Visual textures, machine vision and animal camouflage

The psychophysics of visual texture perception and texture discrimination have been investigated extensively during the past 30 years. Humans have been the main study subjects, but some research on texture perception has involved other species, and there is good reason to think that the most general results from humans apply to other vertebrates as well. Psychophysicists have suggested that some of their findings on human vision reflect adaptive 'tricks' for countering prey camouflage, but this possibility has not been widely communicated to evolutionary biologists. We review the psychophysicists' main conclusions on texture discrimination, and list additional questions that their results raise when animal coats are considered as visual textures. We also suggest ways in which advances in computer vision can be combined with psychophysics to provide new perspectives on the function of animal coat patterns.     

Vibrotactile adaptation impairs discrimination of fine,but not coarse,textures

The effect of vibrotactile adaptation on the ability to discriminate textured surfaces was examined in three experiments. The surfaces were rectilinear arrays of pyramids produced by etching of silicon wafers. Adaptation to 100-Hz vibration severely hampered discrimination of surfaces with spatial periods below 100 &#119 m (Experiment 1), but had little effect on the discrimination of coarser textures (Experiment 2). To determine which vibrotactile channel—Rapidly Adapting or Pacinian—plays the larger role in mediating the discrimination of fine textures, widely separated adapting frequencies (10 and 250 Hz) were used in Experiment 3. The fact that high- but not low-frequency adaptation interfered with discrimination suggests that the Pacinian system contributes importantly to this ability. Taken as a whole, the results of this study strongly support the duplex theory of tactile texture perception, according to which different mechanisms—spatial and vibrotactile—mediate the perception of coarse and fine textures, respectively.     

On the discriminability of hROIs, human visually selected regions-of-interest

Many studies have tried to answer an important question: is it possible to predict human visually selected regions-of-interest (hROIs)? hROIs are defined as the loci of eye fixations and they can be analyzed by their spatial distribution over the visual stimulus and their temporal ordering. We used a simplified set of geometrical spatial kernels and linear filter models as bottom-up conspicuity operators that produce algorithmically selected regions-of-interest, aROIs. As a direct approach we measured the ability of these aROIs to predict human scanpaths. The level of prediction is measured by two similarity indices: S _p for spatial similarity and S _s for temporal ordering similarity. At the same time we assessed the discriminability of the hROI loci, in terms of conspicuity, with respect to non-selected (not of interest) regions of an image. We prove that this discrimination is possible and further correlates with the positional similarity index S _p . Other human scanpath experimental conditions are presented in parsing diagrams and discussed. A general top–down/bottom–up scanpath model is finally formulated.     

Caro-red,a new provitamin a rich tomato

The development and release of a new tomato variety which produces fruit containing approximately ten times the provitamin A content of common red tomatoes is announced. The betacarotene values for Caro-Red are within the lower ranges reported for carrots. Present consumer usage of a variety such as Caro-Red will most likely be confined to use as a garden type where additional variety and flavor are desired.     

Cyclomaltodextrinase, neopullulanase, and maltogenic amylase are nearly indistinguishable from each other

Over 20 enzymes denoted as cyclomaltodextrinase, maltogenic amylase, or neopullulanase that share 40-86% sequence identity with each other are found in public data bases. These enzymes are distinguished from typical alpha-amylases by containing a novel N-terminal domain and exhibiting preferential substrate specificities for cyclomaltodextrins (CDs) over starch. In this research field, a great deal of confusion exists regarding the features distinguishing the three groups of enzymes from one another. Although a different enzyme code has been assigned to each of the three different enzyme names, even a single differentiating enzymatic property has not been documented in the literature. On the other hand, an outstanding question related to this issue concerns the structural basis for the preference of these enzymes for CDs. To clarify the confusion and to address this question, we have determined the structures of two enzymes, one from alkalophilic Bacillus sp. I-5 and named cyclomaltodextrinase and the other from a Thermus species and named maltogenic amylase. The structure of the Bacillus enzyme reveals a dodecameric assembly composed of six copies of the dimer, which is the structural and functional unit of the Thermus enzyme and an enzyme named neopullulanase. The structure of the Thermus enzyme in complex with beta-CD led to the conclusion that Trp47, a well conserved N-terminal domain residue, contributes greatly to the preference for beta-CD. The common dimer formation through the novel N-terminal domain, which contributes to the preference for CDs by lining the active-site cavity, convincingly indicates that the three groups of enzymes are not different enough to preserve the different names and enzyme codes.     

Circadian regulation of visually evoked potentials in the domestic pigeon, Columba livia

The avian circadian and visual systems are integrally related and together influence many aspects of birds' behavior and physiology. Certainly, light cycles and their visual perception are the major zeitgebers for circadian rhythms, but do circadian rhythms affect vision? To assess whether visual function is regulated on a circadian basis, flash-evoked electroretinograms (ERGs) and vision-evoked potentials (VEPs) from the optic tectum (TeO) were recorded simultaneously in domestic pigeons at different circadian phases in a light-dark regime (LD) and in constant darkness (DD), while feeding activity was measured to determine circadian phase. In both LD and DD, the amplitudes of ERG b-waves were higher during the day than at night and latencies of a- and b-waves were longer at night. The median effective intensity for ERG a-wave was marginally higher during the day than during the night, indicating greater sensitivity at night, but this rhythm did not persist in DD. The amplitudes of TeO VEPs were also greater during the day, and latencies were greater at night in LD and DD. Together, the data indicate that a circadian clock regulates pigeon visual function at several integrative levels.     

Stochasticity, invasions, and branching random walks

We link deterministic integrodifference equations to stochastic, individual-based simulations by means of branching random walks. Using standard methods, we determine speeds of invasion for both average densities and furthest-forward individuals. For density-independent branching random walks, demographic stochasticity can produce extinction. Demographic stochasticity does not, however, reduce the overall asymptotic speed of invasion or preclude continually accelerating invasions.     

A method to visually observe and photograph the bovine genital tract in,situ

The ovaries and tubular genital tract were observed through a plexiglass speculum inserted through a standard laparotomy incision in either the right or left paralumbar fossa of eight cows, each repeatedly. The observations were accomplished with the cows in the usual standing position restrained only by a head catch. The cows' feed and water intake were not restricted prior to surgery and none of the cows exhibited any adverse clinical signs post-surgically. The described procedure is simple and inexpensive.     

Expression, purification and preliminary biochemical and structural characterization of the leucine rich repeat namesake domain of leucine rich repeat kinase 2

Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of familial Parkinson's disease. Much research effort has been directed towards the catalytic core region of LRRK2 composed of GTPase (ROC, Ras of complex proteins) and kinase domains and a connecting COR (C-terminus of ROC) domain. In contrast, the precise functions of the protein-protein interaction domains, such as the leucine-rich repeat (LRR) domain, are not known. In the present study, we modeled the LRRK2 LRR domain (LRR_LRRK2) using a template assembly approach, revealing the presence of 14 LRRs. Next, we focused on the expression and purification of LRR_LRRK2 in Escherichia coli. Buffer optimization revealed that the protein requires the presence of a zwitterionic detergent, namely Empigen BB, during solubilization and the subsequent purification and characterization steps. This indicates that the detergent captures the hydrophobic surface patches of LRR_LRRK2 thereby suppressing its aggregation. Circular dichroism (CD) spectroscopy measured 18% α-helices and 21% β-sheets, consistent with predictions from the homology model. Size exclusion chromatography (SEC) and dynamic light scattering measurements showed the presence of a single species, with a Stokes radius corresponding to the model dimensions of a protein monomer. Furthermore, no obvious LRR_LRRK2 multimerization was detected via cross-linking studies. Finally, the LRR_LRRK2 clinical mutations did not influence LRR_LRRK2 secondary, tertiary or quaternary structure as determined via SEC and CD spectroscopy. We therefore conclude that these mutations are likely to affect putative LRR_LRRK2 inter- and intramolecular interactions.     

Separation of nearly identical repeats in shotgun assemblies using defined nucleotide positions, DNPs

An increasingly important problem in genome sequencing is the failure of the commonly used shotgun assembly programs to correctly assemble repetitive sequences. The assembly of non-repetitive regions or regions containing repeats considerably shorter than the average read length is in practice easy to solve, while longer repeats have been a difficult problem. We here present a statistical method to separate arbitrarily long, almost identical repeats, which makes it possible to correctly assemble complex repetitive sequence regions. The differences between repeat units may be as low as 1% and the sequencing error may be up to ten times higher. The method is based on the realization that a comparison of only a part of all overlapping sequences at a time in a data set does not generate enough information for a conclusive analysis. Our method uses optimal multi-alignments consisting of all the overlaps of each read. This makes it possible to determine defined nucleotide positions, DNPs, which constitute the differences between the repeat units. Differences between repeats are distinguished from sequencing errors using statistical methods, where the probabilities of obtaining certain combinations of candidate DNPs are calculated using the information from the multi-alignments. The use of DNPs and combinations of DNPs will allow for optimal and rapid assemblies of repeated regions. This method can solve repeats that differ in only two positions in a read length, which is the theoretical limit for repeat separation. We predict that this method will be highly useful in shotgun sequencing in the future.     

Low intraspecific competitive fitness in a triazine-resistant,nearly nuclear-isogenic line of Brassica napus

The maternally-inherited triazine-resistant biotypes that have appeared usually have had a much reduced competitive fitness. As such studies did not use nuclear isogenic material, we tested rapeseed cv. Regent that had had triazine resistance introduced from Brassica campestris and was then extensively backcrossed to cv. Regent. Seeds of each biotype were alternated at 5-cm spacing to ascertain competitive fitness and various growth parameters were followed. The fresh weight, dry weight, number and weights of siliques (seed pods) and yield of seed of the interplanted triazine-resistant biotype were all less than one-third of the susceptible biotype.     

Expression, purification and preliminary biochemical and structural characterization of the leucine rich repeat namesake domain of leucine rich repeat kinase 2

Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of familial Parkinson's disease. Much research effort has been directed towards the catalytic core region of LRRK2 composed of GTPase (ROC, Ras of complex proteins) and kinase domains and a connecting COR (C-terminus of ROC) domain. In contrast, the precise functions of the protein-protein interaction domains, such as the leucine-rich repeat (LRR) domain, are not known. In the present study, we modeled the LRRK2 LRR domain (LRR(LRRK2)) using a template assembly approach, revealing the presence of 14 LRRs. Next, we focused on the expression and purification of LRR(LRRK2) in Escherichia coli. Buffer optimization revealed that the protein requires the presence of a zwitterionic detergent, namely Empigen BB, during solubilization and the subsequent purification and characterization steps. This indicates that the detergent captures the hydrophobic surface patches of LRR(LRRK2) thereby suppressing its aggregation. Circular dichroism (CD) spectroscopy measured 18% α-helices and 21% β-sheets, consistent with predictions from the homology model. Size exclusion chromatography (SEC) and dynamic light scattering measurements showed the presence of a single species, with a Stokes radius corresponding to the model dimensions of a protein monomer. Furthermore, no obvious LRR(LRRK2) multimerization was detected via cross-linking studies. Finally, the LRR(LRRK2) clinical mutations did not influence LRR(LRRK2) secondary, tertiary or quaternary structure as determined via SEC and CD spectroscopy. We therefore conclude that these mutations are likely to affect putative LRR(LRRK2) inter- and intramolecular interactions.     

NeXML: rich, extensible, and verifiable representation of comparative data and metadata

In scientific research, integration and synthesis require a common understanding of where data come from, how much they can be trusted, and what they may be used for. To make such an understanding computer-accessible requires standards for exchanging richly annotated data. The challenges of conveying reusable data are particularly acute in regard to evolutionary comparative analysis, which comprises an ever-expanding list of data types, methods, research aims, and subdisciplines. To facilitate interoperability in evolutionary comparative analysis, we present NeXML, an XML standard (inspired by the current standard, NEXUS) that supports exchange of richly annotated comparative data. NeXML defines syntax for operational taxonomic units, character-state matrices, and phylogenetic trees and networks. Documents can be validated unambiguously. Importantly, any data element can be annotated, to an arbitrary degree of richness, using a system that is both flexible and rigorous. We describe how the use of NeXML by the TreeBASE and Phenoscape projects satisfies user needs that cannot be satisfied with other available file formats. By relying on XML Schema Definition, the design of NeXML facilitates the development and deployment of software for processing, transforming, and querying documents. The adoption of NeXML for practical use is facilitated by the availability of (1) an online manual with code samples and a reference to all defined elements and attributes, (2) programming toolkits in most of the languages used commonly in evolutionary informatics, and (3) input-output support in several widely used software applications. An active, open, community-based development process enables future revision and expansion of NeXML.     

Expression of synthetic genes coding for completely new, nutritionally rich, artificial proteins

Synthetic genes (A, AB and AHB) constructed and cloned into pKK233-2 vector were recloned from the parent plasmid into the new procaryotic expression vectors pGFY221N and pBI052. Gene AF-B (coding for all amino acids besides phenylalanine) was obtained by 'cassette mutagenesis' from gene AB. The plasmid pGFY221N was constructed from pGFY218L by replacing the PstI by an NcoI site; plasmid pBI052 was derived from pGFY221N through replacing the 221-bp EcoRI/NcoI fragment with a synthetic DNA segment of 52 bp representing the Escherichia coli atpE gene translational initiation region. The genes A, AB, AHB and AF-B in the vector pGFY221N were expressed with a six-amino-acid-long leader sequence; in pBI052 the genes were expressed directly. In vitro expression experiments were successfully with all the genes except with the AHB gene integrated into pGFY221N. In the E. coli minicell system expression was demonstrated with the A gene in pGFY221N and the AF-B and AHB genes in pBI052. Complete translation of the expressed genes AB, AF-B and AHB in either the in vitro or in vivo systems could be shown by using 35S-labelled N-terminal methionine and C-terminal cysteine. Both amino acids occur only once in the peptide sequences.     

Preferred hand use in the japanese macaque troop,arashiyama-R,during visually guided reaching for food pellets

A troop of Japanese macaques, which consisted of about 45 monkeys and was raised at the Primate Research Institute, Kyoto University, was observed during the period from April to June 1988, to evaluate the preferred choice of hand when reaching for food pellets. Nineteen monkeys showed a consistent left-hand preference, 5 monkeys showed a consistent right-hand preference, and the remaining 20 monkeys did not reveal a preference for either hand. Monkeys of more than 8 years of age tended to exhibit a greater left-hand preference with a lower incidence of absence of preference. A tendency to use either left or right hand increased with increasing age: the correlation ratio between age in years and the index to use either hand, designated as the laterality index, was significant (t-test,p<0.001,N=42). Children of mothers with a left-hand preference tended to show a left-hand preference.