DIGE analysis of rat skeletal muscle proteins using nonionic detergent phase extraction of young adult versus aged gastrocnemius tissue

Contractile weakness and loss of muscle mass are critical features of the aging process in mammalians. Age-related fibre wasting has a profound effect on muscle metabolism, fibre type distribution and the overall physiological integrity of the neuromuscular system. This study has used mass spectrometry-based proteomics to investigate the fate of the aging rat muscle proteome. Using nonionic detergent phase extraction, this report shows that the aged gastrocnemius muscle exhibits a generally perturbed protein expression pattern in both the detergent-extracted fraction and the aqueous protein complement from senescent muscle tissue. In the detergent-extracted fraction, the expression of ATP synthase, isocitrate dehydrogenase, enolase, tropomyosin and beta-actin was increased. Different isoforms of creatine kinase and prohibitin showed differential changes. In the aqueous fraction, malate dehydrogenase, sulfotransferase, triosephosphate isomerase, aldolase, cofilin-2 and lactate dehydrogenase showed increased levels. Interestingly, differential effects on dissimilar 2-D spots of the same protein species were shown for Cu/Zn superoxide dismutase, albumin, annexin A4 and phosphoglycolate phosphatase. Mitochondrial Hsp60, Hsp71 and nucleoside diphosphate kinase B exhibited a reduced abundance in aged muscle. The majority of altered proteins were found to be involved in mitochondrial metabolism, glycolysis, metabolic transportation, regulatory processes, the cellular stress response, detoxification mechanisms and muscle contraction

Angiosperm phylogeny: 17 genes, 640 taxa

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/1/ajb20704-sup-0010.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/2/ajb20704.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/3/ajb20704-sup-0001.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/4/ajb20704-sup-0016.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/5/ajb20704-sup-0017.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/6/ajb20704-sup-0021.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/7/ajb20704-sup-0003.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/8/ajb20704-sup-0002.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/9/ajb20704-sup-0011.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/10/ajb20704-sup-0019.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/11/ajb20704-sup-0015.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/12/ajb20704-sup-0006.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/13/ajb20704-sup-0020.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/14/ajb20704-sup-0013.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/15/ajb20704-sup-0004.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/16/ajb20704-sup-0012.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/17/ajb20704-sup-0005.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/18/ajb20704-sup-0018.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/19/ajb20704-sup-0009.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/20/ajb20704-sup-0014.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/21/ajb20704-sup-0007.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/22/ajb20704-sup-0008.pd

Angiosperm Phylogeny: 17 Genes, 640 Taxa

• Premise of the study : Recent analyses employing up to fi ve genes have provided numerous insights into angiosperm phylogeny, but many relationships have remained unresolved or poorly supported. In the hope of improving our understanding of angiosperm phylogeny, we expanded sampling of taxa and genes beyond previous analyses. • Methods : We conducted two primary analyses based on 640 species representing 330 families. The fi rst included 25 260 aligned base pairs (bp) from 17 genes (representing all three plant genomes, i.e., nucleus, plastid, and mitochondrion). The second included 19 846 aligned bp from 13 genes (representing only the nucleus and plastid). • Key results : Many important questions of deep-level relationships in the nonmonocot angiosperms have now been resolved with strong support. Amborellaceae, Nymphaeales, and Austrobaileyales are successive sisters to the remaining angiosperms ( Mesangiospermae ), which are resolved into Chloranthales + Magnoliidae as sister to Monocotyledoneae + [Ceratophyllaceae + Eudicotyledoneae ]. Eudicotyledoneae contains a basal grade subtending Gunneridae . Within Gunneridae , Gunnerales are sister to the remainder ( Pentapetalae ), which comprises (1) Superrosidae , consisting of Rosidae (including Vitaceae) and Saxifragales; and (2) Superasteridae , comprising Berberidopsidales, Santalales, Caryophyllales , Asteridae , and, based on this study, Dilleniaceae (although other recent analyses disagree with this placement). Within the major subclades of Pentapetalae , most deep-level relationships are resolved with strong support. • Conclusions : Our analyses confi rm that with large amounts of sequence data, most deep-level relationships within the angiosperms can be resolved. We anticipate that this well-resolved angiosperm tree will be of broad utility for many areas of biology, including physiology, ecology, paleobiology, and genomics

Provision of Distance Learner Support Services at U.K. Universities: Identification of Best Practice and Institutional Case Study

An investigation of library support for distance learners (DLs) was commissioned and conducted in partnership with the Distance Learning Support Service (DLSS) at Sheffield Hallam University (SHU). It aimed to collect evidence of best practice at U.K. university libraries and develop a better understanding of the needs and expectations of distance learners at SHU. The study used a mixed-methods research strategy. A review of the literature established key themes and informed the design of the data collection tools. Librarians from two different institutions were interviewed, and two separate self-completion questionnaires were distributed to librarians at U.K. universities and DLs at SHU. Sixty-six librarians (forty-one completed in full) and 112 DLs (109 completed in full) responded to the questionnaires distributed. Results showed limited use of synchronous virtual reference and user-education tools. The biggest challenge faced by librarians is collaborating with course tutors. A marked difference exists between what librarians believe are the most significant challenges faced by DLs and what DLs identify as challenges. Librarians need to experiment with technological innovations, such as synchronous virtual referencing tools, to increase the effectiveness and efficiency of future service provision.published or submitted for publicatio

BSPR/EBI 2007 meeting report – Integrative Proteomics: From Molecules to Systems July 25–27, 2007 Wellcome Trust Conference Centre, Hinxton, UK

This report reviews the joint British Society for Proteome Research (BSPR) and European Bioinformatics Institute (EBI) 2007 meeting, ‘Integrative Proteomics: From Molecules to Systems’ which took place at the Wellcome Trust Conference Centre, Hinxton, UK, from 25th to 27th July. The aim of this year's meeting was to explore how the integration of ‘omic’ technologies can lead to a comprehensive understanding of cellular organization, differentiation and signalling. Studies investigating protein–protein interactions and trafficking illustrated how the combination of proteomics and bioinformatics is allowing systems biology to develop as a discipline in its own right

Differential expression of the fast skeletal muscle proteome following chronic low-frequency stimulation

Physiological and biochemical responses of skeletal muscle fibres to enhanced neuromuscular activity under conditions of maximum activation can be studied experimentally by chronic low-frequency stimulation of fast muscles. Stimulation-induced changes in the expression pattern of the rabbit fast skeletal muscle proteome were evaluated by two-dimensional gel electrophoresis and compared to the altered isoform expression profile of established transformation markers such as the Ca2+-ATPase, calsequestrin and the myosin heavy chain. Sixteen muscle proteins exhibited a marked change in their expression level. This included albumin with a 4-fold increase in abundance. In contrast, glycolytic enzymes, such as enolase and aldolase, showed a decreased expression. Concomitant changes were observed with marker elements of the contractile apparatus. While the fast isoforms of troponin T and myosin light chain 2 were drastically down-regulated, their slow counterparts exhibited increased expression. Interestingly, mitochondrial creatine kinase expression increased while the cytosolic isoform of this key muscle enzyme decreased. The expression of the small heat shock protein HSP-B5/alphaB-crystallin and the oxygen carrier protein myoglobin were both increased 2-fold following stimulation. The observed changes indicate that the conversion into fatigue-resistant red fibres depends on: (i) the optimum utilization of free fatty acids via albumin transportation, (ii) a rearrangement of the creatine kinase isozyme pattern for enhanced mitochondrial activity, (iii) an increased availability of oxygen for aerobic metabolism via myoglobin transport, (iv) the conversion of the contractile apparatus to isoforms with slower twitch characteristics and (v) the up-regulation of chaperone-like proteins for stabilising myofibrillar components during the fast-to-slow transition process

Reduced expression of regucalcin in young and aged mdx diaphragm indicates abnormal cytosolic calcium handling in dystrophin-deficient muscle

The cytosolic Ca2+ -binding protein regucalcin is involved in intracellular signaling and present in high abundance in the liver. Here, we could show by comparative mass spectrometry-based proteomics screening of normal versus dystrophic fibres that regucalcin of 33.9 kDa and pI5.2 also exists in diaphragm muscle. Since the expression of sarcolemmal Ca2+ -leak channels and luminal Ca2+ -binding elements is altered in dystrophin-deficient muscle, we initiated this study in order to determine whether additional soluble muscle proteins involved in Ca2+ -handling are affected in muscular dystrophy. Following separation by two-dimensional gel electrophoresis, the spot pattern of the normal versus the mdx diaphragm muscle proteome was evaluated by densitometry. The expression levels of 20 major protein spots were shown to change and their identity determined by mass spectrometry. A 2-fold reduction of regucalcin in mdx diaphragm, as well as in dystrophic limb muscle and heart, was confirmed by immunoblotting in both young and aged mdx mice. The results from our proteomics analysis of dystrophic diaphragm support the concept that abnormal Ca2+ -handling is involved in x-linked muscular dystrophy. The reduction in key Ca2+ -handling proteins may result in an insufficient maintenance of Ca2+ -homeostasis and an abnormal regulation of Ca2+ -dependent enzymes resulting in disturbed intracellular signaling mechanisms in dystrophinopathies

Proteomic profiling of pathological and aged skeletal muscle fibres by peptide mass fingerprinting (Review)

In contrast to the traditional biochemical study of single proteins or isolated pathways in health and disease, technical advances in the high-throughput screening of peptides by mass spectrometry have established new ways of identifying entire cellular protein populations in one swift analytical approach. This review discusses the recent progress in the biochemical analysis of skeletal muscle extracts and outlines the mass spectrometry-based proteomics approach for studying muscle tissues in normal and pathobiochemical processes using peptide mass fingerprinting. Individual topics covered include the most commonly inherited muscle disease, X-linked muscular dystrophy, the physiological process of fast-to-slow fibre transformation, and the role of fibre degeneration in age-related muscle wasting. Recent proteomic profiling studies of dystrophic muscles have revealed new disease markers in dystrophin-deficient fibres, such as adenylate kinase, the Ca2+-binding protein regucalcin and the small heat shock protein cvHSP. Since these muscle proteins are of low abundance, they have not previously been identified as biomarkers of muscular dystrophy, illustrating the increased sensitivity of modern mass spectrometric techniques. This review outlines comparative proteomic techniques that employ conventional labeling methods, such as Coomassie- or silver-staining. In addition, the most advanced proteomic screening approach currently available, fluorescence difference in-gel electrophoresis, is described and its potential for studying muscle proteomes is critically examined. As an alternative suggestion, the two-dimensional analysis of different protein samples separated in parallel on a single second dimension gel is introduced and the usefulness of this technique for direct comparative investigations is explained. The potential of studying protein complex formation by intraproteomics, estimating the composition of subcellular fraction by subproteomics, and analyzing total muscle protein extracts by mass spectrometry-based proteomics, is enormous. Proteomics is one of the most promising new analytical ways of comparing large muscle protein complements and has the potential to decisively improve modern biochemical and biomedical research into neuromuscular disorders