Biology

370 KiB

Open AccessArticle

Myogenic Differential Methylation: Diverse Associations with Chromatin Structure

by Sruti Chandra, Carl Baribault, Michelle Lacey and Melanie Ehrlich

Biology 2014, 3(2), 426-451; https://doi.org/10.3390/biology3020426 - 19 Jun 2014

Cited by 13 | Viewed by 9187

Employing a new algorithm for identifying differentially methylated regions (DMRs) from reduced representation bisulfite sequencing profiles, we identified 1972 hypermethylated and 3250 hypomethylated myogenic DMRs in a comparison of myoblasts (Mb) and myotubes (Mt) with 16 types of nonmuscle cell cultures. DMRs co-localized [...] Read more.

Employing a new algorithm for identifying differentially methylated regions (DMRs) from reduced representation bisulfite sequencing profiles, we identified 1972 hypermethylated and 3250 hypomethylated myogenic DMRs in a comparison of myoblasts (Mb) and myotubes (Mt) with 16 types of nonmuscle cell cultures. DMRs co-localized with a variety of chromatin structures, as deduced from ENCODE whole-genome profiles. Myogenic hypomethylation was highly associated with both weak and strong enhancer-type chromatin, while hypermethylation was infrequently associated with enhancer-type chromatin. Both myogenic hypermethylation and hypomethylation often overlapped weak transcription-type chromatin and Polycomb-repressed-type chromatin. For representative genes, we illustrate relationships between DNA methylation, the local chromatin state, DNaseI hypersensitivity, and gene expression. For example, MARVELD2 exhibited myogenic hypermethylation in transcription-type chromatin that overlapped a silenced promoter in Mb and Mt while TEAD4 had myogenic hypomethylation in intronic subregions displaying enhancer-type or transcription-type chromatin in these cells. For LSP1, alternative promoter usage and active promoter-type chromatin were linked to highly specific myogenic or lymphogenic hypomethylated DMRs. Lastly, despite its myogenesis-associated expression, TBX15 had multiple hypermethylated myogenic DMRs framing its promoter region. This could help explain why TBX15 was previously reported to be underexpressed and, unexpectedly, its promoter undermethylated in placentas exhibiting vascular intrauterine growth restriction. Full article

(This article belongs to the Special Issue DNA Methylation)

► Show Figures

Graphical abstract

253 KiB

Open AccessReview

Causes and Consequences of Age-Related Changes in DNA Methylation: A Role for ROS?

by Franka J. Rang and Johannes Boonstra

Biology 2014, 3(2), 403-425; https://doi.org/10.3390/biology3020403 - 18 Jun 2014

Cited by 50 | Viewed by 8500

Abstract

Recent genome-wide analysis of C-phosphate-G (CpG) sites has shown that the DNA methylome changes with increasing age, giving rise to genome-wide hypomethylation with site‑specific incidences of hypermethylation. This notion has received a lot of attention, as it potentially explains why aged organisms generally [...] Read more.

Recent genome-wide analysis of C-phosphate-G (CpG) sites has shown that the DNA methylome changes with increasing age, giving rise to genome-wide hypomethylation with site‑specific incidences of hypermethylation. This notion has received a lot of attention, as it potentially explains why aged organisms generally have a higher risk of age-related diseases. However, very little is known about the mechanisms that could cause the occurrence of these changes. Moreover, there does not appear to be a clear link between popular theories of aging and alterations in the methylome. Some of the most fruitful of these theories attribute an important role to reactive oxygen species, which seem to be responsible for an increase in oxidative damage to macromolecules, such as DNA, during the lifetime of an organism. In this review, the connection between changes in DNA methylation and these reactive oxygen species is discussed, as well as the effect of these changes on health. Deeper insights into the nature, causes and consequences of the aging methylome might provide a deeper understanding of the molecular mechanisms of aging and eventually contribute to the development of new diagnostic and therapeutic tools. Full article

(This article belongs to the Special Issue DNA Methylation)

► Show Figures

Figure 1

708 KiB

Open AccessArticle

Data Pre-Processing for Label-Free Multiple Reaction Monitoring (MRM) Experiments

by Lisa M. Chung, Christopher M. Colangelo and Hongyu Zhao

Biology 2014, 3(2), 383-402; https://doi.org/10.3390/biology3020383 - 5 Jun 2014

Cited by 3 | Viewed by 8309

Abstract

Multiple Reaction Monitoring (MRM) conducted on a triple quadrupole mass spectrometer allows researchers to quantify the expression levels of a set of target proteins. Each protein is often characterized by several unique peptides that can be detected by monitoring predetermined fragment ions, called [...] Read more.

Multiple Reaction Monitoring (MRM) conducted on a triple quadrupole mass spectrometer allows researchers to quantify the expression levels of a set of target proteins. Each protein is often characterized by several unique peptides that can be detected by monitoring predetermined fragment ions, called transitions, for each peptide. Concatenating large numbers of MRM transitions into a single assay enables simultaneous quantification of hundreds of peptides and proteins. In recognition of the important role that MRM can play in hypothesis-driven research and its increasing impact on clinical proteomics, targeted proteomics such as MRM was recently selected as the Nature Method of the Year. However, there are many challenges in MRM applications, especially data pre‑processing where many steps still rely on manual inspection of each observation in practice. In this paper, we discuss an analysis pipeline to automate MRM data pre‑processing. This pipeline includes data quality assessment across replicated samples, outlier detection, identification of inaccurate transitions, and data normalization. We demonstrate the utility of our pipeline through its applications to several real MRM data sets. Full article

(This article belongs to the Special Issue Advances in Proteomics Methods)

► Show Figures

Figure 1

159 KiB

Open AccessArticle

The Effect of Nutritional Status in the Pathogenesis of Critical Illness Myopathy (CIM)

by Hannah Ogilvie and Lars Larsson

Biology 2014, 3(2), 368-382; https://doi.org/10.3390/biology3020368 - 30 May 2014

Cited by 5 | Viewed by 7453

Abstract

The muscle wasting and loss of specific force associated with Critical Illness Myopathy (CIM) is, at least in part, due to a preferential loss of the molecular motor protein myosin. This acquired myopathy is common in critically ill immobilized and mechanically ventilated intensive [...] Read more.

The muscle wasting and loss of specific force associated with Critical Illness Myopathy (CIM) is, at least in part, due to a preferential loss of the molecular motor protein myosin. This acquired myopathy is common in critically ill immobilized and mechanically ventilated intensive care patients (ICU). There is a growing understanding of the mechanisms underlying CIM, but the role of nutritional factors triggering this serious complication of modern intensive care remains unknown. This study aims at establishing the effect of nutritional status in the pathogenesis of CIM. An experimental ICU model was used where animals are mechanically ventilated, pharmacologically paralysed post-synaptically and extensively monitored for up to 14 days. Due to the complexity of the experimental model, the number of animals included is small. After exposure to this ICU condition, animals develop a phenotype similar to patients with CIM. The results from this study show that the preferential myosin loss, decline in specific force and muscle fiber atrophy did not differ between low vs. eucaloric animals. In both experimental groups, passive mechanical loading had a sparing effect of muscle weight independent on nutritional status. Thus, this study confirms the strong impact of the mechanical silencing associated with the ICU condition in triggering CIM, overriding any potential effects of caloric intake in triggering CIM. In addition, the positive effects of passive mechanical loading on muscle fiber size and force generating capacity was not affected by the nutritional status in this study. However, due to the small sample size these pilot results need to be validated in a larger cohort. Full article

(This article belongs to the Special Issue Muscle Structure and Function)

► Show Figures

Figure 1

690 KiB

Open AccessReview

Advanced Cell Culture Techniques for Cancer Drug Discovery

by Carrie J. Lovitt, Todd B. Shelper and Vicky M. Avery

Biology 2014, 3(2), 345-367; https://doi.org/10.3390/biology3020345 - 30 May 2014

Cited by 216 | Viewed by 31716

Abstract

Human cancer cell lines are an integral part of drug discovery practices. However, modeling the complexity of cancer utilizing these cell lines on standard plastic substrata, does not accurately represent the tumor microenvironment. Research into developing advanced tumor cell culture models in a [...] Read more.

Human cancer cell lines are an integral part of drug discovery practices. However, modeling the complexity of cancer utilizing these cell lines on standard plastic substrata, does not accurately represent the tumor microenvironment. Research into developing advanced tumor cell culture models in a three-dimensional (3D) architecture that more prescisely characterizes the disease state have been undertaken by a number of laboratories around the world. These 3D cell culture models are particularly beneficial for investigating mechanistic processes and drug resistance in tumor cells. In addition, a range of molecular mechanisms deconstructed by studying cancer cells in 3D models suggest that tumor cells cultured in two-dimensional monolayer conditions do not respond to cancer therapeutics/compounds in a similar manner. Recent studies have demonstrated the potential of utilizing 3D cell culture models in drug discovery programs; however, it is evident that further research is required for the development of more complex models that incorporate the majority of the cellular and physical properties of a tumor. Full article

(This article belongs to the Special Issue Screening for Biologically Active Compounds)

► Show Figures

Figure 1

199 KiB

Open AccessArticle

High Intensity Training Improves Health and Physical Function in Middle Aged Adults

by Simon Adamson, Ross Lorimer, James N. Cobley, Ray Lloyd and John Babraj

Biology 2014, 3(2), 333-344; https://doi.org/10.3390/biology3020333 - 12 May 2014

Cited by 37 | Viewed by 17854

Abstract

High intensity training (HIT) is effective at improving health; however, it is unknown whether HIT also improves physical function. This study aimed to determine whether HIT improves metabolic health and physical function in untrained middle aged individuals. Fourteen (three male and eleven female) [...] Read more.

High intensity training (HIT) is effective at improving health; however, it is unknown whether HIT also improves physical function. This study aimed to determine whether HIT improves metabolic health and physical function in untrained middle aged individuals. Fourteen (three male and eleven female) untrained individuals were recruited (control group n = 6: age 42 ± 8 y, weight 64 ± 10 kg, BMI 24 ± 2 kg·m⁻² or HIT group n = 8: age 43 ± 8 y, weight 80 ± 8 kg, BMI 29 ± 5 kg·m⁻²). Training was performed twice weekly, consisting of 10 × 6-second sprints with a one minute recovery between each sprint. Metabolic health (oral glucose tolerance test), aerobic capacity (incremental time to exhaustion on a cycle ergometer) and physical function (get up and go test, sit to stand test and loaded 50 m walk) were determined before and after training. Following eight weeks of HIT there was a significant improvement in aerobic capacity (8% increase in VO₂ peak; p < 0.001), physical function (11%–27% respectively; p < 0.05) and a reduction in blood glucose area under the curve (6% reduction; p < 0.05). This study demonstrates for the first time the potential of HIT as a training intervention to improve skeletal muscle function and glucose clearance as we age. Full article

(This article belongs to the Special Issue Muscle Structure and Function)

► Show Figures

Figure 1

532 KiB

Open AccessArticle

On-Beads Digestion in Conjunction with Data-Dependent Mass Spectrometry: A Shortcut to Quantitative and Dynamic Interaction Proteomics

by Benedetta Turriziani, Amaya Garcia-Munoz, Ruth Pilkington, Cinzia Raso, Walter Kolch and Alexander Von Kriegsheim

Biology 2014, 3(2), 320-332; https://doi.org/10.3390/biology3020320 - 16 Apr 2014

Cited by 110 | Viewed by 19281

Abstract

With the advent of the “-omics” era, biological research has shifted from functionally analyzing single proteins to understanding how entire protein networks connect and adapt to environmental cues. Frequently, pathological processes are initiated by a malfunctioning protein network rather than a single protein. [...] Read more.

With the advent of the “-omics” era, biological research has shifted from functionally analyzing single proteins to understanding how entire protein networks connect and adapt to environmental cues. Frequently, pathological processes are initiated by a malfunctioning protein network rather than a single protein. It is therefore crucial to investigate the regulation of proteins in the context of a pathway first and signaling network second. In this study, we demonstrate that a quantitative interaction proteomic approach, combining immunoprecipitation, in-solution digestion and label-free quantification mass spectrometry, provides data of high accuracy and depth. This protocol is applicable, both to tagged, exogenous and untagged, endogenous proteins. Furthermore, it is fast, reliable and, due to a label-free quantitation approach, allows the comparison of multiple conditions. We further show that we are able to generate data in a medium throughput fashion and that we can quantify dynamic interaction changes in signaling pathways in response to mitogenic stimuli, making our approach a suitable method to generate data for system biology approaches. Full article

(This article belongs to the Special Issue Advances in Proteomics Methods)

► Show Figures

Figure 1

900 KiB

Open AccessArticle

Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L.) Genome

by Navdeep Gill, Matteo Buti, Nolan Kane, Arnaud Bellec, Nicolas Helmstetter, Hélène Berges and Loren H. Rieseberg

Biology 2014, 3(2), 295-319; https://doi.org/10.3390/biology3020295 - 16 Apr 2014

Cited by 18 | Viewed by 13018

Abstract

Sunflower is an important oilseed crop, as well as a model system for evolutionary studies, but its 3.6 gigabase genome has proven difficult to assemble, in part because of the high repeat content of its genome. Here we report on the sequencing, assembly, [...] Read more.

Sunflower is an important oilseed crop, as well as a model system for evolutionary studies, but its 3.6 gigabase genome has proven difficult to assemble, in part because of the high repeat content of its genome. Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs from sunflower to provide additional information on the repeat content of the sunflower genome, assess how repetitive elements in the sunflower genome are organized relative to genes, and compare the genomic distribution of these repeats to that found in other food crops and model species. We also examine the expression of transposable element-related transcripts in EST databases for sunflower to determine the representation of repeats in the transcriptome and to measure their transcriptional activity. Our data confirm previous reports in suggesting that the sunflower genome is >78% repetitive. Sunflower repeats share very little similarity to other plant repeats such as those of Arabidopsis, rice, maize and wheat; overall 28% of repeats are “novel” to sunflower. The repetitive sequences appear to be randomly distributed within the sequenced BACs. Assuming the 96 BACs are representative of the genome as a whole, then approximately 5.2% of the sunflower genome comprises non TE-related genic sequence, with an average gene density of 18kbp/gene. Expression levels of these transposable elements indicate tissue specificity and differential expression in vegetative and reproductive tissues, suggesting that expressed TEs might contribute to sunflower development. The assembled BACs will also be useful for assessing the quality of several different draft assemblies of the sunflower genome and for annotating the reference sequence. Full article

(This article belongs to the Special Issue Insights from Plant Genomes)

► Show Figures

Graphical abstract

931 KiB

Open AccessReview

Screening for Antifibrotic Compounds Using High Throughput System Based on Fluorescence Polarization

by Branko Stefanovic and Lela Stefanovic

Biology 2014, 3(2), 281-294; https://doi.org/10.3390/biology3020281 - 10 Apr 2014

Cited by 6 | Viewed by 6898

Abstract

Fibroproliferative diseases are one of the leading causes of death worldwide. They are characterized by reactive fibrosis caused by uncontrolled synthesis of type I collagen. There is no cure for fibrosis and development of therapeutics that can inhibit collagen synthesis is urgently needed. [...] Read more.

Fibroproliferative diseases are one of the leading causes of death worldwide. They are characterized by reactive fibrosis caused by uncontrolled synthesis of type I collagen. There is no cure for fibrosis and development of therapeutics that can inhibit collagen synthesis is urgently needed. Collagen α1(I) mRNA and α2(I) mRNA encode for type I collagen and they have a unique 5' stem-loop structure in their 5' untranslated regions (5'SL). Collagen 5'SL binds protein LARP6 with high affinity and specificity. The interaction between LARP6 and the 5'SL is critical for biosynthesis of type I collagen and development of fibrosis in vivo. Therefore, this interaction represents is an ideal target to develop antifibrotic drugs. A high throughput system to screen for chemical compounds that can dissociate LARP6 from 5'SL has been developed. It is based on fluorescence polarization and can be adapted to screen for inhibitors of other protein-RNA interactions. Screening of 50,000 chemical compounds yielded a lead compound that can inhibit type I collagen synthesis at nanomolar concentrations. The development, characteristics, and critical appraisal of this assay are presented. Full article

(This article belongs to the Special Issue Screening for Biologically Active Compounds)

► Show Figures

Graphical abstract

789 KiB

Open AccessArticle

Body Size Shifts in Philippine Reef Fishes: Interfamilial Variation in Responses to Protection

by Robert Y. Fidler, Aileen Maypa, Dean Apistar, Alan White and Ralph G. Turingan

Biology 2014, 3(2), 264-280; https://doi.org/10.3390/biology3020264 - 31 Mar 2014

Cited by 6 | Viewed by 7509

Abstract

As a consequence of intense fishing pressure, fished populations experience reduced population sizes and shifts in body size toward the predominance of smaller and early maturing individuals. Small, early-maturing fish exhibit significantly reduced reproductive output and, ultimately, reduced fitness. As part of resource [...] Read more.

As a consequence of intense fishing pressure, fished populations experience reduced population sizes and shifts in body size toward the predominance of smaller and early maturing individuals. Small, early-maturing fish exhibit significantly reduced reproductive output and, ultimately, reduced fitness. As part of resource management and biodiversity conservation programs worldwide, no-take marine protected areas (MPAs) are expected to ameliorate the adverse effects of fishing pressure. In an attempt to advance our understanding of how coral reef MPAs meet their long-term goals, this study used visual census data from 23 MPAs and fished reefs in the Philippines to address three questions: (1) Do MPAs promote shifts in fish body size frequency distribution towards larger body sizes when compared to fished reefs? (2) Do MPA size and (3) age contribute to the efficacy of MPAs in promoting such shifts? This study revealed that across all MPAs surveyed, the distribution of fishes between MPAs and fished reefs were similar; however, large-bodied fish were more abundant within MPAs, along with small, young-of-the-year individuals. Additionally, there was a significant shift in body size frequency distribution towards larger body sizes in 12 of 23 individual reef sites surveyed. Of 22 fish families, eleven demonstrated significantly different body size frequency distributions between MPAs and fished reefs, indicating that shifts in the size spectrum of fishes in response to protection are family-specific. Family-level shifts demonstrated a significant, positive correlation with MPA age, indicating that MPAs become more effective at increasing the density of large-bodied fish within their boundaries over time. Full article

► Show Figures

Figure 1

335 KiB

Open AccessReview

Combustion, Respiration and Intermittent Exercise: A Theoretical Perspective on Oxygen Uptake and Energy Expenditure

by Christopher B. Scott

Biology 2014, 3(2), 255-263; https://doi.org/10.3390/biology3020255 - 28 Mar 2014

Cited by 5 | Viewed by 11318

Abstract

While no doubt thought about for thousands of years, it was Antoine Lavoisier in the late 18th century who is largely credited with the first “modern” investigations of biological energy exchanges. From Lavoisier’s work with combustion and respiration a scientific trend emerges that [...] Read more.

While no doubt thought about for thousands of years, it was Antoine Lavoisier in the late 18th century who is largely credited with the first “modern” investigations of biological energy exchanges. From Lavoisier’s work with combustion and respiration a scientific trend emerges that extends to the present day: the world gains a credible working hypothesis but validity goes missing, often for some time, until later confirmed using proper measures. This theme is applied to glucose/glycogen metabolism where energy exchanges are depicted as conversion from one form to another and, transfer from one place to another made by both the anaerobic and aerobic biochemical pathways within working skeletal muscle, and the hypothetical quantification of these components as part of an oxygen (O₂) uptake measurement. The anaerobic and aerobic energy exchange components of metabolism are represented by two different interpretations of O₂ uptake: one that contains a glycolytic component (1 L O₂ = 21.1 kJ) and one that does not (1 L O₂ = 19.6 kJ). When energy exchange transfer and oxygen-related expenditures are applied separately to exercise and recovery periods, an increased energy cost for intermittent as compared to continuous exercise is hypothesized to be a direct result. Full article

(This article belongs to the Special Issue Muscle Structure and Function)

► Show Figures

Figure 1

219 KiB

Open AccessReview

RNA Splicing Factors and RNA-Directed DNA Methylation

by Chao-Feng Huang and Jian-Kang Zhu

Biology 2014, 3(2), 243-254; https://doi.org/10.3390/biology3020243 - 26 Mar 2014

Cited by 14 | Viewed by 10890

Abstract

RNA-directed histone and/or DNA modification is a conserved mechanism for the establishment of epigenetic marks from yeasts and plants to mammals. The heterochromation formation in yeast is mediated by RNAi-directed silencing mechanism, while the establishment of DNA methylation in plants is through the [...] Read more.

RNA-directed histone and/or DNA modification is a conserved mechanism for the establishment of epigenetic marks from yeasts and plants to mammals. The heterochromation formation in yeast is mediated by RNAi-directed silencing mechanism, while the establishment of DNA methylation in plants is through the RNA-directed DNA methylation (RdDM) pathway. Recently, splicing factors are reported to be involved in both RNAi-directed heterochromatin formation in yeast and the RdDM pathway in plants. In yeast, splicing factors may provide a platform for facilitating the siRNA generation through an interaction with RDRC and thereby affect the heterochromatin formation, whereas in plants, various splicing factors seem to act at different steps in the RdDM pathway. Full article

(This article belongs to the Special Issue DNA Methylation)

► Show Figures

Figure 1

Journal Menu

Journal Browser

Biology, Volume 3, Issue 2 (June 2014) – 12 articles , Pages 243-451

Further Information

Guidelines

MDPI Initiatives

Follow MDPI