A structural change in the kinesin motor protein that drives motility

Kinesin motors power many motile processes by converting ATP energy into unidirectional motion along microtubules. The force-generating and enzymatic properties of conventional kinesin have been extensively studied; however, the structural basis of movement is unknown. Here we have detected and visualized a large conformational change of an approximately 15-amino-acid region (the neck linker) in kinesin using electron paramagnetic resonance, fluorescence resonance energy transfer, pre-steady state kinetics and cryo-electron microscopy. This region becomes immobilized and extended towards the microtubule 'plus' end when kinesin binds microtubules and ATP, and reverts to a more mobile conformation when gamma-phosphate is released after nucleotide hydrolysis. This conformational change explains both the direction of kinesin motion and processive movement by the kinesin dimer.     

A validation study of a variable weighting algorithm for cluster analysis

De Soete (1986, 1988) proposed a variable weighting procedure when Euclidean distance is used as the dissimilarity measure with an ultrametric hierarchical clustering method. The algorithm produces weighted distances which approximate ultrametric distances as closely as possible in a least squares sense. The present simulation study examined the effectiveness of the De Soete procedure for an applications problem for which it was not originally intended. That is, to determine whether or not the algorithm can be used to reduce the influence of variables which are irrelevant to the clustering present in the data. The simulation study examined the ability of the procedure to recover a variety of known underlying cluster structures. The results indicate that the algorithm is effective in identifying extraneous variables which do not contribute information about the true cluster structure. Weights near 0.0 were typically assigned to such extraneous variables. Furthermore, the variable weighting procedure was not adversely effected by the presence of other forms of error in the data. In general, it is recommended that the variable weighting procedure be used for applied analyses when Euclidean distance is employed with ultrametric hierarchical clustering methods.     

A study of standardization of variables in cluster analysis

A methodological problem in applied clustering involves the decision of whether or not to standardize the input variables prior to the computation of a Euclidean distance dissimilarity measure. Existing results have been mixed with some studies recommending standardization and others suggesting that it may not be desirable. The existence of numerous approaches to standardization complicates the decision process. The present simulation study examined the standardization problem. A variety of data structures were generated which varied the intercluster spacing and the scales for the variables. The data sets were examined in four different types of error environments. These involved error free data, error perturbed distances, inclusion of outliers, and the addition of random noise dimensions. Recovery of true cluster structure as found by four clustering methods was measured at the correct partition level and at reduced levels of coverage. Results for eight standardization strategies are presented. It was found that those approaches which standardize by division by the range of the variable gave consistently superior recovery of the underlying cluster structure. The result held over different error conditions, separation distances, clustering methods, and coverage levels. The traditionalz-score transformation was found to be less effective in several situations.     

Climate-driven trends in contemporary ocean productivity

Contributing roughly half of the biosphere's net primary production (NPP), photosynthesis by oceanic phytoplankton is a vital link in the cycling of carbon between living and inorganic stocks. Each day, more than a hundred million tons of carbon in the form of CO2 are fixed into organic material by these ubiquitous, microscopic plants of the upper ocean, and each day a similar amount of organic carbon is transferred into marine ecosystems by sinking and grazing. The distribution of phytoplankton biomass and NPP is defined by the availability of light and nutrients (nitrogen, phosphate, iron). These growth-limiting factors are in turn regulated by physical processes of ocean circulation, mixed-layer dynamics, upwelling, atmospheric dust deposition, and the solar cycle. Satellite measurements of ocean colour provide a means of quantifying ocean productivity on a global scale and linking its variability to environmental factors. Here we describe global ocean NPP changes detected from space over the past decade. The period is dominated by an initial increase in NPP of 1,930 teragrams of carbon a year (Tg C yr(-1)), followed by a prolonged decrease averaging 190 Tg C yr(-1). These trends are driven by changes occurring in the expansive stratified low-latitude oceans and are tightly coupled to coincident climate variability. This link between the physical environment and ocean biology functions through changes in upper-ocean temperature and stratification, which influence the availability of nutrients for phytoplankton growth. The observed reductions in ocean productivity during the recent post-1999 warming period provide insight on how future climate change can alter marine food webs.     

Myosin VI is an actin-based motor that moves backwards.

Myosins and kinesins are molecular motors that hydrolyse ATP to track along actin filaments and microtubules, respectively. Although the kinesin family includes motors that move towards either the plus or minus ends of microtubules, all characterized myosin motors move towards the barbed (+) end of actin filaments. Crystal structures of myosin II (refs 3-6) have shown that small movements within the myosin motor core are transmitted through the 'converter domain' to a 'lever arm' consisting of a light-chain-binding helix and associated light chains. The lever arm further amplifies the motions of the converter domain into large directed movements. Here we report that myosin VI, an unconventional myosin, moves towards the pointed (-) end of actin. We visualized the myosin VI construct bound to actin using cryo-electron microscopy and image analysis, and found that an ADP-mediated conformational change in the domain distal to the motor, a structure likely to be the effective lever arm, is in the opposite direction to that observed for other myosins. Thus, it appears that myosin VI achieves reverse-direction movement by rotating its lever arm in the opposite direction to conventional myosin lever arm movement.