Integrating phenotypic and expression profiles to map arsenic-response networks

Background  

Arsenic is a nonmutagenic carcinogen affecting millions of people. The cellular impact of this metalloid in Saccharomyces cerevisiae was determined by profiling global gene expression and sensitivity phenotypes. These data were then mapped to a metabolic network composed of all known biochemical reactions in yeast, as well as the yeast network of 20,985 protein-protein/protein-DNA interactions.     

Complex phenotypic profiles leading to ozone sensitivity in Arabidopsis thaliana mutants

Genetically tractable model plants offer the possibility of defining the plant O₃ response at the molecular level. To this end, we have isolated a collection of ozone (O₃)-sensitive mutants of Arabidopsis thaliana . Mutant phenotypes and genetics were characterized. Additionally, parameters associated with O₃ sensitivity were analysed, including stomatal conductance, sensitivity to and accumulation of reactive oxygen species, antioxidants, stress gene-expression and the accumulation of stress hormones. Each mutant has a unique phenotypic profile, with O₃ sensitivity caused by a unique set of alterations in these systems. O₃ sensitivity in these mutants is not caused by gross deficiencies in the antioxidant pathways tested here. The rcd3 mutant exhibits misregulated stomata. All mutants exhibited changes in stress hormones consistent with the known hormonal roles in defence and cell death regulation. One mutant, dubbed re-8 , is an allele of the classic leaf development mutant reticulata and exhibits phenotypes dependent on light conditions. This study shows that O₃ sensitivity can be determined by deficiencies in multiple interacting plant systems and provides genetic evidence linking these systems.     

Fiber-type differences in muscle mitochondrial profiles

Although striated muscles differ in mitochondrial content, the extent of fiber-type specific mitochondrial specializations is not well known. To address this issue, we compared mitochondrial structural and functional properties in red muscle (RM), white muscle (WM), and cardiac muscle of rainbow trout. Overall preservation of the basic relationships between oxidative phosphorylation complexes among fiber types was confirmed by kinetic analyses, immunoblotting of native holoproteins, and spectroscopic measurements of cytochrome content. Fiber-type differences in mitochondrial properties were apparent when parameters were expressed per milligram mitochondrial protein. However, the differences diminished when expressed relative to cytochrome oxidase (COX), possibly a more meaningful denominator than mitochondrial protein. Expressed relative to COX, there were no differences in oxidative phosphorylation enzyme activities, pyruvate-based respiratory rates, H2O2 production, or state 4 proton leak respiration. These data suggest most mitochondrial qualitative properties are conserved across fiber types. However, there remained modest differences ( approximately 50%) in stoichiometries of selected enzymes of the Krebs cycle, beta-oxidation, and antioxidant enzymes. There were clear differences in membrane fluidity (RM > cardiac, WM) and proton conductance (H+/min/mV/U COX: WM > RM > cardiac). The pronounced differences in mitochondrial content between fiber types could be attributed to a combination of differences in myonuclear domain and modest effects on the expression of nuclear- and mitochondrially encoded respiratory genes. Collectively, these studies suggest constitutive pathways that transcend fiber types are primarily responsible for determining most quantitative and qualitative properties of mitochondria.     

Mitochondrial network of skeletal muscle fiber

Highly specialized muscle fibers require a unique spatial organization of the mitochondrial network. Mitochondrial morphology is largely determined by the fusion and fission of these organelles. This review summarizes the current concepts of mitochondrial dynamics mechanisms and structural features of the mitochondrial network in striated muscle tissue. The role of mitochondria and their dynamics in muscle fiber physiology are also discussed.     

Conversion of rat muscle fiber types

Summary Rats were used in this study to determine the time course of conversion of muscle fiber types. The right or left gastrocnemius muscle was removed thereby causing an overload on the ipsilateral soleus and plantaris muscles. The contralateral limb served as a control. The type II to type I fiber conversion was followed histochemically in the soleus and plantaris muscles for one to six weeks following surgery. Muscle sections were stained for myofibrillar actomyosin ATPase and NADH tetrazolium reductase. The type I population in the soleus muscle was 99.3% six weeks after synergist removal. The plantaris muscle underwent a two fold increase in the percentage of type I fibers after six weeks. Transitional fibers were prominent in the plantaris muscle and reached their peak at 4% (P<0.05) of the total population, four weeks after surgery.This research was funded in part by grants from The Graduate School at Washington State University, and The Society of the Sigma Xi     

Morphological aspects of muscle fiber regeneration

Although striated muscle displays remarkable regenerative potential, the three-dimensional cytoarchitecture of the regenerated myofibers is different from that of myofibers formed during fetal development. It has been demonstrated with spaced, serial ultrathin sections that the regenerating myotubes that occur spontaneously (i.e., without secondary trauma) in dystrophic (dy2J) murine muscle and the regenerating fibers found in free whole-muscle transplants of normal, murine extensor digitorum longus muscles branch and recombine, forming a complex syncytium. Multiple motor end-plate regions are observed on the branched syncytia found in dystrophic muscle. Branched fibers persist in long-term grafts and are found with a frequency that indicates that they should be of physiological significance. Although the number of myofibers found in long-term grafts is approximately 68% of that found in control muscle, comparison of the diameter distributions of the regenerated muscle fibers with age-matched control fibers indicates that many of the regenerating fibers fail to achieve normal size. Type IIb fibers appear to be more growth inhibited than type IIa fibers. The size of the motoneuron pool to grafted muscles is smaller than that to control muscles.     

血管平滑肌细胞表型调节机制的研究进展

血管平滑肌细胞（VSMC）的增殖和迁移是动脉粥样硬化斑块形成、高血压和血管再狭窄的共同病理特征,而VSMC表型转化是VSMC增殖和迁移的基础,研究VSMC表型调节的分子机制,对上述疾病的防治具有重要意义。本文对VSMC表型转化的影响因素、信号转导途径和转录因子的研究进展作一综述。     

Regulation and characteristics of vascular smooth muscle cell phenotypic diversity

Vascular smooth muscle cells can perform both contractile and synthetic functions, which are associated with and characterised by changes in morphology, proliferation and migration rates, and the expression of different marker proteins. The resulting phenotypic diversity of smooth muscle cells appears to be a function of innate genetic programmes and environmental cues, which include biochemical factors, extracellular matrix components, and physical factors such as stretch and shear stress. Because of the diversity among smooth muscle cells, blood vessels attain the flexibility that is necessary to perform efficiently under different physiological and pathological conditions. In this review, we discuss recent literature demonstrating the extent and nature of smooth muscle cell diversity in the vascular wall and address the factors that affect smooth muscle cell phenotype. (Neth Heart J 2007;15:100-8.)     

Nascent muscle fiber appearance in overloaded chicken slow-tonic muscle

The application of a weight overload to the humerus of chickens induces a hypertrophy of anterior latissimus dorsi (ALD) muscle fibers. This growth is accompanied by a rapid and almost complete replacement of one slow-tonic myosin isoform, SM-1, by another slow-tonic isoform, SM-2. In addition, a population of small fibers appears mainly in extrafascicular spaces and, concurrently, three additional myosin bands are detected by gel electrophoresis. Five antibodies against myosin heavy chain (MHC) isoforms were selected as immunocytochemical probes to determine the cellular location and nature of these myosins. The antibodies react with ventricular, fast skeletal muscle and either SM-1 or SM-2, or both the slow-tonic MHCs. The antifast and antiventricular antibodies react with myosin present in the 10-day embryonic ALD muscle but do not react with myosin in posthatch ALD muscle. The small fibers in overloaded muscle contain a myosin isoform characteristically expressed during the embryonic stage of ALD muscle development and therefore are named nascent myofibers. Some of the nascent myofibers do not react with the antibody to both slow-tonic MHCs, indicating the lack of the normal adult slow-tonic myosins which are expressed in 10-day embryos. In order to explore the origin of the nascent fibers, an electron microscopic study was performed. Stereological analysis of the existing fibers shows a stimulation of numbers and sizes of satellite cells. In addition, the volume occupied by nonmuscle and undifferentiated cells increases dramatically. Myotube formation with incipient myofibrils is seen in extrafascicular spaces. These data suggest that new muscle fiber formation accompanies hypertrophy in overloaded chicken ALD muscle and the process may involve satellite cell migration.     

Metabolic and phenotypic adaptations of diaphragm muscle fibers with inactivation

Zhan, Wen-Zhi, Hirofumi Miyata, Y. S. Prakash, and Gary C. Sieck. Metabolic and phenotypic adaptations of diaphragm musclefibers with inactivation. J. Appl.Physiol. 82(4):1145-1153, 1997.We hypothesizedthat metabolic adaptations to muscle inactivity are most pronouncedwhen neurotrophic influence is disrupted. In ratdiaphragm muscle(Dia_m), 2 wk ofunilateral denervation or tetrodotoxin nerve blockade resulted in areduction in succinate dehydrogenase (SDH) activity of type I, IIa, andIIx fibers (~50, 70, and 24%, respectively) and a decrease in SDHvariability among fibers (~63%). In contrast, inactivity induced byspinal cord hemisection at C₂ (ST)resulted in much less change in SDH activity of type I and IIa fibers(~27 and 24%, respectively) and only an ~30% reduction in SDHvariability among fibers. Actomyosin adenosinetriphosphatase (ATPase)activities of type I, IIx, and IIb fibers in denervated andtetrodotoxin-treated Dia_m werereduced by ~20, 45, and 60%, respectively, and actomyosin ATPasevariability among fibers was ~60% lower. In contrast, onlyactomyosin ATPase activity of type IIb fibers was reduced (~20%) inST Dia_m. These results suggestthat disruption of neurotrophic influence has a greater impact onmuscle fiber metabolic properties than inactivity per se.