged 40-69 years were recruited between 2006 and 2010 and underwent retinal imaging. Macular retinal nerve fibre layer (mRNFL), ganglion cell-inner plexiform layer (GCIPL), and inner nuclear layer (INL) thicknesses were extracted from fovea--centred OCT. Linear mixed effects models were fitted to examine the association between prevalent PD and retinal thicknesses. Hazard ratios for the association between time to PD diagnosis and retinal thicknesses were estimated using frailty models.// Results: Within the AlzEye cohort, there were 700 individuals with prevalent PD and 105,770 controls (mean age 65.5 ± 13.5 years, 51.7% female). Individuals with prevalent PD had thinner GCIPL (-2.12 μm, 95% confidence interval: -3.17, -1.07, p = 8.2 × 10⁻⁵) and INL (-0.99 μm, 95% confidence interval: -1.52, -0.47, p = 2.1 × 10⁻⁴). The UK Biobank included 50,405 participants (mean age 56.1 ± 8.2 years, 54.7% female), of whom 53 developed PD at a mean of 2653 ± 851 days. Thinner GCIPL (hazard ratio: 0.62 per standard deviation increase, 95% confidence interval: 0.46, 0.84, p=0.002) and thinner INL (hazard ratio: 0.70, 95% confidence interval: 0.51, 0.96, p=0.026) were also associated with incident PD.// Discussion: Individuals with PD have reduced thickness of the INL and GCIPL of the retina. Involvement of these layers several years before clinical presentation highlight a potential role for retinal imaging for at-risk stratification of PD

Avoiding Coral Reef Functional Collapse Requires Local and Global Action

oral reefs face multiple anthropogenic threats, from pollution and overfishing to the dual effects of greenhouse gas emissions: rising sea temperature and ocean acidification [1]. While the abundance of coral has declined in recent decades [2, 3], the implications for humanity are difficult to quantify because they depend on ecosystem function rather than the corals themselves. Most reef functions and ecosystem services are founded on the ability of reefs to maintain their three-dimensional structure through net carbonate accumulation [4]. Coral growth only constitutes part of a reef's carbonate budget; bioerosion processes are influential in determining the balance between net structural growth and disintegration [5, 6]. Here, we combine ecological models with carbonate budgets and drive the dynamics of Caribbean reefs with the latest generation of climate models. Budget reconstructions using documented ecological perturbations drive shallow (6-10 m) Caribbean forereefs toward an increasingly fragile carbonate balance. We then projected carbonate budgets toward 2080 and contrasted the benefits of local conservation and global action on climate change. Local management of fisheries (specifically, no-take marine reserves) and the watershed can delay reef loss by at least a decade under "business-as-usual" rises in greenhouse gas emissions. However, local action must be combined with a low-carbon economy to prevent degradation of reef structures and associated ecosystem services

Genome modeling system: A knowledge management platform for genomics

In this work, we present the Genome Modeling System (GMS), an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled with reliable and repeatable analysis pipelines. The GMS also serves as a platform for bioinformatics development, allowing a large team to collaborate on data analysis, or an individual researcher to leverage the work of others effectively within its data management system. Rather than separating ad-hoc analysis from rigorous, reproducible pipelines, the GMS promotes systematic integration between the two. As a demonstration of the GMS, we performed an integrated analysis of whole genome, exome and transcriptome sequencing data from a breast cancer cell line (HCC1395) and matched lymphoblastoid line (HCC1395BL). These data are available for users to test the software, complete tutorials and develop novel GMS pipeline configurations. The GMS is available at https://github.com/genome/gms

Cotton in the new millennium: advances, economics, perceptions and problems

Cotton is the most significant natural fibre and has been a preferred choice of the textile industry and consumers since the industrial revolution began. The share of man-made fibres, both regenerated and synthetic fibres, has grown considerably in recent times but cotton production has also been on the rise and accounts for about half of the fibres used for apparel and textile goods. To cotton’s advantage, the premium attached to the presence of cotton fibre and the general positive consumer perception is well established, however, compared to commodity man-made fibres and high performance fibres, cotton has limitations in terms of its mechanical properties but can help to overcome moisture management issues that arise with performance apparel during active wear. This issue of Textile Progress aims to: i. Report on advances in cotton cultivation and processing as well as improvements to conventional cotton cultivation and ginning. The processing of cotton in the textile industry from fibre to finished fabric, cotton and its blends, and their applications in technical textiles are also covered. ii. Explore the economic impact of cotton in different parts of the world including an overview of global cotton trade. iii. Examine the environmental perception of cotton fibre and efforts in organic and genetically-modified (GM) cotton production. The topic of naturally-coloured cotton, post-consumer waste is covered and the environmental impacts of cotton cultivation and processing are discussed. Hazardous effects of cultivation, such as the extensive use of pesticides, insecticides and irrigation with fresh water, and consequences of the use of GM cotton and cotton fibres in general on the climate are summarised and the effects of cotton processing on workers are addressed. The potential hazards during cotton cultivation, processing and use are also included. iv. Examine how the properties of cotton textiles can be enhanced, for example, by improving wrinkle recovery and reducing the flammability of cotton fibre

Marine Biodiversity in the Caribbean: Regional Estimates and Distribution Patterns

This paper provides an analysis of the distribution patterns of marine biodiversity and summarizes the major activities of the Census of Marine Life program in the Caribbean region. The coastal Caribbean region is a large marine ecosystem (LME) characterized by coral reefs, mangroves, and seagrasses, but including other environments, such as sandy beaches and rocky shores. These tropical ecosystems incorporate a high diversity of associated flora and fauna, and the nations that border the Caribbean collectively encompass a major global marine biodiversity hot spot. We analyze the state of knowledge of marine biodiversity based on the geographic distribution of georeferenced species records and regional taxonomic lists. A total of 12,046 marine species are reported in this paper for the Caribbean region. These include representatives from 31 animal phyla, two plant phyla, one group of Chromista, and three groups of Protoctista. Sampling effort has been greatest in shallow, nearshore waters, where there is relatively good coverage of species records; offshore and deep environments have been less studied. Additionally, we found that the currently accepted classification of marine ecoregions of the Caribbean did not apply for the benthic distributions of five relatively well known taxonomic groups. Coastal species richness tends to concentrate along the Antillean arc (Cuba to the southernmost Antilles) and the northern coast of South America (Venezuela – Colombia), while no pattern can be observed in the deep sea with the available data. Several factors make it impossible to determine the extent to which these distribution patterns accurately reflect the true situation for marine biodiversity in general: (1) highly localized concentrations of collecting effort and a lack of collecting in many areas and ecosystems, (2) high variability among collecting methods, (3) limited taxonomic expertise for many groups, and (4) differing levels of activity in the study of different taxa

Multi-ancestry genome-wide association meta-analysis of Parkinson?s disease

Although over 90 independent risk variants have been identified for Parkinson’s disease using genome-wide association studies, most studies have been performed in just one population at a time. Here we performed a large-scale multi-ancestry meta-analysis of Parkinson’s disease with 49,049 cases, 18,785 proxy cases and 2,458,063 controls including individuals of European, East Asian, Latin American and African ancestry. In a meta-analysis, we identified 78 independent genome-wide significant loci, including 12 potentially novel loci (MTF2, PIK3CA, ADD1, SYBU, IRS2, USP8, PIGL, FASN, MYLK2, USP25, EP300 and PPP6R2) and fine-mapped 6 putative causal variants at 6 known PD loci. By combining our results with publicly available eQTL data, we identified 25 putative risk genes in these novel loci whose expression is associated with PD risk. This work lays the groundwork for future efforts aimed at identifying PD loci in non-European populations