Cortical maps: where theory meets experiments

Primary visual cortex (V1) has remarkably systematic functional maps. One commonly used class of computational models proposes that such maps are generated by a mechanism that projects the multiple dimensions of neuronal responses smoothly onto the two dimensions of cortex. In this issue of Neuron, Mriganka Sur and colleagues find a close match between such model predictions and measurements from ferret V1.     

The highly processive kinesin-8, Kip3, switches microtubule protofilaments with a bias toward the left

Kinesin-1 motor proteins walk parallel to the protofilament axes of microtubules as they step from one tubulin dimer to the next. Is protofilament tracking an inherent property of processive kinesin motors, like kinesin-1, and what are the structural determinants underlying protofilament tracking? To address these questions, we investigated the tracking properties of the processive kinesin-8, Kip3. Using in vitro gliding motility assays, we found that Kip3 rotates microtubules counterclockwise around their longitudinal axes with periodicities of ∼1 μm. These rotations indicate that the motors switch protofilaments with a bias toward the left. Molecular modeling suggests 1), that the protofilament switching may be due to kinesin-8 having a longer neck linker than kinesin-1, and 2), that the leftward bias is due the asymmetric geometry of the motor neck linker complex.The founding member of the kinesin superfamily, the cargo-transporting kinesin-1, has been studied in great detail. Dimeric kinesin-1 constructs 1) are mechanical processive, taking ∼100 of 8-nm steps in a hand-over-hand fashion without detaching from the microtubule; and 2), walk parallel to the axis of microtubule protofilaments as they step from one tubulin dimer to the next. The latter was inferred from gliding motility assays, where microtubules propelled by motors bound to a planar substrate surface rotated around their longitudinal axis with periodicities corresponding to the helical course of the protofilaments in supertwisted microtubules (1,2). Interestingly, protofilament tracking of kinesin-1 is lost in nonprocessive, monomeric constructs (3). There, and also for other nonprocessive microtubule motors such as the kinesin-14 Ncd (4) or axonemal dynein (5), significantly shorter pitches of microtubule rotations in gliding motility assays were observed. As suggested previously (6) this may indicate that protofilament tracking is an inherent property of processive microtubule motors.To explore this idea further, we investigated the rotations of 14-protofilament microtubules (left-handed helical pitch of ∼8 μm (2)) in gliding motility assays using kinesin-8 that has been observed to perform ≈12 μm-long processive runs in vitro (7). Streptavidin-coated quantum dots (QDs), sparsely bound to the microtubules, served as reporters of microtubule rotations (Fig. 1 A). Information on the three-dimensional paths of the QDs—and thus on microtubule rotations—were obtained from 1), two-dimensional tracking of the QDs with nanometer precision in x and y (8), in combination with 2), z information derived from fluorescence-interference contrast (FLIC) (2) (Fig. 1, B–D). FLIC originates from destructive and constructive interference effects close to reflecting surfaces and gives rise to a modulation of the detected intensity of a fluorescent object depending on its height above the surface. Specifically, the microtubule-attached QDs appear dark when they are in close proximity to the surface (i.e., when being located between the microtubule and the surface) but brighten up significantly when being further away (i.e., when on the microtubule lattice pointing away from the surface). In our experiments, we observed counterclockwise rotations (looking from the trailing microtubule plus-end in the direction toward the leading minus-end) with an average pitch of 0.93 μm ± 0.20 μm (mean ± SD, N = 75; N is the number of complete rotations obtained from 15 gliding microtubules). Considering the geometry of the assay, the counterclockwise directionality of the rotations corresponds to the motors stepping with a perpetual bias (∼1 protofilament switch event per forward movement over 10 tubulin dimers) toward the left.Open in a separate windowFigure 1Monitoring Kip3-driven microtubule rotations in gliding motility assays. (A) Schematic of the experimental setup. Imaging is performed on top of a reflective silicon surface using fluorescence interference contrast (FLIC) microscopy (2). (B) Maximum projection of the fluorescence signal of a microtubule-attached quantum dot in the Kip3 gliding motility assay. (C) FLIC intensity (red) and lateral distance from the microtubule path (blue) of the quantum dot shown in panel B versus traveled distance along the microtubule path. The periodic FLIC signal is indicative of repeated up- and down-motion. (D) Schematic of the deduced Kip3 path (red) in comparison to the protofilament axis (green) on a 14-protofilament microtubule.The behavior observed in our experiments is in stark contrast to kinesin-1, for which counterclockwise rotations with an average pitch of 7.9 μm were previously observed using the same experimental technique (2). Consequently, the question arises: which structural determinants decide whether a kinesin acts as a strict protofilament tracker (and—if it does not—from where the directional bias of the off-axis stepping originates)? Assuming motility in a hand-over-hand fashion, it will matter which binding sites on the microtubule lattice are within reach of the forward swinging motor head. This reach is primarily set by the neck linkers, the structural elements that connect the two motor heads to the coiled-coil neck domain. More precisely, the reach is a function of the length of the neck linkers and their three-dimensional path dictated by the volumes that are occupied by the motor heads when bound to the microtubule. Based on primary sequence alignment between Kip3 with other members of the kinesin-8 family and prediction of the start of the coiled-coil dimerization domain with the program PCOILS, we assigned the neck linker region to the amino acids K436–H452 (i.e., 17 amino acids). Accounting for neck linker docking of the rear motor head (K436–Q447) (9), the corresponding length of the neck linkers between both heads, composed of five amino acids from the undocked part of the rear-head neck linker and 17 amino acids from the front-head neck linker, is estimated to be 85 Å (see the Supporting Material).We then modeled all configurations of Kip3 with both heads bound simultaneously to adjacent tubulin dimers (Fig. 2, A and B, and see the Supporting Material). The estimated three-dimensional distances between the positions where the neck linkers protrude from the motor heads, respecting the volumes of the heads (Fig. 2 C, gray column; see also the Supporting Material), are measures for the minimally required neck linker lengths for each two-head bound configuration. Comparison between the three-dimensional distances obtained from the model and the available neck linker length (85 Å) suggests that a forward-swinging Kip3 head can most readily reach the tubulin dimer in the front (53 Å needed) and can switch to the protofilament on the left (79 Å for left and 93 Å for front-left needed), but it has difficulties in stepping to the protofilament on the right, which would require a longer neck-linker than it actually exhibits (103 Å for front-right and 105 Å for right needed). The main reason why these long neck-linker distances are required (i.e., >100 Å) is that, to reach the tubulin dimer on the right (or front-right), the neck linker has to bend over the humpy back of the front head (see Fig. 2 B, right and front-right). On the contrary, to reach the tubulin dimer on the left (or front-left), this detour is avoided (see Fig. 2 B, left and front-left). The model-derived preference for left-stepping over right-stepping is in agreement with our experimental observations.Open in a separate windowFigure 2Virtual three-dimensional reconstruction of Kip3 stepping. (A) Tubulin dimer: composed of alpha-tubulin (α) and beta-tubulin (β) monomers, with the unstructured surface-exposed E-Hooks (e). Kip3 front head: Shown with undocked neck linker (U) and following coiled-coil (cc) dimerization domain. Kip3 rear head: Shown with docked (D) and undocked (U) neck linker parts. (B) Illustration of different Kip3 configurations bound with both heads to adjacent tubulin dimers (first heptad repeat of the coiled coil region is artificially unfolded to illustrate all binding configurations). (C) Estimated three-dimensional distances between the positions where the neck linkers protrude from the motor heads, respecting the volumes of the heads (nomenclature as in panel B). For comparison, the direct distances between the tubulin dimers are given.Modeling as described can be applied for kinesin-1, whose neck linkers are three-amino-acids shorter than the neck linkers of Kip3. Whereas the modeled minimally required neck linker lengths for each two-head-bound configuration are almost identical to the values for Kip3, we estimate an available neck linker length of 63 Å (see the Supporting Material), which explains the strict forward stepping of kinesin-1.In summary, we have shown what to our knowledge is the first example of a highly processive kinesin motor (run length of several μm) switching between protofilaments of microtubules. Our modeling suggests that protofilament switching may be due to kinesin-8 having a longer neck linker than kinesin-1 so that it is able to reach the extra distance required to change protofilaments. The leftward bias cannot be explained by the geometry of the microtubule lattice alone (Fig. 2 C, last column) but follows from the additional consideration of the asymmetric geometry of the motor neck linker complex. A leftward torque component, which may be present in the powerstrokes of the individual heads (3,4), may further promote the leftward bias but is not strictly necessary. While our results were under review, left-handed spiraling along microtubules of beads coated with a modified kinesin-1 (with extended neck linkers (10)) was reported (11); the handedness of the bead rotations is consistent with the handedness of our microtubule rotations and our model.Our results may also provide an alternative explanation for the short-pitch, counterclockwise rotations of microtubules gliding on surfaces coated by dimeric kinesin-5 (Eg5) motors (6). The authors of this report attributed the short pitch to the low processivity of Eg5, arguing that during processive episodes the motor follows the protofilament axis, but when detaching generates an off-axis force leading to microtubule rotation. Considering the structure of Eg5 (neck linker length of 18 amino acids (12)), protofilament switching may, however, also be possible during the processive episodes. For kinesin-2 (neck linker length of 17 amino acids, although reduced in length by ∼5 Å due to proline in cis-conformation at position 13 (12,13)), the propensity to switch protofilaments is controversially discussed and may depend on the stability of the neck domain (11,14).Previously, Kip3, has been found to depolymerize microtubules in a length-dependent manner (7). The underlying mechanism has been described by an antenna model, where Kip3 binds along the entire microtubule lattice and subsequently walks to the microtubule plus-end relying on its high processivity that is ∼20 times the run length of kinesin-1. During such long runs, motors in vivo are expected to frequently encounter obstacles, such as microtubule-associated proteins. In the case of kinesin-1, shown to follow the microtubule''s protofilament axis (1), obstacles cause motor stalling or accelerated detachment. It is exciting to speculate that Kip3 uses protofilament switching to bypass obstacles on the microtubule surface avoiding premature motor release or stalling that could reduce the efficiency of targeting and subsequent depolymerization of the microtubule plus-ends.     

Arabidopsis cytokinin-resistant mutant, cnr1, displays altered auxin responses and sugar sensitivity

Based upon the phenotype of young, dark-grown seedlings, a cytokinin-resistant mutant, cnr1, has been isolated, which displays altered cytokinin- and auxin-induced responses. The mutant seedlings possess short hypocotyls and open apical hooks (in dark), and display agravitropism, hyponastic cotyledons, reduced shoot growth, compact rosettes and short roots with increased adventitious branching and reduced number of root hairs. A number of these features invariably depend upon auxin/cytokinin ratio but the cnr1 mutant retains normal sensitivity towards auxin as well as auxin polar transport inhibitor, TIBA, although upregulation of primary auxin-responsive Aux/IAA genes is reduced. The mutant shows resistance towards cytokinin in hypocotyl/root growth inhibition assays, displays reduced regeneration in tissue cultures (cytokinin response) and decreased sensitivity to cytokinin for anthocyanin accumulation. It is thus conceivable that due to reduced sensitivity to cytokinin, the cnr1 mutant also shows altered auxin response. Surprisingly, the mutant retains normal sensitivity to cytokinin for induction of primary response genes, the type-A Arabidopsis response regulators, although the basal level of their expression was considerably reduced as compared to the wild-type. The zeatin and zeatin riboside levels, as estimated by HPLC, and the cytokinin oxidase activity were comparable in the cnr1 mutant and the wild-type. The hypersensitivity to red light (in hypocotyl growth inhibition assay), partial photomorphogenesis in dark, and hypersensitivity to sugars, are some other features displayed by the cnr1 mutant. The lesion in the cnr1 mutant has been mapped to the top of chromosome 1 where no other previously known cytokinin-resistant mutant has been mapped, indicating that the cnr1 mutant defines a novel locus involved in hormone, light and sugar signalling.     

A framework for characterizing overlap of communication and computation in parallel applications

Effective overlap of computation and communication is a well understood technique for latency hiding and can yield significant performance gains for applications on high-end computers. In this paper, we propose an instrumentation framework for message-passing systems to characterize the degree of overlap of communication with computation in the execution of parallel applications. The inability to obtain precise time-stamps for pertinent communication events is a significant problem, and is addressed by generation of minimum and maximum bounds on achieved overlap. The overlap measures can aid application developers and system designers in investigating scalability issues. The approach has been used to instrument two MPI implementations as well as the ARMCI system. The implementation resides entirely within the communication library and thus integrates well with existing approaches that operate outside the library. The utility of the framework is demonstrated by analyzing communication-computation overlap for micro-benchmarks and the NAS benchmarks, and the insights obtained are used to modify the NAS SP benchmark, resulting in improved overlap.

Rapid expression and activation of MMP-2 and MMP-9 upon exposure of human breast cancer cells (MCF-7) to fibronectin in serum free medium

Interactions between tumour cells and the extracellular matrix (ECM) strongly influence tumour development, affecting cell survival, proliferation and migration. Many of these interactions are mediated through a family of cell surface receptors named integrins. Fibronectin and its integrin receptors play important roles in tumour development. The alpha5beta 1 integrin interacts with the central cell adhesive region of fibronectin and requires both the RGD and synergy sites for maximal binding. Matrix metalloproteinases (MMPs) are a family of zinc dependent endopeptidases. They are capable of digesting the different components of the ECM and basement membrane. The ECM gives structural support to cells and plays a central role in cell adhesion, differentiation, proliferation and migration. Binding of ECM to integrins modulates expression and activity of the different MMPs. Our experimental findings demonstrate that cultivation of human breast cancer cells, MCF-7, in serum free medium in the presence of fibronectin upregulates the activity of MMP-2 and MMP-9. Blocking of alpha5beta 1 integrin with anti-alpha5 monoclonal antibody inhibits the fibronectin-induced MMP activation response appreciably. This strongly indicates alpha5beta 1 mediated signalling events in activation of MMP-2 and MMP-9. Phosphorylation of FAK and PI-3 kinase and the nuclear translocation of ERK and NF-kappaB upon fibronectin binding demonstrate possible participation of the FAK/PI-3K/ERK signalling pathways in the regulation of MMP-2 activity.     

Chlorophyllase in <Emphasis Type="Italic">Piper betle</Emphasis> L. has a role in chlorophyll homeostasis and senescence dependent chlorophyll breakdown

Total chlorophyll content and chlorophyllase (chlorophyll-chlorophyllido hydrolase EC 3.1.1.14) activity in fresh leaves of Piper betle L. landrace KS was, respectively, twofold higher and eight fold lower than KV, showing negative correlation between chlorophyll and chlorophyllase activity. Specific chlorophyllase activity was nearly eightfold more in KV than KS. ORF of 918 nt was found in cloned putative chlorophyllase cDNAs from KV and KS. The gene was present as single copy in both the landraces. The encoded polypeptide of 306 amino acids differed only at two positions between the KV and KS; 203 (cysteine to tyrosine) and 301 (glutamine to glycine). Difference in chlorophyllase gene expression between KV and KS was evident in fresh and excised leaves. Up regulation of chlorophyllase gene by ABA and down regulation by BAP was observed in both the landraces; however, there was quantitative difference between KV and KS. Data suggests that chlorophyllase in P. betle is involved in chlorophyll homeostasis and chlorophyll loss during post harvest senescence.     

Road to Royalty – Transition of Potential Queen to Queen in the Primitively Eusocial Wasp Ropalidia marginata

Ropalidia marginata, a primitively eusocial wasp, is different from typical primitively eusocial species in having docile queens who cannot be using dominance to maintain reproductive monopoly and instead appear to use a pheromone from the Dufour's gland to do so. When a docile queen is removed from her colony, one of the workers (potential queen, PQ) becomes highly aggressive, and if the queen is not returned, gradually loses her aggression and becomes the new docile queen within a few days. We hypothesized that the decrease in aggression of the PQ with time since queen removal should be correlated with her change in ovaries and pheromone profile. Because the Dufour's gland hydrocarbon composition in R. marginata can be correlated with fertility, this also gave us an opportunity to test whether PQ is different from workers in her Dufour's gland hydrocarbons. In this study, we therefore trace the road to royalty in R. marginata, that is, the transition of the PQ during queen establishment, in terms of her ovaries, aggression, and Dufour's gland hydrocarbons. Our study focuses on queen establishment, which is important for understanding how reproductive conflict can be manifested and resolved.     

Genetic polymorphism of Baylisascaris procyonis in host infrapopulations and component populations in the Central USA

Baylisascaris procyonis is a nematode of significant concern to public and domestic animal health as well as wildlife management. The population genetics of B. procyonis is poorly understood. To gain insights into patterns of genetic diversity within (infrapopulation level) and among (component population level) raccoon (Procyon lotor) hosts, and specifically to assess the relative importance of indirect and direct transmission of the parasite for explaining observed population structure, we collected 69 B. procyonis from 17 wild raccoons inhabiting five counties in Missouri and Arkansas, USA. Informative regions of mitochondrial (CO1, CO2) and nuclear (28S, ITS2) genes were amplified and the distribution and genetic variability of these genes were assessed within and across raccoons. Concatenation of the CO1 and CO2 mtDNA sequences resulted in 5 unique haplotypes, with haplotype diversity 0.456?±?0.068. The most common haplotype occurred in 94% of raccoons and 72.5% of B. procyonis. Sequences for 28S rDNA revealed four unique nuclear genotypes, the most common found in 100% of raccoons and 82.6% of B. procyonis. ITS2 genotypes were assessed using fragment analysis, and there was a 1:1 correspondence between 28S and ITS-2 genotypes. Infrapopulation variation in haplotypes and genotypes was high and virtually all hosts infected with multiple sequenced nematodes also harbored multiple haplotypes and genotypes. There was a positive relationship between the size of the analyzed infrapopulation (i.e., the number of nematodes analyzed) and the number of haplotypes identified in an individual. Collectively this work emphasizes the importance of indirect transmission in the lifecycle to this parasite.     

Independent and combined abiotic stresses affect the physiology and expression patterns of DREB genes differently in stress‐susceptible and resistant genotypes of banana

In tropics, combined stresses of drought and heat often reduce crop productivity in plants like Musa acuminata L. We compared responses of two contrasting banana genotypes, namely the drought‐sensitive Grand Nain (GN; AAA genome) and drought tolerant Hill banana (HB; AAB genome) to individual drought, heat and their combination under controlled and field conditions. Drought and combined drought and heat treatments caused greater reduction in leaf relative water content and greater increase in ion leakage and H₂O₂ content in GN plants, especially in early stages, while the responses were more pronounced in HB at later stages. A combination of drought and heat increased the severity of responses. Real‐time expression patterns of the A‐1 and A‐2 group DEHYDRATION‐RESPONSIVE ELEMENT BINDING (DREB) genes revealed greater changes in expression in leaves of HB plants for both the individual stresses under controlled conditions compared to GN plants. A combination of heat and drought, however, activated most DREB genes in GN but surprisingly suppressed their expression in HB in controlled and field conditions. Its response seems correlated to a better stomatal control over transpiration in HB and a DREB‐independent pathway for the more severe combined stresses unlike in GN. Most of the DREB genes had abscisic acid (ABA)‐responsive elements in their promoters and were also activated by ABA suggesting at least partial dependence on ABA. This study provides valuable information on physiological and molecular responses of the two genotypes to individual and combined drought and heat stresses.