Cyanobacteria and Biosequestration: The Effects of High CO2 Levels on Calcifying Strains of Synechococcus

Increased carbon dioxide levels in the atmosphere and its influence on climate change is a growing concern in the scientific, political, and social communities. Methods of mitigation are being tested to explore carbon capture and storage through the biosynthesis of stable carbon-containing compounds using different strains of calcifying cyanobacteria. By utilizing marine genera, the cyanobacteria could potentially be grown in brine waste waters, conserving valuable fresh water resources. In this experiment, two strains of Synechococcus were cultured in flasks with varying levels of CO2: air, 5% CO2, and 15% CO2. Growth of each culture was monitored by measuring optical density and pH level, as calcification requires an alkaline environment. Morphological characteristics of each culture were analyzed through light microscopy and scanning electron microscopy to compare differences in cell surface and association. Preliminary results have shown inconsistent morphology and growth. Cultures started from previous experiments lacked duplication of observed filamentous morphology, but exhibited better growth in high CO2 levels. The incubation of cultures in media with varying levels of calcium chloride will be used to analyze and compare the sequestration of carbon through calcium carbonate production. Analysis of the chemical composition of precipitates in the media and the S-layer of cells will verify the presence of calcium carbonate. Methods include the use of SEM-EDX (energy-dispersive X-ray spectroscopy) and polarized light microscopy. If experimental outcomes verify efficient production of calcium carbonate from sources of high CO2, these cyanobacteria may be viable systems for capturing carbon

Directly e-mailing authors of newly published papers encourages community curation

Much of the data within Model Organism Databases (MODs) comes from manual curation of the primary research literature. Given limited funding and an increasing density of published material, a significant challenge facing all MODs is how to efficiently and effectively prioritize the most relevant research papers for detailed curation. Here, we report recent improvements to the triaging process used by FlyBase. We describe an automated method to directly e-mail corresponding authors of new papers, requesting that they list the genes studied and indicate (‘flag’) the types of data described in the paper using an online tool. Based on the author-assigned flags, papers are then prioritized for detailed curation and channelled to appropriate curator teams for full data extraction. The overall response rate has been 44% and the flagging of data types by authors is sufficiently accurate for effective prioritization of papers. In summary, we have established a sustainable community curation program, with the result that FlyBase curators now spend less time triaging and can devote more effort to the specialized task of detailed data extraction

Wheat root length and not branching is altered in the presence of neighbours, including blackgrass.

The effect of neighbouring plants on crop root system architecture may directly interfere with water and nutrient acquisition, yet this important and interesting aspect of competition remains poorly understood. Here, the effect of the weed blackgrass (Alopecurus myosuroides Huds.) on wheat (Triticum aestivum L.) roots was tested, since a low density of this species (25 plants m-2) can lead to a 10% decrease in wheat yield and herbicide resistance is problematic. We used a simplified growth system based on gelled medium, to grow wheat alongside a neighbour, either another wheat plant, a blackgrass or Brachypodium dystachion individual (a model grass). A detailed analysis of wheat seminal root system architecture showed that the presence of a neighbour principally affected the root length, rather than number or diameter under a high nutrient regime. In particular, the length of first order lateral roots decreased significantly in the presence of blackgrass and Brachypodium. However, this effect was not noted when wheat plants were grown in low nutrient conditions. This suggests that wheat may be less sensitive to the presence of blackgrass when grown in low nutrient conditions. In addition, nutrient availability to the neighbour did not modulate the neighbour effect on wheat root architecture.This work was supported by European Union FP7 Marie Curie International Reintegration Grant, the Gatsby Charitable Foundation, the Broodbank Trust and the Newton Trust University of Cambridge

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Experimental setup for investigating the effect of a neighbour on wheat RSA.

<p>(a) Wheat plant grown in homogeneous MS medium with 0.12% (w/v) phytagel alongside a blackgrass individual. (b) Focal wheat plants were grown under different treatments. (c) Wheat roots system extracted from the medium, laid flat on a transparent plate for scanning. (d) Inverted images with dark roots on a white background, and traced using SmartRoot [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178176#pone.0178176.ref036" target="_blank">36</a>]. (e) Second experimental setup, with the focal (<i>i</i>.<i>e</i>., plant of interest) wheat grown in low nutrient (LN) medium and its neighbour (either w, wheat or bd, <i>Brachypodium</i> or bg, blackgrass) grown in a patch of LN or high nutrient (HN) medium.</p

Description of root system architecture parameters.

<p>Description of root system architecture parameters.</p

Seminal root characteristics of wheat grown in LN conditions, in the presence of a different neighbour with a LN or HN patch.

<p>The focal wheat plant was grown in low nutrient (LN) medium while its neighbours (w, wheat; bd, <i>Brachypodium</i>; bg, blackgrass) were grown in a patch of low (LN, black triangles) or high nutrient (HN, white squares) medium. (a) Seminal root length, individual root data (black filled circles) and treatment means (red diamonds). (b) Seminal root number mean ± se. (c) Cumulative length of seminals, mean ± se. (d) Lateral root density in the ramified region, individual root data (black filled circles) and treatment means (red diamonds). Data shown are from three separate experiments, <i>n</i> = 7–10 plants. Significance levels of main factors (N, neighbour, P, patch) and their interactions (N x P) are shown. Significant differences amongst neighbours are indicated below the x-axis,^<b>.</b> <i>p</i> < 0.1, * <i>p</i> < 0.05, <i>n</i>.<i>s</i>., not significant.</p

Total fresh weight and root to shoot ratio of wheat and neighbours grown in heterogeneous nutrient conditions.

<p>The focal wheat plant was grown in low nutrient (LN) medium while its neighbours (w, wheat; bd, <i>Brachypodium</i>; bg, blackgrass) were grown in a patch of low (LN, black triangles) or high nutrient (HN, white squares) medium. (a) FW and (b) root to shoot ratio of the focal wheat plant grown in different competitive conditions (w, wheat alone; w-w, wheat against wheat; w-bd, wheat against <i>Brachypodium</i>; w-bg, wheat against blackgrass). (c) FW and (d) root to shoot ratio of neighbours. Data shown as mean ± se, <i>n</i> = 7–10 plants from three separate experiments, except for root to shoot ratio of plant of interest where <i>n</i> = 5–10 from two separate experiments. Significance levels of main factors (N, neighbour, P, patch) and their interactions (N x P) are shown. Significant differences amongst neighbours are indicated below the x-axis,^<b>.</b> <i>p</i> < 0.1, * <i>p</i> < 0.05, ** <i>p</i> < 0.01, *** <i>p</i> < 0.001, <i>n</i>.<i>s</i>., not significant.</p

Characteristics of lateral roots of wheat grown in high nutrient conditions and in the presence of different neighbours (w, wheat alone; w-w, wheat against wheat; w-bd, wheat against <i>Brachypodium</i>; w-bg, wheat against blackgrass).

<p>(a) Mean length for first order laterals ± se. (b) Frequency distribution of first order lateral root length. (c) Mean length for second order laterals ± se. (d) Frequency distribution of second order lateral root length. (e) Mean cumulative length of first and second order laterals ± se. Data obtained from 11–12 plants per treatment in three separate experiments;^<b>.</b> <i>p</i> < 0.1, * <i>p</i> < 0.05, ** <i>p</i> < 0.01.</p