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Biology, Volume 2, Issue 4 (December 2013), Pages 1189-1496

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Research

Jump to: Review

Open AccessArticle Pol IV-Dependent siRNA Production is Reduced in Brassica rapa
Biology 2013, 2(4), 1210-1223; doi:10.3390/biology2041210
Received: 27 August 2013 / Revised: 24 September 2013 / Accepted: 25 September 2013 / Published: 30 September 2013
Cited by 4 | PDF Full-text (511 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Plants produce a diverse array of small RNA molecules capable of gene regulation, including Pol IV-dependent short interfering (p4-si)RNAs that trigger transcriptional gene silencing. Small RNA transcriptomes are available for many plant species, but mutations affecting the synthesis of Pol IV-dependent siRNAs [...] Read more.
Plants produce a diverse array of small RNA molecules capable of gene regulation, including Pol IV-dependent short interfering (p4-si)RNAs that trigger transcriptional gene silencing. Small RNA transcriptomes are available for many plant species, but mutations affecting the synthesis of Pol IV-dependent siRNAs are characterized only in Arabidopsis and maize, leading to assumptions regarding nature of p4-siRNAs in all other species. We have identified a mutation in the largest subunit of Pol IV, NRPD1, that impacts Pol IV activity in Brassica rapa, an agriculturally important relative of the reference plant Arabidopsis. Using this mutation we characterized the Pol IV-dependent and Pol IV-independent small RNA populations in B. rapa. In addition, our analysis demonstrates reduced production of p4-siRNAs in B. rapa relative to Arabidopsis. B. rapa genomic regions are less likely to generate p4-siRNAs than Arabidopsis but more likely to generate Pol IV-independent siRNAs, including 24 nt RNAs mapping to transposable elements. These observations underscore the diversity of small RNAs produced by plants and highlight the importance of genetic studies during small RNA analysis. Full article
(This article belongs to the Special Issue Insights from Plant Genomes)
Open AccessArticle A Laboratory Assessment of Factors That Affect Bacterial Adhesion to Contact Lenses
Biology 2013, 2(4), 1268-1281; doi:10.3390/biology2041268
Received: 18 July 2013 / Revised: 1 October 2013 / Accepted: 29 October 2013 / Published: 1 November 2013
Cited by 3 | PDF Full-text (184 KB) | HTML Full-text | XML Full-text
Abstract
Adhesion of pathogenic microbes, particularly bacteria, to contact lenses is implicated in contact lens related microbial adverse events. Various in vitro conditions such as type of bacteria, the size of initial inoculum, contact lens material, nutritional content of media, and incubation period [...] Read more.
Adhesion of pathogenic microbes, particularly bacteria, to contact lenses is implicated in contact lens related microbial adverse events. Various in vitro conditions such as type of bacteria, the size of initial inoculum, contact lens material, nutritional content of media, and incubation period can influence bacterial adhesion to contact lenses and the current study investigated the effect of these conditions on bacterial adhesion to contact lenses. There was no significant difference in numbers of bacteria that adhered to hydrogel etafilcon A or silicone hydrogel senofilcon A contact lenses. Pseudomonas aeruginosa adhered in higher numbers compared to Staphylococcus aureus. Within a genera/species, adhesion of different bacterial strains did not differ appreciably. The size of initial inoculum, nutritional content of media, and incubation period played significant roles in bacterial adhesion to lenses. A set of in vitro assay conditions to help standardize adhesion between studies have been recommended. Full article
Open AccessArticle Algorithms for Hidden Markov Models Restricted to Occurrences of Regular Expressions
Biology 2013, 2(4), 1282-1295; doi:10.3390/biology2041282
Received: 28 June 2013 / Revised: 8 October 2013 / Accepted: 5 November 2013 / Published: 8 November 2013
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Abstract
Hidden Markov Models (HMMs) are widely used probabilistic models, particularly for annotating sequential data with an underlying hidden structure. Patterns in the annotation are often more relevant to study than the hidden structure itself. A typical HMM analysis consists of annotating the [...] Read more.
Hidden Markov Models (HMMs) are widely used probabilistic models, particularly for annotating sequential data with an underlying hidden structure. Patterns in the annotation are often more relevant to study than the hidden structure itself. A typical HMM analysis consists of annotating the observed data using a decoding algorithm and analyzing the annotation to study patterns of interest. For example, given an HMM modeling genes in DNA sequences, the focus is on occurrences of genes in the annotation. In this paper, we define a pattern through a regular expression and present a restriction of three classical algorithms to take the number of occurrences of the pattern in the hidden sequence into account. We present a new algorithm to compute the distribution of the number of pattern occurrences, and we extend the two most widely used existing decoding algorithms to employ information from this distribution. We show experimentally that the expectation of the distribution of the number of pattern occurrences gives a highly accurate estimate, while the typical procedure can be biased in the sense that the identified number of pattern occurrences does not correspond to the true number. We furthermore show that using this distribution in the decoding algorithms improves the predictive power of the model. Full article
(This article belongs to the Special Issue Developments in Bioinformatic Algorithms)
Open AccessArticle Dynamic Programming Used to Align Protein Structures with a Spectrum Is Robust
Biology 2013, 2(4), 1296-1310; doi:10.3390/biology2041296
Received: 3 October 2013 / Revised: 23 October 2013 / Accepted: 8 November 2013 / Published: 20 November 2013
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Abstract
Several efficient algorithms to conduct pairwise comparisons among large databases of protein structures have emerged in the recent literature. The central theme is the design of a measure between the Cα atoms of two protein chains, from which dynamic programming is [...] Read more.
Several efficient algorithms to conduct pairwise comparisons among large databases of protein structures have emerged in the recent literature. The central theme is the design of a measure between the Cα atoms of two protein chains, from which dynamic programming is used to compute an alignment. The efficiency and efficacy of these algorithms allows large-scale computational studies that would have been previously impractical. The computational study herein shows that the structural alignment algorithm eigen-decomposition alignment with the spectrum (EIGAs) is robust against both parametric and structural variation. Full article
(This article belongs to the Special Issue Developments in Bioinformatic Algorithms)
Open AccessArticle Changes in RNA Splicing in Developing Soybean (Glycine max) Embryos
Biology 2013, 2(4), 1311-1337; doi:10.3390/biology2041311
Received: 20 September 2013 / Revised: 6 November 2013 / Accepted: 12 November 2013 / Published: 21 November 2013
Cited by 4 | PDF Full-text (920 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Developing soybean seeds accumulate oils, proteins, and carbohydrates that are used as oxidizable substrates providing metabolic precursors and energy during seed germination. The accumulation of these storage compounds in developing seeds is highly regulated at multiple levels, including at transcriptional and post-transcriptional [...] Read more.
Developing soybean seeds accumulate oils, proteins, and carbohydrates that are used as oxidizable substrates providing metabolic precursors and energy during seed germination. The accumulation of these storage compounds in developing seeds is highly regulated at multiple levels, including at transcriptional and post-transcriptional regulation. RNA sequencing was used to provide comprehensive information about transcriptional and post-transcriptional events that take place in developing soybean embryos. Bioinformatics analyses lead to the identification of different classes of alternatively spliced isoforms and corresponding changes in their levels on a global scale during soybean embryo development. Alternative splicing was associated with transcripts involved in various metabolic and developmental processes, including central carbon and nitrogen metabolism, induction of maturation and dormancy, and splicing itself. Detailed examination of selected RNA isoforms revealed alterations in individual domains that could result in changes in subcellular localization of the resulting proteins, protein-protein and enzyme-substrate interactions, and regulation of protein activities. Different isoforms may play an important role in regulating developmental and metabolic processes occurring at different stages in developing oilseed embryos. Full article
(This article belongs to the Special Issue Insights from Plant Genomes)
Open AccessArticle Portraying the Expression Landscapes of B-CellLymphoma-Intuitive Detection of Outlier Samples and of Molecular Subtypes
Biology 2013, 2(4), 1411-1437; doi:10.3390/biology2041411
Received: 1 August 2013 / Revised: 1 October 2013 / Accepted: 5 November 2013 / Published: 2 December 2013
Cited by 4 | PDF Full-text (2597 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
We present an analytic framework based on Self-Organizing Map (SOM) machine learning to study large scale patient data sets. The potency of the approach is demonstrated in a case study using gene expression data of more than 200 mature aggressive B-cell lymphoma [...] Read more.
We present an analytic framework based on Self-Organizing Map (SOM) machine learning to study large scale patient data sets. The potency of the approach is demonstrated in a case study using gene expression data of more than 200 mature aggressive B-cell lymphoma patients. The method portrays each sample with individual resolution, characterizes the subtypes, disentangles the expression patterns into distinct modules, extracts their functional context using enrichment techniques and enables investigation of the similarity relations between the samples. The method also allows to detect and to correct outliers caused by contaminations. Based on our analysis, we propose a refined classification of B-cell Lymphoma into four molecular subtypes which are characterized by differential functional and clinical characteristics. Full article
(This article belongs to the Special Issue Developments in Bioinformatic Algorithms)
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Open AccessArticle Application of Fluorescence Two-Dimensional Difference In-Gel Electrophoresis as a Proteomic Biomarker Discovery Tool in Muscular Dystrophy Research
Biology 2013, 2(4), 1438-1464; doi:10.3390/biology2041438
Received: 24 September 2013 / Revised: 5 November 2013 / Accepted: 12 November 2013 / Published: 2 December 2013
Cited by 8 | PDF Full-text (1149 KB) | HTML Full-text | XML Full-text
Abstract
In this article, we illustrate the application of difference in-gel electrophoresis for the proteomic analysis of dystrophic skeletal muscle. The mdx diaphragm was used as a tissue model of dystrophinopathy. Two-dimensional gel electrophoresis is a widely employed protein separation method in proteomic [...] Read more.
In this article, we illustrate the application of difference in-gel electrophoresis for the proteomic analysis of dystrophic skeletal muscle. The mdx diaphragm was used as a tissue model of dystrophinopathy. Two-dimensional gel electrophoresis is a widely employed protein separation method in proteomic investigations. Although two-dimensional gels usually underestimate the cellular presence of very high molecular mass proteins, integral membrane proteins and low copy number proteins, this method is extremely powerful in the comprehensive analysis of contractile proteins, metabolic enzymes, structural proteins and molecular chaperones. This gives rise to two-dimensional gel electrophoretic separation as the method of choice for studying contractile tissues in health and disease. For comparative studies, fluorescence difference in-gel electrophoresis has been shown to provide an excellent biomarker discovery tool. Since aged diaphragm fibres from the mdx mouse model of Duchenne muscular dystrophy closely resemble the human pathology, we have carried out a mass spectrometry-based comparison of the naturally aged diaphragm versus the senescent dystrophic diaphragm. The proteomic comparison of wild type versus mdx diaphragm resulted in the identification of 84 altered protein species. Novel molecular insights into dystrophic changes suggest increased cellular stress, impaired calcium buffering, cytostructural alterations and disturbances of mitochondrial metabolism in dystrophin-deficient muscle tissue. Full article
(This article belongs to the Special Issue Advances in Proteomics Methods)
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Open AccessArticle Exploiting a Reference Genome in Terms of Duplications: The Network of Paralogs and Single Copy Genes in Arabidopsis thaliana
Biology 2013, 2(4), 1465-1487; doi:10.3390/biology2041465
Received: 25 September 2013 / Revised: 19 November 2013 / Accepted: 20 November 2013 / Published: 9 December 2013
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Abstract
Arabidopsis thaliana became the model organism for plant studies because of its small diploid genome, rapid lifecycle and short adult size. Its genome was the first among plants to be sequenced, becoming the reference in plant genomics. However, the Arabidopsis genome is [...] Read more.
Arabidopsis thaliana became the model organism for plant studies because of its small diploid genome, rapid lifecycle and short adult size. Its genome was the first among plants to be sequenced, becoming the reference in plant genomics. However, the Arabidopsis genome is characterized by an inherently complex organization, since it has undergone ancient whole genome duplications, followed by gene reduction, diploidization events and extended rearrangements, which relocated and split up the retained portions. These events, together with probable chromosome reductions, dramatically increased the genome complexity, limiting its role as a reference. The identification of paralogs and single copy genes within a highly duplicated genome is a prerequisite to understand its organization and evolution and to improve its exploitation in comparative genomics. This is still controversial, even in the widely studied Arabidopsis genome. This is also due to the lack of a reference bioinformatics pipeline that could exhaustively identify paralogs and singleton genes. We describe here a complete computational strategy to detect both duplicated and single copy genes in a genome, discussing all the methodological issues that may strongly affect the results, their quality and their reliability. This approach was used to analyze the organization of Arabidopsis nuclear protein coding genes, and besides classifying computationally defined paralogs into networks and single copy genes into different classes, it unraveled further intriguing aspects concerning the genome annotation and the gene relationships in this reference plant species. Since our results may be useful for comparative genomics and genome functional analyses, we organized a dedicated web interface to make them accessible to the scientific community. Full article
(This article belongs to the Special Issue Insights from Plant Genomes)
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Open AccessArticle Root-Zone Glyphosate Exposure Adversely Affects Two Ditch Species
Biology 2013, 2(4), 1488-1496; doi:10.3390/biology2041488
Received: 11 September 2013 / Revised: 6 December 2013 / Accepted: 10 December 2013 / Published: 18 December 2013
Cited by 2 | PDF Full-text (136 KB) | HTML Full-text | XML Full-text
Abstract
Glyphosate, one of the most applied herbicides globally, has been extensively studied for its effects on non-target organisms. In the field, following precipitation, glyphosate runs off into agricultural ditches where it infiltrates into the soil and thus may encounter the roots of [...] Read more.
Glyphosate, one of the most applied herbicides globally, has been extensively studied for its effects on non-target organisms. In the field, following precipitation, glyphosate runs off into agricultural ditches where it infiltrates into the soil and thus may encounter the roots of vegetation. These edge-of-field ditches share many characteristics with wetlands, including the ability to reduce loads of anthropogenic chemicals through uptake, transformation, and retention. Different species within the ditches may have a differential sensitivity to exposure of the root zone to glyphosate, contributing to patterns of abundance of ruderal species. The present laboratory experiment investigated whether two species commonly found in agricultural ditches in southcentral United States were affected by root zone glyphosate in a dose-dependent manner, with the objective of identifying a sublethal concentration threshold. The root zone of individuals of Polygonum hydropiperoides and Panicum hemitomon were exposed to four concentrations of glyphosate. Leaf chlorophyll content was measured, and the ratio of aboveground biomass to belowground biomass and survival were quantified. The findings from this study showed that root zone glyphosate exposure negatively affected both species including dose-dependent reductions in chlorophyll content. P. hydropiperdoides showed the greatest negative response, with decreased belowground biomass allocation and total mortality at the highest concentrations tested. Full article

Review

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Open AccessReview Algorithms for Computing the Triplet and Quartet Distances for Binary and General Trees
Biology 2013, 2(4), 1189-1209; doi:10.3390/biology2041189
Received: 15 July 2013 / Revised: 29 August 2013 / Accepted: 13 September 2013 / Published: 26 September 2013
Cited by 1 | PDF Full-text (1353 KB) | HTML Full-text | XML Full-text
Abstract
Distance measures between trees are useful for comparing trees in a systematic manner, and several different distance measures have been proposed. The triplet and quartet distances, for rooted and unrooted trees, respectively, are defined as the number of subsets of three or [...] Read more.
Distance measures between trees are useful for comparing trees in a systematic manner, and several different distance measures have been proposed. The triplet and quartet distances, for rooted and unrooted trees, respectively, are defined as the number of subsets of three or four leaves, respectively, where the topologies of the induced subtrees differ. These distances can trivially be computed by explicitly enumerating all sets of three or four leaves and testing if the topologies are different, but this leads to time complexities at least of the order n3 or n4 just for enumerating the sets. The different topologies can be counte dimplicitly, however, and in this paper, we review a series of algorithmic improvements that have been used during the last decade to develop more efficient algorithms by exploiting two different strategies for this; one based on dynamic programming and another based oncoloring leaves in one tree and updating a hierarchical decomposition of the other. Full article
(This article belongs to the Special Issue Developments in Bioinformatic Algorithms)
Open AccessReview Elucidation of Nuclear and Organellar Genomes of Gossypium hirsutum: Furthering Studies of Species Evolution and Applications for Crop Improvement
Biology 2013, 2(4), 1224-1241; doi:10.3390/biology2041224
Received: 18 September 2013 / Revised: 3 October 2013 / Accepted: 8 October 2013 / Published: 18 October 2013
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Abstract
Plant genomes are larger and more complex than other eukaryotic organisms, due to small and large duplication events, recombination and subsequent reorganization of the genetic material. Commercially important cotton is the result of a polyploidization event between Old and New World cottons [...] Read more.
Plant genomes are larger and more complex than other eukaryotic organisms, due to small and large duplication events, recombination and subsequent reorganization of the genetic material. Commercially important cotton is the result of a polyploidization event between Old and New World cottons that occurred over one million years ago. Allotetraploid cotton has properties that are dramatically different from its progenitors—most notably, the presence of long, spinnable fibers. Recently, the complete genome of a New World cotton ancestral species, Gossypium raimondii, was completed. Future genome sequencing efforts are focusing on an Old World progenitor, G. arboreum. This sequence information will enable us to gain insights into the evolution of the cotton genome that may be used to understand the evolution of other plant species. The chloroplast genomes of multiple cotton species and races have been determined. This information has also been used to gain insight into the evolutionary history of cotton. Analysis of the database of nuclear and organellar sequences will facilitate the identification of potential genes of interest and subsequent development of strategies for improving cotton. Full article
(This article belongs to the Special Issue Insights from Plant Genomes)
Open AccessReview The Role of the Bacterial Flagellum in Adhesion and Virulence
Biology 2013, 2(4), 1242-1267; doi:10.3390/biology2041242
Received: 30 July 2013 / Revised: 27 September 2013 / Accepted: 30 September 2013 / Published: 25 October 2013
Cited by 17 | PDF Full-text (425 KB) | HTML Full-text | XML Full-text
Abstract
The bacterial flagellum is a complex apparatus assembled of more than 20 different proteins. The flagellar basal body traverses the cell wall, whereas the curved hook connects the basal body to the whip-like flagellar filament that protrudes several µm from the bacterial [...] Read more.
The bacterial flagellum is a complex apparatus assembled of more than 20 different proteins. The flagellar basal body traverses the cell wall, whereas the curved hook connects the basal body to the whip-like flagellar filament that protrudes several µm from the bacterial cell. The flagellum has traditionally been regarded only as a motility organelle, but more recently it has become evident that flagella have a number of other biological functions. The major subunit, flagellin or FliC, of the flagellum plays a well-documented role in innate immunity and as a dominant antigen of the adaptive immune response. Importantly, flagella have also been reported to function as adhesins. Whole flagella have been indicated as significant in bacterial adhesion to and invasion into host cells. In various pathogens, e.g., Escherichia coli, Pseudomonas aeruginosa and Clostridium difficile, flagellin and/or the distally located flagellar cap protein have been reported to function as adhesins. Recently, FliC of Shiga-toxigenic E. coli was shown to be involved in cellular invasion via lipid rafts. Here, we examine the latest or most important findings regarding flagellar adhesive and invasive properties, especially focusing on the flagellum as a potential virulence factor. Full article
(This article belongs to the Special Issue Bacterial Adhesion)
Open AccessReview DNA Damage Response in Plants: Conserved and Variable Response Compared to Animals
Biology 2013, 2(4), 1338-1356; doi:10.3390/biology2041338
Received: 12 September 2013 / Revised: 8 November 2013 / Accepted: 12 November 2013 / Published: 21 November 2013
Cited by 8 | PDF Full-text (613 KB) | HTML Full-text | XML Full-text
Abstract
The genome of an organism is under constant attack from endogenous and exogenous DNA damaging factors, such as reactive radicals, radiation, and genotoxins. Therefore, DNA damage response systems to sense DNA damage, arrest cell cycle, repair DNA lesions, and/or induce programmed cell [...] Read more.
The genome of an organism is under constant attack from endogenous and exogenous DNA damaging factors, such as reactive radicals, radiation, and genotoxins. Therefore, DNA damage response systems to sense DNA damage, arrest cell cycle, repair DNA lesions, and/or induce programmed cell death are crucial for maintenance of genomic integrity and survival of the organism. Genome sequences revealed that, although plants possess many of the DNA damage response factors that are present in the animal systems, they are missing some of the important regulators, such as the p53 tumor suppressor. These observations suggest differences in the DNA damage response mechanisms between plants and animals. In this review the DNA damage responses in plants and animals are compared and contrasted. In addition, the function of SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1), a plant-specific transcription factor that governs the robust response to DNA damage, is discussed. Full article
(This article belongs to the Special Issue Insights from Plant Genomes)
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Open AccessReview Next Generation Characterisation of Cereal Genomes for Marker Discovery
Biology 2013, 2(4), 1357-1377; doi:10.3390/biology2041357
Received: 16 August 2013 / Revised: 29 October 2013 / Accepted: 8 November 2013 / Published: 25 November 2013
Cited by 4 | PDF Full-text (364 KB) | HTML Full-text | XML Full-text
Abstract
Cereal crops form the bulk of the world’s food sources, and thus their importance cannot be understated. Crop breeding programs increasingly rely on high-resolution molecular genetic markers to accelerate the breeding process. The development of these markers is hampered by the complexity [...] Read more.
Cereal crops form the bulk of the world’s food sources, and thus their importance cannot be understated. Crop breeding programs increasingly rely on high-resolution molecular genetic markers to accelerate the breeding process. The development of these markers is hampered by the complexity of some of the major cereal crop genomes, as well as the time and cost required. In this review, we address current and future methods available for the characterisation of cereal genomes, with an emphasis on faster and more cost effective approaches for genome sequencing and the development of markers for trait association and marker assisted selection (MAS) in crop breeding programs. Full article
(This article belongs to the Special Issue Insights from Plant Genomes)
Open AccessReview Insights into Chromatin Structure and Dynamics in Plants
Biology 2013, 2(4), 1378-1410; doi:10.3390/biology2041378
Received: 30 October 2013 / Revised: 15 November 2013 / Accepted: 18 November 2013 / Published: 28 November 2013
Cited by 2 | PDF Full-text (697 KB) | HTML Full-text | XML Full-text
Abstract
The packaging of chromatin into the nucleus of a eukaryotic cell requires an extraordinary degree of compaction and physical organization. In recent years, it has been shown that this organization is dynamically orchestrated to regulate responses to exogenous stimuli as well as [...] Read more.
The packaging of chromatin into the nucleus of a eukaryotic cell requires an extraordinary degree of compaction and physical organization. In recent years, it has been shown that this organization is dynamically orchestrated to regulate responses to exogenous stimuli as well as to guide complex cell-type-specific developmental programs. Gene expression is regulated by the compartmentalization of functional domains within the nucleus, by distinct nucleosome compositions accomplished via differential modifications on the histone tails and through the replacement of core histones by histone variants. In this review, we focus on these aspects of chromatin organization and discuss novel approaches such as live cell imaging and photobleaching as important tools likely to give significant insights into our understanding of the very dynamic nature of chromatin and chromatin regulatory processes. We highlight the contribution plant studies have made in this area showing the potential advantages of plants as models in understanding this fundamental aspect of biology. Full article
(This article belongs to the Special Issue Insights from Plant Genomes)

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