Laminar Cortical Dynamics of Visual Form and Motion Interactions During Coherent Object Motion Perception

How do visual form and motion processes cooperate to compute object motion when each process separately is insufficient? A 3D FORMOTION model specifies how 3D boundary representations, which separate figures from backgrounds within cortical area V2, capture motion signals at the appropriate depths in MT; how motion signals in MT disambiguate boundaries in V2 via MT-to-Vl-to-V2 feedback; how sparse feature tracking signals are amplified; and how a spatially anisotropic motion grouping process propagates across perceptual space via MT-MST feedback to integrate feature-tracking and ambiguous motion signals to determine a global object motion percept. Simulated data include: the degree of motion coherence of rotating shapes observed through apertures, the coherent vs. element motion percepts separated in depth during the chopsticks illusion, and the rigid vs. non-rigid appearance of rotating ellipses.

Boundary, Brightness, and Depth Interactions During Preattentive Representation and Attentive Recognition of Figure and Ground

This article applies a recent theory of 3-D biological vision, called FACADE Theory, to explain several percepts which Kanizsa pioneered. These include 3-D pop-out of an occluding form in front of an occluded form, leading to completion and recognition of the occluded form; 3-D transparent and opaque percepts of Kanizsa squares, with and without Varin wedges; and interactions between percepts of illusory contours, brightness, and depth in response to 2-D Kanizsa images. These explanations clarify how a partially occluded object representation can be completed for purposes of object recognition, without the completed part of the representation necessarily being seen. The theory traces these percepts to neural mechanisms that compensate for measurement uncertainty and complementarity at individual cortical processing stages by using parallel and hierarchical interactions among several cortical processing stages. These interactions are modelled by a Boundary Contour System (BCS) that generates emergent boundary segmentations and a complementary Feature Contour System (FCS) that fills-in surface representations of brightness, color, and depth. The BCS and FCS interact reciprocally with an Object Recognition System (ORS) that binds BCS boundary and FCS surface representations into attentive object representations. The BCS models the parvocellular LGN→Interblob→Interstripe→V4 cortical processing stream, the FCS models the parvocellular LGN→Blob→Thin Stripe→V4 cortical processing stream, and the ORS models inferotemporal cortex.

Quadruped Gait Transitions from a Neural Pattern Generator with Arousal Modulated Interactions

A four-channel neural pattern generator is described in which both the frequency and the relative phase of oscillations are controlled by a scalar arousal or GO signal. The generator is used to simulate quadruped gaits; in particular, rapid transitions are simulated in the order - walk, trot, pace, and gallop - that occurs in the cat. Precise switching control is achieved by using an arousal dependent modulation of the model's inhibitory interactions. This modulation generates a different functional connectivity in a single network at different arousal levels.

A Neural Theory of Attentive Visual Search: Interactions of Boundary, Surface, Spatial, and Object Representations

Visual search data are given a unified quantitative explanation by a model of how spatial maps in the parietal cortex and object recognition categories in the inferotemporal cortex deploy attentional resources as they reciprocally interact with visual representations in the prestriate cortex. The model visual representations arc organized into multiple boundary and surface representations. Visual search in the model is initiated by organizing multiple items that lie within a given boundary or surface representation into a candidate search grouping. These items arc compared with object recognition categories to test for matches or mismatches. Mismatches can trigger deeper searches and recursive selection of new groupings until a target object io identified. This search model is algorithmically specified to quantitatively simulate search data using a single set of parameters, as well as to qualitatively explain a still larger data base, including data of Aks and Enns (1992), Bravo and Blake (1990), Chellazzi, Miller, Duncan, and Desimone (1993), Egeth, Viri, and Garbart (1984), Cohen and Ivry (1991), Enno and Rensink (1990), He and Nakayarna (1992), Humphreys, Quinlan, and Riddoch (1989), Mordkoff, Yantis, and Egeth (1990), Nakayama and Silverman (1986), Treisman and Gelade (1980), Treisman and Sato (1990), Wolfe, Cave, and Franzel (1989), and Wolfe and Friedman-Hill (1992). The model hereby provides an alternative to recent variations on the Feature Integration and Guided Search models, and grounds the analysis of visual search in neural models of preattentive vision, attentive object learning and categorization, and attentive spatial localization and orientation.

Laminar Cortical Dynamics of Visual Form and Motion Interactions During Coherent Object Motion Perception

How do visual form and motion processes cooperate to compute object motion when each process separately is insufficient? Consider, for example, a deer moving behind a bush. Here the partially occluded fragments of motion signals available to an observer must be coherently grouped into the motion of a single object. A 3D FORMOTION model comprises five important functional interactions involving the brain’s form and motion systems that address such situations. Because the model’s stages are analogous to areas of the primate visual system, we refer to the stages by corresponding anatomical names. In one of these functional interactions, 3D boundary representations, in which figures are separated from their backgrounds, are formed in cortical area V2. These depth-selective V2 boundaries select motion signals at the appropriate depths in MT via V2-to-MT signals. In another, motion signals in MT disambiguate locally incomplete or ambiguous boundary signals in V2 via MT-to-V1-to-V2 feedback. The third functional property concerns resolution of the aperture problem along straight moving contours by propagating the influence of unambiguous motion signals generated at contour terminators or corners. Here, sparse “feature tracking signals” from, e.g., line ends, are amplified to overwhelm numerically superior ambiguous motion signals along line segment interiors. In the fourth, a spatially anisotropic motion grouping process takes place across perceptual space via MT-MST feedback to integrate veridical feature-tracking and ambiguous motion signals to determine a global object motion percept. The fifth property uses the MT-MST feedback loop to convey an attentional priming signal from higher brain areas back to V1 and V2. The model's use of mechanisms such as divisive normalization, endstopping, cross-orientation inhibition, and longrange cooperation is described. Simulated data include: the degree of motion coherence of rotating shapes observed through apertures, the coherent vs. element motion percepts separated in depth during the chopsticks illusion, and the rigid vs. non-rigid appearance of rotating ellipses.

Emergence of Tri-Phasic Muscle Activation from the Non-linear Interactions of Central and Spinal Neural Network Circuits

The origin of the tri-phasic burst pattern, observed in the EMGs of opponent muscles during rapid self-terminated movements, has been controversial. Here we show by computer simulation that the pattern emerges from interactions between a central neural trajectory controller (VITE circuit) and a peripheral neuromuscularforce controller (FLETE circuit). Both neural models have been derived from simple functional constraints that have led to principled explanations of a wide variety of behavioral and neurobiological data, including, as shown here, the generation of tri-phasic bursts.

Normal and Amnesis Learning, Recognition, and Memory by a Neural Model of Cortico-Hippocampal Interactions

The processes by which humans and other primates learn to recognize objects have been the subject of many models. Processes such as learning, categorization, attention, memory search, expectation, and novelty detection work together at different stages to realize object recognition. In this article, Gail Carpenter and Stephen Grossberg describe one such model class (Adaptive Resonance Theory, ART) and discuss how its structure and function might relate to known neurological learning and memory processes, such as how inferotemporal cortex can recognize both specialized and abstract information, and how medial temporal amnesia may be caused by lesions in the hippocampal formation. The model also suggests how hippocampal and inferotemporal processing may be linked during recognition learning.

Physico-chemical properties and component interactions in high solids food systems

The present study aimed to investigate interactions of components in the high solids systems during storage. The systems included (i) lactose–maltodextrin (MD) with various dextrose equivalents at different mixing ratios, (ii) whey protein isolate (WPI)–oil [olive oil (OO) or sunflower oil (SO)] at 75:25 ratio, and (iii) WPI–oil– {glucose (G)–fructose (F) 1:1 syrup [70% (w/w) total solids]} at a component ratio of 45:15:40. Crystallization of lactose was delayed and increasingly inhibited with increasing MD contents and higher DE values (small molecular size or low molecular weight), although all systems showed similar glass transition temperatures at each aw. The water sorption isotherms of non-crystalline lactose and lactose–MD (0.11 to 0.76 aw) could be derived from the sum of sorbed water contents of individual amorphous components. The GAB equation was fitted to data of all non-crystalline systems. The protein–oil and protein–oil–sugar materials showed maximum protein oxidation and disulfide bonding at 2 weeks of storage at 20 and 40°C. The WPI–OO showed denaturation and preaggregation of proteins during storage at both temperatures. The presence of G–F in WPI–oil increased Tonset and Tpeak of protein aggregation, and oxidative damage of the protein during storage, especially in systems with a higher level of unsaturated fatty acids. Lipid oxidation and glycation products in the systems containing sugar promoted oxidation of proteins, increased changes in protein conformation and aggregation of proteins, and resulted in insolubility of solids or increased hydrophobicity concomitantly with hardening of structure, covalent crosslinking of proteins, and formation of stable polymerized solids, especially after storage at 40°C. We found protein hydration transitions preceding denaturation transitions in all high protein systems and also the glass transition of confined water in protein systems using dynamic mechanical analysis.

Characterisation of bacteriophage-host interactions in Lactococcus lactis

Lactococcus lactis is used extensively world-wide for the production of fermented dairy products. Bacteriophages (phages) infecting L. lactis can result in slow or incomplete fermentations, or may even cause total fermentation failure. Therefore, bacteriophages disrupting L. lactis fermentation are of economic concern. This thesis employed a multifaceted approach to investigate various molecular aspects of phage-host interaction in L. lactis. The genome sequence of an Irish dairy starter strain, the prophage-cured L. lactis subsp. cremoris UC509.9, was studied. The 2,250,427 bp circular chromosome represents the smallest among its sequenced lactococcal equivalents. The genome displays clear genetic adaptation to the dairy niche in the form of extensive reductive evolution. Gene prediction identified 2066 protein-encoding genes, including 104 which showed significant homology to transposase-specifying genes. Over 9 % of the identified genes appear to be inactivated through stop codons or frame shift mutations. Many pseudogenes were found in genes that are assigned to carbohydrate and amino acid transport and metabolism orthologous groups, reflecting L. lactis UC509.9’s adaptation to the lactose and casein-rich dairy environment. Sequence analysis of the eight plasmids of L. lactis revealed extensive adaptation to the dairy environment. Key industrial phenotypes were mapped and novel lactococcal plasmid-associated genes highlighted. In addition to chromosomally-encoded bacteriophage resistance systems, six functional such systems were identified, including two abortive infection systems, AbiB and AbiD1, explaining the observed phage resistance of L. lactis UC509.9 Molecular analysis suggests that the constitutive expression of AbiB is not lethal to cells, suggesting the protein is expressed in an un/inactivated form. Analysis of 936 species phage sk1-escape mutants of AbiB revealed that all such mutants harbour mutations in orf6, which encodes the major capsid protein. Results suggest that the major capsid protein is required for activation of the AbiB system, although this requires furrther investigations. Temporal transcriptomes of L. lactis UC509.9 undergoing lytic infection with either one of two distinct bacteriophages, Tuc2009 and c2, was determined and compared to the transcriptome of uninfected UC509.9 cells. Whole genome microarrays performed at various time-points post-infection demonstrated a rather modest impact on host transcription. Alterations in the UC509.9 transcriptome during lytic infection appear phage-specific, with a relatively small number of differentially transcribed genes shared between infection with either Tuc2009 or c2. Transcriptional profiles of both bacteriophages during lytic infection was shown to generally correlate with previous studies and allowed the confirmation of previously predicted promoter sequences. Bioinformatic analysis of genomic regions encoding the presumed cell wall polysaccharide (CW PS) biosynthesis gene cluster of several strains of L. lactis was performed. Results demonstrate the presence of three dominant genetic types of this gene cluster, termed type A, B and C. These regions were used for the development of a multiplex PCR to identify CW PS genotype of various lactococcal strains. Analysis of 936 species phage receptor binding protein phylogeny (RBP) and CW PS genotype revealed an apparent correlation between RBP phylogeny and CW PS type, thereby providing a partial explanation for the observed narrow host range of 936 phages. Further analysis of the genetic locus encompassing the presumed CW PS biosynthesis operon of eight strains identified as belonging to the CW PS C (geno)type, revealed the presence of a variable region among the examined strains. The obtained comparative analysis allowed for the identification of five subgroups of the C type, named C1 to C5. We purified an acidic polysaccharide from the cell wall of L. lactis 3107 (C2 subtype) and confirmed that it is structurally different from the CW PS of the C1 subtype L. lactis MG1363. Combinations of genes from the variable region of C2 subtype were amplified from L. lactis 3107 and introduced into a mutant of the C1 subtype L. lactis NZ9000 (a direct derivative of MG1363) deficient in CW PS biosynthesis. The resulting recombinant mutant synthesized a CW PS with a composition characteristic for that of the C2 subtype L. lactis 3107 and not the wildtype C1 L. lactis NZ9000. The recombinant mutant exhibited a changed phage resistance/sensitivity profile consistent with that of L. lactis 3107, which unambiguously demonstrated that L. lactis 3107 CW PS is the host cell surface receptor of two bacteriophages belonging to the P335 species as well as phages that are member of the 936 species. The research presented in this thesis has significantly advanced our understanding of L. lactis bacteriophage-host interactions in several ways. Firstly, the examination of plasmidencoded bacteriophage resistance systems has allowed inferences to be made regarding the mode of action of AbiB, thereby providing a platform for further elucidation of the molecular trigger of this system. Secondly, the phage infection transcriptome data presented, in addition to previous work, has made L. lactis a model organism in terms of transcriptomic studies of bacteriophage-host interactions. And finally, the research described in this thesis has for the first time explicitly revealed the nature of a carbohydrate bacteriophage receptor in L. lactis, while also providing a logical explanation for the observed narrow host ranges exhibited by 936 and P335 phages. Future research in discerning the structures of other L. lactis CW PS, combined with the determination of the molecular interplay between receptor binding proteins of these phages and CW PS will allow an in depth understanding of the mechanism by which the most prevalent lactococcal phages identify and adsorb to their specific host.

The impact of host-microbe interactions on murine colonic secretomotor function

The overall objective of this thesis was to gain further insight into the mechanisms underlying commensal microbial influences on intestinal ion transport. In this regard, I examined the impact of commensal host-microbe interactions on colonic secretomotor function in mouse. I first examined the influence of two different probiotic (microorganisms which, when given in adequate amounts, can confer health benefits upon the host) strains, Bifidobacterium infantis 35624 and L. salivarius UCC118 on active colonic ion transport in the mouse, using the Ussing Chamber. I found that both probiotics appear to have converging effects on ion transport at a functional level. However, L. salivarius UCC118 may preferentially inhibit neurally-evoked ion transport. Next I examined the impact of the host microbiota itself on both baseline and stimulated colonic secretomotor function as well as probiotic induced changes in ion transport. I provide further evidence that the microbiota is capable of mediating alterations in colonic ion transport, and specifically suggests that it can influence cAMP-mediated responses. Finally, it has been well documented that many probiotics elicit their effects via secreted bioactives, therefore, I studied the effects of microbially produced GABA, contained in supernatants from the commensal microbe Lactobacillus brevis DPC6108, on colonic secretomotor function. In conclusion, I believe that commensal microbes have an important and strain specific functional influence on colonic ion transport and secretomotor function and these effects can be mediated via extracellular bioactives. Moreover, I believe that functional ex-vivo studies such as those carried out in this thesis have a critical role to play in our future understanding of host-microbe interactions in the gut.

Exploring the physicochemical basis of cheese texture, rheology and functionality, with emphasis on cation-casein interactions

The physicochemical properties of cheese and milk gels are greatly influenced by molecular interactions between the casein proteins involving calcium. Novel experiments were designed to investigate the relationship between insoluble caseinbound cations and rheological properties of Cheddar cheese and rennet-induced milk gels. Cheddar cheese and rennet-induced milk gels were supplemented with Mg2+ or Sr2+ to compare their effects on their rheological properties to those previously reported in literature for Ca2+ supplementation. Sr2+ displayed behaviour similar to Ca2+ as observed by its ability to increase the rigidity of cheese and rennet milk gels and also decrease cheese meltability. Mg+2 had no influence on cheese rheological properties and was greatly inferior to Ca2+ and Sr2+ in its ability to increase rennet milk gel elasticity. Cheddar cheese was supplemented with the calcium-chelating salts trisodium citrate, disodium hydrogen phosphate or disodium EDTA, in an attempt to reduce the CCP content of cheese and thereby modify its rheological and functional properties. TSC and EDTA were successful in decreasing cheese CCP, whereas DSP caused an initial increase in CCP content. Cheddar cheese was supplemented with chlorides of iron, copper and zinc at salting to investigate the effects of concentrations of these elements in excess of those found innately or commonly in fortification studies, with emphasis on mineral equilibria changes and resultant alteration of rheological properties. Zinc addition was the only added metal that significantly influenced cheese rheological properties, leading to an increase in cheese rigidity and decreased cheese melt at elevated temperatures. Gum tragacanth was used as a fat-replacer in the manufacture of reduced-fat Cheddar cheese, in an attempt to improve the rheological, functional and sensory properties of reduced-fat Cheddar. Overall, the experimental work reported in this thesis generated new knowledge and theories about how casein-mineral interactions influence rheological properties of casein systems.

The relevance of bacterial isoprenoid biosynthetic pathways for host-microbe interactions

This thesis was undertaken to investigate the relevance of two bacterial isoprenoid biosynthetic pathways (Mevalonate (MVAL) and 2-C-methyl-D-erythritol 4-phosphate (MEP)) for host-microbe interactions. We determined a significant reduction in microbial diversity in the murine gut microbiota (by next generation sequencing) following oral administration of a common anti-cholesterol drug Rosuvastatin (RSV) that targets mammalian and bacterial HMG-CoA reductase (HMG-R) for inhibition of MVAL formation. In tandem we identified significant hepatic and intestinal off-target alterations to the murine metabolome indicating alterations in inflammation, bile acid profiles and antimicrobial peptide synthesis with implications on community structure of the gastrointestinal microbiota in statin-treated animals. However we found no effect on local Short Chain Fatty Acid biosynthesis (metabolic health marker in our model). We demonstrated direct inhibition of bacterial growth in-vitro by RSV which correlated with reductions in bacterial MVAL formation. However this was only at high doses of RSV. Our observations demonstrate a significant RSV-associated impact on the gut microbiota prompting similar human analysis. Successful deletion of another MVAL pathway enzyme (HMG-CoA synthase (mvaS)) involved in Listeria monocytogenes EGDe isoprenoid biosynthesis determined that the enzyme is non-essential for normal growth and in-vivo pathogenesis of this pathogen. We highlight potential evidence for alternative means of synthesis of the HMG-CoA substrate that could render mvaS activity redundant under our test conditions. Finally, we showed by global gene expression analysis (Massive Analysis of cDNA Ends (MACE RNA-seq) a significant role for the penultimate MEP pathway metabolite (E)-4-hydroxy-3-methyl-2-but-2-enyl pyrophosphate (HMBPP) in significant up regulation of genes of immunity and antigen presentation in THP-1 cells at nanomolar levels. We infected THP-1 cells with wild type or HMBPP under/over-producing L. monoctyogenes EGDe mutants and determined subtle effects of HMBPP upon overall host responses to Listeria infection. Overall our findings provide greater insights regarding bacterial isoprenoid biosynthetic pathways for host-microbe/microbe-host dialogue.

Infant milk formula manufacture: process and compositional interactions in high dry matter wet-mixes

Infant milk formula (IMF) is fortified milk with composition based on the nutrient content in human mother's milk, 0 to 6 months postpartum. Extensive medical and clinical research has led to advances in the nutritional quality of infant formula; however, relatively few studies have focused on interactions between nutrients and the manufacturing process. The objective of this research was to investigate the impact of composition and processing parameters on physical behaviour of high dry matter (DM) IMF systems with a view to designing more sustainable manufacturing processes. The study showed that commercial IMF, with similar compositions, manufactured by different processes, had markedly different physical properties in dehydrated or reconstituted state. Commercial products made with hydrolysed protein were more heat stable compared to products made with intact protein, however, emulsion quality was compromised. Heat-induced denaturation of whey proteins resulted in increased viscosity of wet-mixes, an effect that was dependant on both whey concentration and interactions with lactose and caseins. Expanding on fundamental laboratory studies, a novel high velocity steam injection process was developed whereby high DM (60%) wet-mixes with lower denaturation/viscosity compared to conventional processes could be achieved; powders produced using this process were of similar quality to those manufactured conventionally. Hydrolysed proteins were also shown to be an effective way of reducing viscosity in heat-treated high DM wet-mixes. In particular, using a whey protein concentrate whereby β-Lactoglobulin was selectively hydrolysed, i.e., α-Lactalbumin remained intact, reduced viscosity of wet-mixes during processing while still providing good emulsification. The thesis provides new insights into interactions between nutrients and/or processing which influence physical stability of IMF both in concentrated liquid and powdered form. The outcomes of the work have applications in such areas as; increasing the DM content of spray drier feeds in order to save energy, and, controlling final powder quality.

Intrastereomic proteins from the asteroid Asterias rubens. separation, partial characterization ,and interactions with growing calcite crystals

info:eu-repo/semantics/published

Binding of MetJ repressor to specific and nonspecific DNA and effect of S-adenosylmethionine on these interactions.

We have used analytical ultracentrifugation to characterize the binding of the methionine repressor protein, MetJ, to synthetic oligonucleotides containing zero to five specific recognition sites, called metboxes. For all lengths of DNA studied, MetJ binds more tightly to repeats of the consensus sequence than to naturally occurring metboxes, which exhibit a variable number of deviations from the consensus. Strong cooperative binding occurs only in the presence of two or more tandem metboxes, which facilitate protein-protein contacts between adjacent MetJ dimers, but weak affinity is detected even with DNA containing zero or one metbox. The affinity of MetJ for all of the DNA sequences studied is enhanced by the addition of SAM, the known cofactor for MetJ in the cell. This effect extends to oligos containing zero or one metbox, both of which bind two MetJ dimers. In the presence of a large excess concentration of metbox DNA, the effect of cooperativity is to favor populations of DNA oligos bound by two or more MetJ dimers rather than a stochastic redistribution of the repressor onto all available metboxes. These results illustrate the dynamic range of binding affinity and repressor assembly that MetJ can exhibit with DNA and the effect of the corepressor SAM on binding to both specific and nonspecific DNA.