Depth cue combination in spontaneous eye movements.

Where we look when we scan visual scenes is an old question that continues to inspire both fundamental and applied research. Recently, it has been reported that depth is an important variable in driving eye movements: the directions of spontaneous saccades tend to follow depth gradients, or, equivalently, surface tilts (L. Jansen, S. Onat, & P. König, 2009; M. Wexler & N. Ouarti, 2008). This has been found to hold for both simple and complex scenes and for a variety of depth cues. However, it is not known whether saccades are aligned with individual depth cues, or with a combination of depth cues. If saccades do follow a combination of depth cues, then it is interesting to ask whether this combination follows the same rules as the well-studied case of depth cue combination in conscious perception. We showed subjects surfaces inclined in depth, in which perspective and binocular disparity cues specified different plane orientations, with different degrees of both small and large conflict between the two sets of cues. We recorded subjects' spontaneous saccades while they scanned the scene, as well as their reports of perceived plane orientation. We found that distributions of spontaneous saccade directions followed the same pattern of depth cue combination as perceived surface orientation: a weighted linear combination of cues for small conflicts, and cue dominance for large conflicts. The weights assigned to the cues varied considerably from one subject to the next but were strongly correlated for saccades and perception; moreover, for both perception and saccades, cue weights could be modified by manipulating cue reliability in a way compatible with Bayesian theories of optimal cue combination. We also measured vergence, which allowed us to calculate the orientation of the plane fitted to points scanned in depth. Contrary to perception and saccades, vergence was dominated by a single cue, binocular disparity.

The Fur-like protein Mur of Rhizobium leguminosarum is a Mn(2+)-responsive transcriptional regulator.

In wild-type Rhizobium leguminosarum, the sitABCD operon specifies a Mn(2+) transporter whose expression is severely reduced in cells grown in the presence of this metal. Mutations in the R. leguminosarum gene, mur (manganese uptake regulator), whose product resembles the Fur transcriptional regulator, cause high-level expression of sitABCD in the presence of Mn(2+). In gel-shift mobility assays, purified R. leguminosarum Mur protein bound to at least two regions near the sitABCD promoter region, although this DNA has no conventional consensus Fur-binding sequences (fur boxes). Thus, in contrast to gamma-proteobacteria, where Fur binds Fe(2+), the R. leguminosarum Fur homologue, Mur, act as a Mn(2)-responsive transcriptional regulator.

Fur is not the global regulator of iron uptake genes in Rhizobium leguminosarum.

Rhizobium leguminosarum fur mutants were unaffected in Fe-dependent regulation of several operons that specify different Fe uptake systems, yet cloned R. leguminosarum fur partially corrected an Escherichia coli fur mutant and R. leguminosarum Fur protein bound to canonical fur boxes. The lack of a phenotype in fur mutants is not due to functional redundancy with Irr, another member of the Fur superfamily found in the rhizobia, since irr fur double mutants are also unaffected in Fe-responsive regulation of several operons involved in Fe uptake. Neither Irr nor Fur is needed for symbiotic N(2) fixation on peas. As in Bradyrhizobium japonicum, irr mutants accumulated protoporphyrin IX. R. leguminosarum irr is not regulated by Fur and its Irr protein lacks the motif needed for haem-dependent post-translational modification that occurs in B. japonicum Irr. The similarities and differences in the Fur superfamily in the rhizobia and other Gram-negative bacteria are discussed.

Structural studies of the Fur protein from Rhizobium leguminosarum.

The X-ray crystal structure of the apo-form of the Fur protein from Rhizobium leguminosarum has been solved at 2.7 A resolution. Small-angle X-ray scattering was used to give information on the solution conformation of the protein. The Fur homodimer folds into two domains. The N-terminal domain is formed from the packing of two helix-turn-helix motifs while the C-terminal domain appears primarily to stabilize the dimeric state of the protein.

The vbs genes that direct synthesis of the siderophore vicibactin in Rhizobium leguminosarum: their expression in other genera requires ECF sigma factor RpoI.

A cluster of eight genes, vbsGSO, vbsADL, vbsC and vbsP, are involved in the synthesis of vicibactin, a cyclic, trihydroxamate siderophore made by the symbiotic bacterium Rhizobium leguminosarum. None of these vbs genes was required for symbiotic N2 fixation on peas or Vicia. Transcription of vbsC, vbsGSO and vbsADL (but not vbsP) was enhanced by growth in low levels of Fe. Transcription of vbsGSO and vbsADL, but not vbsP or vbsC, required the closely linked gene rpoI, which encodes an ECF sigma factor of RNA polymerase. Transfer of the cloned vbs genes, plus rpoI, to Rhodobacter, Paracoccus and Sinorhizobium conferred the ability to make vicibactin on these other genera. We present a biochemical genetic model of vicibactin synthesis, which accommodates the phenotypes of different vbs mutants and the homologies of the vbs gene products. In this model, VbsS, which is similar to many non-ribosomal peptide synthetase multienzymes, has a central role. It is proposed that VbsS activates L-N5-hydroxyornithine via covalent attachment as an acyl thioester to a peptidyl carrier protein domain. Subsequent VbsA-catalysed acylation of the hydroxyornithine, followed by VbsL-mediated epimerization and acetylation catalysed by VbsC, yields the vicibactin subunit, which is then trimerized and cyclized by the thioesterase domain of VbsS to give the completed siderophore.

The stationarity hypothesis: an allocentric criterion in visual perception.

Having long considered that extraretinal information plays little or no role in spatial vision, the study of structure from motion (SfM) has confounded a moving observer perceiving a stationary object with a non-moving observer perceiving a rigid object undergoing equal and opposite motion. However, recently it has been shown that extraretinal information does play an important role in the extraction of structure from motion by enhancing motion cues for objects that are stationary in an allocentric, world-fixed reference frame (Nature 409 (2001) 85). Here, we test whether stationarity per se is a criterion in SfM by pitting it against rigidity. We have created stimuli that, for a moving observer, offer two interpretations: one that is rigid but non-stationary, another that is more stationary or less rigid. In two experiments, with subjects reporting either structure or motion, we show that stationary, non-rigid solutions are preferred over rigid, non-stationary solutions; and that when no perfectly stationary solutions is available, the visual system prefers the solution that is most stationary. These results demonstrate that allocentric criteria, derived from extra-retinal information, participate in reconstructing the visual scene.

The Rhizobium leguminosarum tonB gene is required for the uptake of siderophore and haem as sources of iron.

In the N2-fixing bacterium Rhizobium leguminosarum, mutations in a homologue of tonB (tonB(Rl)) block the import of vicibactin and haem as iron sources in free-living bacteria. TonB(Rl) mutants were normal for growth with ferric dicitrate and slightly reduced for growth with haemoglobin as sole iron sources. The deduced TonB(Rl) product is larger than that of (for example) Escherichia coli, on account of an extended N-terminal domain. Transcription of tonB(Rl) was enhanced in low-Fe growth conditions; this was not controlled by Fur, nor RpoI, an Fe-regulated extracytoplasmic sigma factor. Upstream of tonB(Rl) and transcribed divergently is an operon, hmuPSTUV, whose products are homologous to ABC transporters involved in haem uptake in pathogenic bacteria. Expression of hmuPSTUV was enhanced in low-Fe conditions, and hmu mutants show slightly diminished growth on haem as sole Fe source, suggesting that there is more than one system for the uptake of this molecule. hmuPSTUV expression appears to be from three closely linked promoters. Downstream of hmuPSTUV, a gene that may encode an extracytoplasmic sigma factor was identified, but this gene, rpoZ, did not affect the transcription of tonB(Rl) or hmuPSTUV. Mutations in tonB(Rl), hmu genes and rpoZ did not affect symbiotic N(2) fixation in peas.

Metals and the rhizobial-legume symbiosis--uptake, utilization and signalling.

In this review, we consider how the nitrogen-fixing root nodule bacteria, the 'rhizobia', acquire various metals, paying particular attention to the uptake of iron. We also review the literature pertaining to the roles of molybdenum and nickel in the symbiosis with legumes. We highlight some gaps in our knowledge, for example the lack of information on how rhizobia acquire molybdenum. We examine the means whereby different metals affect rhizobial physiology and the role of metals as signals for gene regulation. We describe the ways in which genetics has shown (or not) if, and how, particular metal uptake and/or metal-mediated signalling pathways are required for the symbiotic interaction with legumes.

How long can cryopreserved skin be stored to maintain adequate graft performance?

Skin graft preservation for the purpose of delayed application is still a basic tool in burn treatment and plastic and reconstructive surgery. As the demand for skin allografts has increased the responsibility for processing, storage and evaluation of graft performance of preserved skin has become an important issue of banking organizations. The present experiments were undertaken to determine how long can cryopreserved cadaveric skin be stored to maintain adequate graft performance? We applied a mouse recipient model, developed by us: Human cadaveric skin cryopreserved and stored for 5,6 or 7 years was grafted on Balb/c mice, and primary take was evaluated by gross observation and predetermined histologic criteria after 7 days. The results demonstrate that graft performance of cryopreserved skin decreased with time, as reflected in the lower percent of samples with high score of separate histologic criteria after prolonged storage. Nevertheless, paired comparison analysis between cryopreserved and fresh skin indicated that this decrease was not significant for storage of 5 years; whereas it was highly significant for 6 years of storage. Linear regression analysis indicated that there was no correlation between the score of the histologic criteria and storage period for upto 65 months. These results are in line with the paired comparison analysis. We feel that our in vivo model and analysis may be used as an evaluation procedure for transplantation performance of banked skin.

Self-motion and the perception of stationary objects.

One of the ways that we perceive shape is through seeing motion. Visual motion may be actively generated (for example, in locomotion), or passively observed. In the study of the perception of three-dimensional structure from motion, the non-moving, passive observer in an environment of moving rigid objects has been used as a substitute for an active observer moving in an environment of stationary objects; this 'rigidity hypothesis' has played a central role in computational and experimental studies of structure from motion. Here we show that this is not an adequate substitution because active and passive observers can perceive three-dimensional structure differently, despite experiencing the same visual stimulus: active observers' perception of three-dimensional structure depends on extraretinal information about their own movements. The visual system thus treats objects that are stationary (in an allocentric, earth-fixed reference frame) differently from objects that are merely rigid. These results show that action makes an important contribution to depth perception, and argue for a revision of the rigidity hypothesis to incorporate the special case of stationary objects.