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Analysis of T-DNA/Host-Plant DNA Junction Sequences in Single-Copy Transgenic Barley Lines

Author(s):Joanne G. Bartlett -- Mark A. Smedley -- Wendy A. Harwood
Journal: Biology
Publisher:
Abstract
| Pages: 39-55
Sequencing across the junction between an integrated transfer DNA (T-DNA) and a host plant genome provides two important pieces of information. The junctions themselves provide information regarding the proportion of T-DNA which has integrated into the host plant genome, whilst the transgene flanking sequences can be used to study the local genetic environment of the integrated transgene. In addition, this information is important in the safety assessment of GM crops and essential for GM traceability. In this study, a detailed analysis was carried out on the right-border T-DNA junction sequences of single-copy independent transgenic barley lines. T-DNA truncations at the right-border were found to be relatively common and affected 33.3% of the lines. In addition, 14.3% of lines had rearranged construct sequence after the right border break-point. An in depth analysis of the host-plant flanking sequences revealed that a significant proportion of the T-DNAs integrated into or close to known repetitive elements. However, this integration into repetitive DNA did not have a negative effect on transgene expression.

Polar Microalgae: New Approaches towards Understanding Adaptations to an Extreme and Changing Environment

Author(s):Barbara R. Lyon -- Thomas Mock
Journal: Biology
Publisher:
Abstract
| Pages: 56-80
Polar Regions are unique and highly prolific ecosystems characterized by extreme environmental gradients. Photosynthetic autotrophs, the base of the food web, have had to adapt physiological mechanisms to maintain growth, reproduction and metabolic activity despite environmental conditions that would shut-down cellular processes in most organisms. High latitudes are characterized by temperatures below the freezing point, complete darkness in winter and continuous light and high UV in the summer. Additionally, sea-ice, an ecological niche exploited by microbes during the long winter seasons when the ocean and land freezes over, is characterized by large salinity fluctuations, limited gas exchange, and highly oxic conditions. The last decade has been an exciting period of insights into the molecular mechanisms behind adaptation of microalgae to the cryosphere facilitated by the advancement of new scientific tools, particularly “omics” techniques. We review recent insights derived from genomics, transcriptomics, and proteomics studies. Genes, proteins and pathways identified from these highly adaptable polar microbes have far-reaching biotechnological applications. Furthermore, they may provide insights into life outside this planet, as well as glimpses into the past. High latitude regions also have disproportionately large inputs into global biogeochemical cycles and are the region most sensitive to climate change.

Polar Microbiology: Recent Advances and Future Perspectives

Author(s):Pabulo Henrique Rampelotto
Journal: Biology
Publisher:
Abstract
| Pages: 81-84
Polar microbiology is a thriving branch of science with the potential to provide new insights into a wide range of basic and applied issues in biology. In this context, it is timely to review and highlight the progress so far and discuss exciting future perspectives. In this special issue, some of the leaders in the field have described their work, ideas and findings in a collection of reviews and original research articles with studies ranging from one of the oldest permafrost areas on Earth, located in Siberia, to the accretion ice of Lake Vostok, located in Antarctica. Altogether, these articles provide a comprehensive and reliable source of information on the current advances and future perspectives in this exciting field of research. In this Editorial, I present a brief overview on the theme [...]

R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms

Author(s):Frank Kramer -- Michaela Bayerlová -- Tim Beißbarth
Journal: Biology
Publisher:
Abstract
| Pages: 85-100
Putting new findings into the context of available literature knowledge is one approach to deal with the surge of high-throughput data results. Furthermore, prior knowledge can increase the performance and stability of bioinformatic algorithms, for example, methods for network reconstruction. In this review, we examine software packages for the statistical computing framework R, which enable the integration of pathway data for further bioinformatic analyses. Different approaches to integrate and visualize pathway data are identified and packages are stratified concerning their features according to a number of different aspects: data import strategies, the extent of available data, dependencies on external tools, integration with further analysis steps and visualization options are considered. A total of 12 packages integrating pathway data are reviewed in this manuscript. These are supplemented by five R-specific packages for visualization and six connector packages, which provide access to external tools.

High-Throughput Screen of Natural Product Libraries for Hsp90 Inhibitors

Author(s):Jason Davenport -- Maurie Balch -- Lakshmi Galam -- Antwan Girgis -- Jessica Hall -- Brian S. J. Blagg -- Robert L. Matts
Journal: Biology
Publisher:
Abstract
| Pages: 101-138
Hsp90 has become the target of intensive investigation, as inhibition of its function has the ability to simultaneously incapacitate proteins that function in pathways that represent the six hallmarks of cancer. While a number of Hsp90 inhibitors have made it into clinical trials, a number of short-comings have been noted, such that the search continues for novel Hsp90 inhibitors with superior pharmacological properties. To identify new potential Hsp90 inhibitors, we have utilized a high-throughput assay based on measuring Hsp90-dependent refolding of thermally denatured luciferase to screen natural compound libraries. Over 4,000 compounds were screen with over 100 hits. Data mining of the literature indicated that 51 compounds had physiological effects that Hsp90 inhibitors also exhibit, and/or the ability to downregulate the expression levels of Hsp90-dependent proteins. Of these 51 compounds, seven were previously characterized as Hsp90 inhibitors. Four compounds, anthothecol, garcinol, piplartine, and rottlerin, were further characterized, and the ability of these compounds to inhibit the refolding of luciferase, and reduce the rate of growth of MCF7 breast cancer cells, correlated with their ability to suppress the Hsp90-dependent maturation of the heme-regulated eIF2α kinase, and deplete cultured cells of Hsp90-dependent client proteins. Thus, this screen has identified an additional 44 compounds with known beneficial pharmacological properties, but with unknown mechanisms of action as possible new inhibitors of the Hsp90 chaperone machine.

Miniaturized Bioaffinity Assessment Coupled to Mass Spectrometry for Guided Purification of Bioactives from Toad and Cone Snail

Author(s):Ferry Heus -- Reka A. Otvos -- Ruud L. E. G. Aspers -- Rene van Elk -- Jenny I. Halff -- Andreas W. Ehlers -- Sébastien Dutertre -- Richard J. Lewis -- Sybren Wijmenga -- August B. Smit -- Wilfried M.
Journal: Biology
Publisher:
Abstract
| Pages: 139-156
A nano-flow high-resolution screening platform, featuring a parallel chip-based microfluidic bioassay and mass spectrometry coupled to nano-liquid chromatography, was applied to screen animal venoms for nicotinic acetylcholine receptor like (nAChR) affinity by using the acetylcholine binding protein, a mimic of the nAChR. The potential of this microfluidic platform is demonstrated by profiling the Conus textilevenom proteome, consisting of over 1,000 peptides. Within one analysis (<90 min, 500 ng venom injected), ligands are detected and identified. To show applicability for non-peptides, small molecular ligands such as steroidal ligands were identified in skin secretions from two toad species (Bufo alvarius and Bufo marinus). Bioactives from the toad samples were subsequently isolated by MS-guided fractionation. The fractions analyzed by NMR and a radioligand binding assay with α7-nAChR confirmed the identity and bioactivity of several new ligands.

McArdle Disease and Exercise Physiology

Author(s):Yu Kitaoka
Journal: Biology
Publisher:
Abstract
| Pages: 157-166
McArdle disease (glycogen storage disease Type V; MD) is a metabolic myopathy caused by a deficiency in muscle glycogen phosphorylase. Since muscle glycogen is an important fuel for muscle during exercise, this inborn error of metabolism provides a model for understanding the role of glycogen in muscle function and the compensatory adaptations that occur in response to impaired glycogenolysis. Patients with MD have exercise intolerance with symptoms including premature fatigue, myalgia, and/or muscle cramps. Despite this, MD patients are able to perform prolonged exercise as a result of the “second wind” phenomenon, owing to the improved delivery of extra-muscular fuels during exercise. The present review will cover what this disease can teach us about exercise physiology, and particularly focuses on the compensatory pathways for energy delivery to muscle in the absence of glycogenolysis.

In Vitro High Throughput Screening, What Next? Lessons from the Screening for Aurora Kinase Inhibitors

Author(s):Thi-My-Nhung Hoang -- Hong-Lien Vu -- Ly-Thuy-Tram Le -- Chi-Hung Nguyen -- Annie Molla
Journal: Biology
Publisher:
Abstract
| Pages: 167-175
Based on in vitro assays, we performed a High Throughput Screening (HTS) to identify kinase inhibitors among 10,000 small chemical compounds. In this didactic paper, we describe step-by-step the approach to validate the hits as well as the major pitfalls encountered in the development of active molecules. We propose a decision tree that could be adapted to most in vitro HTS.

Acknowledgement to Reviewers of Biology in 2013

Author(s):Biology Editorial Office
Journal: Biology
Publisher:
Abstract
| Pages: 176-177
The editors of Biology would like to express their sincere gratitude to the following reviewers for assessing manuscripts in 2013. [...]
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