Quiescent fibroblasts exhibit high metabolic activity

Many cells in mammals exist in the state of quiescence, which is characterized by reversible exit from the cell cycle. Quiescent cells are widely reported to exhibit reduced size, nucleotide synthesis, and metabolic activity. Much lower glycolytic rates have been reported in quiescent compared with proliferating lymphocytes. In contrast, we show here that primary human fibroblasts continue to exhibit high metabolic rates when induced into quiescence via contact inhibition. By monitoring isotope labeling through metabolic pathways and quantitatively identifying fluxes from the data, we show that contact-inhibited fibroblasts utilize glucose in all branches of central carbon metabolism at rates similar to those of proliferating cells, with greater overflow flux from the pentose phosphate pathway back to glycolysis. Inhibition of the pentose phosphate pathway resulted in apoptosis preferentially in quiescent fibroblasts. By feeding the cells labeled glutamine, we also detected a "backwards" flux in the tricarboxylic acid cycle from α-ketoglutarate to citrate that was enhanced in contact-inhibited fibroblasts; this flux likely contributes to shuttling of NADPH from the mitochondrion to cytosol for redox defense or fatty acid synthesis. The high metabolic activity of the fibroblasts was directed in part toward breakdown and resynthesis of protein and lipid, and in part toward excretion of extracellular matrix proteins. Thus, reduced metabolic activity is not a hallmark of the quiescent state. Quiescent fibroblasts, relieved of the biosynthetic requirements associated with generating progeny, direct their metabolic activity to preservation of self integrity and alternative functions beneficial to the organism as a whole.     

Use of Acadian marine plant extract powder from Ascophyllum nodosum in tissue culture of Kappaphycus varieties

Three varieties of Kappaphycus alvarezii (Kapilaran, KAP), Tambalang purple (PUR), Adik-adik (AA), and one variety of Kappaphycus striatum var. sacol (green sacol (GS) were used to determine the efficiency of Acadian marine plant extract powder (AMPEP) as a culture medium at different concentrations, for the regeneration of young plants of Kappaphycus varieties, using tissue culture techniques for the production of seed stock for nursery and outplanting purposes for the commercial cultivation of carrageenophytes. A shorter duration for shoot formation was observed when the explant was treated with AMPEP + Plant Growth Regulator (PGR = PAA + zeatin at 1 mg L⁻¹) compared to AMPEP when used singly. However, four explants responded differently to the number of days required for shoot formation. The KAP variety took 46 days to form shoots at 3–4 mg L⁻¹ AMPEP + PGR; while PUR required 21 days at 3–5 mg L⁻¹ AMPEP and 3–4 mg L⁻¹ AMPEP + PGR. AA required 17 days at 3–5 mg L⁻¹ AMPEP and AMPEP + PGR; and GS 25 days at 1 mg L⁻¹ AMPEP + PGR. It was observed that among the four explants used, PUR and AA initiated shoot formation with the use of AMPEP only at higher concentrations (3–5 mg L⁻¹) after a shorter period. Only PUR responded positively to ESS/2 for shoot initiation. The use of AMPEP alone and/or in combination with PGR as a culture medium in the propagation of microplantlets using tissue culture technique is highly encouraging.     

Historical trends in frog populations in New Zealand based on public perceptions

Surveys were distributed to New Zealand land users in 1998 and 2008 to acquire information about New Zealand frogs with the aim of compiling and mapping their distribution and inferred population trends without costly and time-consuming field surveys. The overall frog population trend was reported as declining, with possible causes reported as an increase in agriculture, an increase in the distribution of predatory fish and disease. The resultant maps could be used for four main purposes: 1) to identify regions where Litoria populations are known to occur, which can be eliminated when considering suitable regions for translocation of Leiopelma; 2) to identify growing or stable populations of Litoria species, which may assist future disease surveys, population monitoring and to identify sources of genetic material that may serve as an Ark for declining Australian populations; 3) to highlight populations that are in decline to enable effective targeting of detailed disease studies; and 4) to approximate the stability of amphibian populations in the absence of more accurate, but costly, scientific monitoring.     

A novel harmony search-K means hybrid algorithm for clustering gene expression data

Recent progress in bioinformatics research has led to the accumulation of huge quantities of biological data at various data sources. The DNA microarray technology makes it possible to simultaneously analyze large number of genes across different samples. Clustering of microarray data can reveal the hidden gene expression patterns from large quantities of expression data that in turn offers tremendous possibilities in functional genomics, comparative genomics, disease diagnosis and drug development. The k- ¬means clustering algorithm is widely used for many practical applications. But the original k-¬means algorithm has several drawbacks. It is computationally expensive and generates locally optimal solutions based on the random choice of the initial centroids. Several methods have been proposed in the literature for improving the performance of the k-¬means algorithm. A meta-heuristic optimization algorithm named harmony search helps find out near-global optimal solutions by searching the entire solution space. Low clustering accuracy of the existing algorithms limits their use in many crucial applications of life sciences. In this paper we propose a novel Harmony Search-K means Hybrid (HSKH) algorithm for clustering the gene expression data. Experimental results show that the proposed algorithm produces clusters with better accuracy in comparison with the existing algorithms.     

Impact of AMPEP on the growth and occurrence of epiphytic Neosiphonia infestation on two varieties of commercially cultivated Kappaphycus alvarezii grown at different depths in the Philippines

Two varieties of the carrageenophyte Kappaphycus alvarezii (Tungawan, TUNG; and Giant tambalang, GTAM) from Zamboanga Sibugay, Philippines were used to test the efficacy of Acadian Marine Plant Extract Powder (AMPEP) as source of nutrients for growth, and to determine if applications had any effect on the percent occurrence of an epiphytic infestation of the red alga Neosiphonia sp. at four different depths in the sea. Results showed that the use of AMPEP significantly (P < 0.05) increased the growth rate of both Kappaphycus varieties tested but decreased the percent occurrence of Neosiphonia sp. The percent occurrence of Neosiphonia sp. infection (6–50% at all depths) of both Kappaphycus varieties with AMPEP treatment was significantly lower than the controls (i.e., 10–75% at all depths). Both the growth rate of the cultivated seaweed and the percent occurrence of the epiphytes decreased as the cultivation depth increased. Plants dipped in AMPEP and suspended at the surface had the highest growth rates (i.e., 4.1%, TUNG; 3.1%, GTAM) after 45 days; those without AMPEP dipping had the highest percent occurrence of Neosiphonia infection (viz. 70–75%). The occurrence of Neosiphonia infestation was found to be correlated with changes in irradiance and salinity at the depths observed. The results suggested that both varieties of K. alvarezii used in this study have the fastest growth rate when grown immediately at the water surface. However, in order to minimize damage caused by the occurrence of epiphytic Neosiphonia, K. alvarezii should be grown within a depth range of 50–100 cm. These observations are important for the improved management of Kappaphycus for commercial farming. Furthermore, the use of AMPEP treatments for enhancement of growth and reduction deleterious Neosiphonia sp. infections is encouraging.     

Studies of esterase 6 in Drosophila melanogaster. XVIII. Biochemical differences between the slow and fast allozymes

Most natural populations of Drosophila melanogaster are polymorphic for two major electrophoretic variants at the esterase-6 locus. The frequency of the EST 6F allozyme is greatest in populations in warmer latitudes, whereas the EST 6S allozyme is predominant in colder latitudes. Latitudinal clines in electromorph frequencies are found on three continents. Purified preparations of the allozymes have been characterized for their pH optimum, substrate specificity, organophosphate inhibition, alcohol activation, thermal stability, and kinetic parameters. These and previous analyses of the EST 6 allozymes reveal that the two variants have differences in their physical and kinetic properties that may provide a basis for the selective maintenance of the polymorphisms and an explanation of the clinal variation observed in natural populations.      

A microRNA network regulates proliferative timing and extracellular matrix synthesis during cellular quiescence in fibroblasts

Background

Although quiescence (reversible cell cycle arrest) is a key part in the life history and fate of many mammalian cell types, the mechanisms of gene regulation in quiescent cells are poorly understood. We sought to clarify the role of microRNAs as regulators of the cellular functions of quiescent human fibroblasts.

Results

Using microarrays, we discovered that the expression of the majority of profiled microRNAs differed between proliferating and quiescent fibroblasts. Fibroblasts induced into quiescence by contact inhibition or serum starvation had similar microRNA profiles, indicating common changes induced by distinct quiescence signals. By analyzing the gene expression patterns of microRNA target genes with quiescence, we discovered a strong regulatory function for miR-29, which is downregulated with quiescence. Using microarrays and immunoblotting, we confirmed that miR-29 targets genes encoding collagen and other extracellular matrix proteins and that those target genes are induced in quiescence. In addition, overexpression of miR-29 resulted in more rapid cell cycle re-entry from quiescence. We also found that let-7 and miR-125 were upregulated in quiescent cells. Overexpression of either one alone resulted in slower cell cycle re-entry from quiescence, while the combination of both together slowed cell cycle re-entry even further.

Conclusions

microRNAs regulate key aspects of fibroblast quiescence including the proliferative state of the cells as well as their gene expression profiles, in particular, the induction of extracellular matrix proteins in quiescent fibroblasts.