Fatty acid synthase modulates homeostatic responses to myocardial stress

Fatty acid synthase (FAS) promotes energy storage through de novo lipogenesis and participates in signaling by the nuclear receptor PPARα in noncardiac tissues. To determine if de novo lipogenesis is relevant to cardiac physiology, we generated and characterized FAS knockout in the myocardium (FASKard) mice. FASKard mice develop normally, manifest normal resting heart function, and have normal cardiac PPARα signaling as well as fatty acid oxidation. However, they decompensate with stress. Most die within 1 h of transverse aortic constriction, probably due to arrhythmia. Voltage clamp measurements of FASKard cardiomyocytes show hyperactivation of L-type calcium channel current that could not be reversed with palmitate supplementation. Of the classic regulators of this current, Ca(2+)/calmodulin-dependent protein kinase II (CaMKII) but not protein kinase A signaling is activated in FASKard hearts, and knockdown of FAS in cultured cells activates CaMKII. In addition to being intolerant of the stress of acute pressure, FASKard hearts were also intolerant of the stress of aging, reflected as persistent CaMKII hyperactivation, progression to dilatation, and premature death by ～1 year of age. CaMKII signaling appears to be pathogenic in FASKard hearts because inhibition of its signaling in vivo rescues mice from early mortality after transverse aortic constriction. FAS was also increased in two mechanistically distinct mouse models of heart failure and in the hearts of humans with end stage cardiomyopathy. These data implicate a novel relationship between FAS and calcium signaling in the heart and suggest that FAS induction in stressed myocardium represents a compensatory response to protect cardiomyocytes from pathological calcium flux.     

Helix-dipole effects in peptide self-assembly to amyloid

The formation of amyloid fibrils is associated with incurable diseases including Alzheimer's, Parkinson's, and type 2 diabetes. Important mechanistic details of the self-assembly are unknown partly because of the absence of a clear structural characterization of intermediates. There is experimental evidence, however, for α-helical intermediates that has come primarily from circular dichroism spectroscopy. Here, we strengthen the evidence for helical intermediates by demonstrating helix-dipole effects in the early events of self-assembly. Previously, we showed that capped peptides containing the part of the islet amyloid polypeptide that may be responsible for the initial intermolecular contacts (Acetyl-R(11)LANFLVHSSNNFGA(25)-NH(2) and Acetyl-R(11)LANFLVHSGNNFGA(25)-NH(2) which contains the S20G mutation associated with early onset type 2 diabetes) self-assemble via helical intermediates [Liu et al. (2010) J. Am. Chem. Soc.132, 18223-18232]. We demonstrate here that when the peptides are uncapped, they do not self-assemble as indicated primarily by circular dichroism and nuclear magnetic resonance data. Self-assembly is restored when the charge on α-NH(3)(+) of Arg11 is eliminated but not when the charge on α-COO(-) of Ala25 is removed, consistent with the helicity of the peptides skewed toward the N-terminus. Our results strengthen the hypothesis that α-helical intermediates are on pathway to amyloid formation and indicate that the helix dipole is an attractive target for inhibiting the formation of α-helical assemblies.     

Genetic variability and population structure of grey wolf (<Emphasis Type="Italic">Canis lupus</Emphasis>) in Serbia

Results of previous morphometric and genetic analyses of grey wolf (Canis lupus L.) population from Serbia indicated different patterns of population subdivision. In order to explore population structure, level of genetic variability, genetic drift, inbreeding and signals of bottleneck for grey wolves from Serbia, we applied highly polymorphic genetic markers (microsatellites). Obtained data are valuable in determination of conservation units and creation of appropriate management plans. We have amplified 18 highly polymorphic microsatellites, in a total sample of 75 grey wolves, from different localities across Serbia and multilocus genotypes were analyzed using appropriate software. Observed values of the basic genetic parameters (H_O = 0.69; H_E = 0.75) indicated moderate level of genetic variability, similar to genetic variability in other populations belonging to the Dinaric-Balkan population of grey wolf. In STRUCTURE analysis, although ΔK was estimated to be at first peak K = 2, and second peak K = 4, CLUMPAK analyses showed that there’s no structuring for any of assumed K, and therefore the population of grey wolf from Serbia may be considered as one continuous population and treated as one conservation unit in future management plans. Signals of bottleneck haven’t been observed (Wilcoxon test two phase mutation model p = 0.247; and stepwise mutation model p = 0.815).     

Grazed wet meadows are sink habitats for the southern dunlin (Calidris alpina schinzii) due to nest trampling by cattle

The effect of habitat management is commonly evaluated by measuring population growth, which does not distinguish changes in reproductive success from changes in survival or the effects of immigration or emigration. Management has rarely been evaluated considering complete life cycle of the target organisms, including also possible negative impacts from management. We evaluated the effectiveness of cattle grazing in the restoration of coastal meadows as a breeding habitat for small and medium‐sized ground‐nesting birds by examining the size and demography of a southern dunlin (Calidris alpina schinzii) breeding population. Using a stochastic renesting model that includes within‐season variation in breeding parameters, we evaluated the effect of grazing time and stocking rates on reproduction. The census data indicated that the population was stable when nest trampling was prevented, but detailed demographic models showed that the population on managed meadows was a sink that persisted by attracting immigrants. Even small reductions in reproductive success caused by trampling were detrimental to long‐term viability. We suggest that the best management strategy is to postpone grazing to after the 19th of June, which is about three weeks later than what is optimal from the farmer's point of view. The differing results from the two evaluation approaches warn against planning and evaluating management only based on census population size and highlight the need to consider target‐specific life history characteristics and demography. Even though grazing management is crucial for creating and maintaining suitable habitats, we found that it was insufficient in maintaining a viable population without additional measures that increase nest success. In the presently studied case and in populations with similar breeding cycles, impacts from nest trampling can be avoided by starting grazing when about 70% of the breeding season has past.     

GC-MS analysis and in vitro antioxidant and enzyme inhibitory activities of essential oil from aerial parts of endemic Thymus spathulifolius Hausskn. et Velen

We investigated the antioxidant and enzyme inhibitory activities and chemical composition of the hydro-distilled essential oil (0.35% yield) from aerial parts of Thymus spathulifolius. Antioxidant capacity of the oil was assessed by different methods including free radical scavenging (DPPH and ABTS), reducing power (FRAP and CUPRAC) and phosphomolybdenum assay. Inhibitory activities were analyzed against acetylcholinesterase (AChE), butyrylcholinesterase (BChE), α-amylase, α-glucosidase, and tyrosinase. Twenty-one constituents were identified representing 97.2% of the total oil with thymol (50.5%), borneol (16.7%) and carvacrol (7.7%) as the major components. The essential oil exhibited good antioxidant activity with IC₅₀ values of 3.82 and 0.22?mg/mL determined by free radical scavenging DPPH and ABTS, respectively. EC₅₀ values of FRAP and CUPRAC were found to be 0.12 and 0.34?mg/mL, respectively. The results of the present study support the uses of T. spathulifolius essential oil as a source of natural antioxidants and bioactivities for functional foods and phytomedicines.     

Compressed suffix tree--a basis for genome-scale sequence analysis

Summary: Suffix tree is one of the most fundamental data structuresin string algorithms and biological sequence analysis. Unfortunately,when it comes to implementing those algorithms and applyingthem to real genomic sequences, often the main memory size becomesthe bottleneck. This is easily explained by the fact that whilea DNA sequence of length n from alphabet = {A, C, G, T } canbe stored in n log ||= 2n bits, its suffix tree occupies O(nlog n) bits. In practice, the size difference easily reachesfactor 50. We provide an implementation of the compressed suffix tree veryrecently proposed by Sadakane (Theory of Computing Systems,in press). The compressed suffix tree occupies space proportionalto the text size, i.e. O(n log} | |) bits, and supports alltypical suffix tree operations with at most log n factor slowdown.Our experiments show that, e.g. on a 10 MB DNA sequence, thecompressed suffix tree takes 10% of the space of normal suffixtree. Typical operations are slowed down by factor 60. Availability: The C++ implementation under GNU license is availableat http://www.cs.helsinki.fi/group/suds/cst/. An example programimplementing a typical pattern discovery task is included. Experimentalresults in this note correspond to version 0.95. Contact: vmakinen{at}cs.helsinki.fi     

Peak alignment using restricted edit distances

A peak is a pair of real values (x,y), where x is the time when peak of height y is registered. In the peak alignment problem, we are given two sequences of peaks, and our task is to align the sequences allowing some basic edit operations on the peaks. We study an instance of the peak alignment problem that arises in the analysis of Mass Spectrometry data in Systems Biology. There the measurement technique guarantees that two peaks (x,y), (x',y') can only be considered the same if x is close enough to x', and y is close enough to y'. We review some methods to do alignment under such restrictions on matches.