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Biology, Volume 1, Issue 3

2012 December - 24 articles

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Articles (24)

  • Article
  • Open Access
10 Citations
7,793 Views
15 Pages

14 December 2012

Changes in the potential habitat of five allopatric species of threatened Macrozamia cycads under scenarios of increased ambient temperature were examined. A lack of seed dispersal, poor recruitment, low seedling survival, obligate pollinator mutuali...

  • Article
  • Open Access
554 Citations
24,445 Views
11 Pages

FLEXBAR—Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms

  • Matthias Dodt,
  • Johannes T. Roehr,
  • Rina Ahmed and
  • Christoph Dieterich

14 December 2012

Quantitative and systems biology approaches benefit from the unprecedented depth of next-generation sequencing. A typical experiment yields millions of short reads, which oftentimes carry particular sequence tags. These tags may be: (a) specific to t...

  • Article
  • Open Access
33 Citations
13,590 Views
27 Pages

14 December 2012

The possible loss of whole branches from the tree of life is a dramatic, but under-studied, biological implication of climate change. The tree of life represents an evolutionary heritage providing both present and future benefits to humanity, often i...

  • Article
  • Open Access
6 Citations
7,075 Views
12 Pages

13 December 2012

An understanding of the climate conditions governing spatial variation in the reproductive performance of plants can provide important information about the factors characterizing plant community structure, especially in the context of climate change...

  • Review
  • Open Access
10 Citations
9,085 Views
11 Pages

Genetic and Epigenetic Regulation of CCR5 Transcription

  • Rutger J. Wierda and
  • Peter J. Van den Elsen

13 December 2012

The chemokine receptor CCR5 regulates trafficking of immune cells of the lymphoid and the myeloid lineage (such as monocytes, macrophages and immature dendritic cells) and microglia. Because of this, there is an increasing recognition of the importan...

  • Review
  • Open Access
46 Citations
11,145 Views
63 Pages

10 December 2012

Large tracts of lowlands have been drained to expand extensive agriculture into areas that were historically categorized as wasteland. This expansion in agriculture necessarily coincided with changes in ecosystem structure, biodiversity, and nutrient...

  • Article
  • Open Access
10 Citations
9,013 Views
12 Pages

Whole Genome Sequencing and a New Bioinformatics Platform Allow for Rapid Gene Identification in D. melanogaster EMS Screens

  • Michael A. Gonzalez,
  • Derek Van Booven,
  • William Hulme,
  • Rick H. Ulloa,
  • Rafael F. Acosta Lebrigio,
  • Jeannette Osterloh,
  • Mary Logan,
  • Marc Freeman and
  • Stephan Zuchner

5 December 2012

Forward genetic screens in Drosophila melanogaster using ethyl methanesulfonate (EMS) mutagenesis are a powerful approach for identifying genes that modulate specific biological processes in an in vivo setting. The mapping of genes that contain rando...

  • Review
  • Open Access
7 Citations
17,288 Views
16 Pages

Recruitment of Transcription Complexes to Enhancers and the Role of Enhancer Transcription

  • Jared S. Stees,
  • Fred Varn,
  • Suming Huang,
  • John Strouboulis and
  • Jörg Bungert

5 December 2012

Enhancer elements regulate the tissue- and developmental-stage-specific expression of genes. Recent estimates suggest that there are more than 50,000 enhancers in mammalian cells. At least a subset of enhancers has been shown to recruit RNA polymeras...

  • Article
  • Open Access
9 Citations
9,242 Views
30 Pages

23 November 2012

Species endemic to mountains on oceanic islands are subject to a number of existing threats (in particular, invasive species) along with the impacts of a rapidly changing climate. The Lord Howe Island endemic palm Hedyscepe canterburyana is restricte...

  • Review
  • Open Access
24 Citations
9,910 Views
16 Pages

The Role of DNA Methylation in Common Skeletal Disorders

  • Jesús Delgado-Calle and
  • José A. Riancho

22 November 2012

Bone is a complex connective tissue characterized by a calcified extracellular matrix. This mineralized matrix is constantly being formed and resorbed throughout life, allowing the bone to adapt to daily mechanical loads and maintain skeletal propert...

  • Article
  • Open Access
13 Citations
7,589 Views
22 Pages

A Systematic Survey and Characterization of Enhancers that Regulate Sox3 in Neuro-Sensory Development in Comparison with Sox2 Enhancers

  • Naoko Nishimura,
  • Yoshifumi Kamimura,
  • Yoshiko Ishida,
  • Tatsuya Takemoto,
  • Hisato Kondoh and
  • Masanori Uchikawa

22 November 2012

Development of neural and sensory primordia at the early stages of embryogenesis depends on the activity of two B1 Sox transcription factors, Sox2 and Sox3. The embryonic expression patterns of the Sox2 and Sox3 genes are similar, yet they show gene-...

  • Review
  • Open Access
35 Citations
15,461 Views
30 Pages

19 November 2012

After entry into the target cell, the human immunodeficiency virus type I (HIV) integrates into the host genome and becomes a proviral eukaryotic transcriptional unit. Transcriptional regulation of provirus gene expression is critical for HIV replica...

  • Review
  • Open Access
47 Citations
15,906 Views
10 Pages

16 November 2012

RNA-sequencing (RNA-seq) has become the tool of choice for transcriptomics. Several recent studies demonstrate its successful adaption to single cell analysis. This allows new biological insights into cell differentiation, cell-to-cell variation and...

  • Article
  • Open Access
6 Citations
7,025 Views
19 Pages

14 November 2012

Many migratory birds have changed their timing of arrival at breeding grounds in response to recent climate change. Understanding the adaptive value and the demographic consequences of these shifts are key challenges. To address these questions we ex...

  • Article
  • Open Access
83 Citations
15,916 Views
22 Pages

6 November 2012

Intertidal mangrove ecosystems are sensitive to climate change impacts, particularly to associated relative sea level rise. Human stressors and low tidal range add to vulnerability, both characteristics of the Doula Estuary, Cameroon. To investigate...

  • Review
  • Open Access
51 Citations
12,173 Views
20 Pages

5 November 2012

In many European estuaries, extensive areas of intertidal habitats consist of bare mudflats and sandflats that harbour a very high abundance and biomass of macrobenthic invertebrates. The high stocks of macrobenthos in turn provide important food sou...

  • Review
  • Open Access
17 Citations
10,934 Views
18 Pages

25 October 2012

How have animals evolved new body designs (morphological evolution)? This requires explanations both for simple morphological changes, such as differences in pigmentation and hair patterns between different Drosophila populations and species, and als...

  • Article
  • Open Access
30 Citations
10,974 Views
22 Pages

The Population Genomics of Sunflowers and Genomic Determinants of Protein Evolution Revealed by RNAseq

  • Sébastien Renaut,
  • Christopher J. Grassa,
  • Brook T. Moyers,
  • Nolan C. Kane and
  • Loren H. Rieseberg

25 October 2012

Few studies have investigated the causes of evolutionary rate variation among plant nuclear genes, especially in recently diverged species still capable of hybridizing in the wild. The recent advent of Next Generation Sequencing (NGS) permits investi...

  • Review
  • Open Access
11 Citations
9,452 Views
15 Pages

Recent Advances and Future Perspectives in Microbial Phototrophy in Antarctic Sea Ice

  • Eileen Y. Koh,
  • Andrew R. Martin,
  • Andrew McMinn and
  • Ken G. Ryan

22 October 2012

Bacteria that utilize sunlight to supplement metabolic activity are now being described in a range of ecosystems. While it is likely that phototrophy provides an important competitive advantage, the contribution that these microorganisms make to the...

  • Review
  • Open Access
51 Citations
22,358 Views
21 Pages

Inhibitors of HIV-1 Reverse Transcriptase—Associated Ribonuclease H Activity

  • Tatiana Ilina,
  • Krystal LaBarge,
  • Stefan G. Sarafianos,
  • Rieko Ishima and
  • Michael A. Parniak

19 October 2012

HIV-1 enzyme reverse transcriptase (RT) is a major target for antiviral drug development, with over half of current FDA-approved therapeutics against HIV infection targeting the DNA polymerase activity of this enzyme. HIV-1 RT is a multifunctional en...

  • Article
  • Open Access
2 Citations
6,982 Views
13 Pages

16 October 2012

Unravelling the role of neuromessenger processes in learning and memory has long interested researchers. We investigated the effects of an acetylcholinesterase blocker, Methyl Parathion (MeP), on honeybee learning. We used visual and olfactory tasks...

  • Review
  • Open Access
24 Citations
15,230 Views
13 Pages

Genome Walking by Next Generation Sequencing Approaches

  • Mariateresa Volpicella,
  • Claudia Leoni,
  • Alessandra Costanza,
  • Immacolata Fanizza,
  • Antonio Placido and
  • Luigi R. Ceci

1 October 2012

Genome Walking (GW) comprises a number of PCR-based methods for the identification of nucleotide sequences flanking known regions. The different methods have been used for several purposes: from de novo sequencing, useful for the identification of un...

  • Review
  • Open Access
261 Citations
33,167 Views
24 Pages

Genotyping-by-Sequencing in Plants

  • Stéphane Deschamps,
  • Victor Llaca and
  • Gregory D. May

25 September 2012

The advent of next-generation DNA sequencing (NGS) technologies has led to the development of rapid genome-wide Single Nucleotide Polymorphism (SNP) detection applications in various plant species. Recent improvements in sequencing throughput combine...

  • Article
  • Open Access
5 Citations
8,161 Views
11 Pages

Bioinformatics Analysis of the FREM1 Gene—Evolutionary Development of the IL-1R1 Co-Receptor, TILRR

  • Richard C. Hudson,
  • Caroline Gray,
  • Endre Kiss-Toth,
  • Timothy J. A. Chico and
  • Eva E. Qwarnstrom

25 September 2012

The TLRs and IL-1 receptors have evolved to coordinate the innate immune response following pathogen invasion. Receptors and signalling intermediates of these systems are generally characterised by a high level of evolutionary conservation. The recen...

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Biology - ISSN 2079-7737