Orientation enhancement in early visual processing can explain time course of brightness contrast and White’s illusion

Dynamics of orientation tuning in V1 indicates that computational model of V1 should not only comprise of bank of static spatially oriented filters but also include the contribution for dynamical response facilitation or suppression along orientation. Time evolution of orientation response in V1 can emerge due to time- dependent excitation and lateral inhibition in the orientation domain. Lateral inhibition in the orientation domain suggests that Ernst Mach’s proposition can be applied for the enhancement of initial orientation distribution that is generated due to interaction of visual stimulus with spatially oriented filters and subcortical temporal filter. Oriented spatial filtering that appears much early ( $<$ 70 ms) in the sequence of visual information processing can account for many of the brightness illusions observed at steady state. It is therefore expected that time evolution of orientation response might be reflecting in the brightness percept over time. Our numerical study suggests that only spatio-temporal filtering at early phase can explain experimentally observed temporal dynamics of brightness contrast illusion. But, enhancement of orientation response at early phase of visual processing is the key mechanism that can guide visual system to predict the brightness by “Max-rule” or “Winner Takes All” (WTA) estimation and thus producing White’s illusions at any exposure.     

Is visual processing in the dorsal stream accessible to consciousness?

There are two highly interconnected clusters of visually responsive areas in the primate cortex. These two clusters have relatively few interconnections with each other, though those interconnections are undoubtedly important. One of the two main clusters (the dorsal stream) links the primary visual cortex (V1) to superior regions of the occipito-parietal cortex, while the other (the ventral stream) links V1 to inferior regions of the occipito-temporal cortex. According to our current understanding of the functional anatomy of these two systems, the dorsal stream's principal role is to provide real-time 'bottom-up' visual guidance of our movements online. In contrast, the ventral stream, in conjunction with top-down information from visual and semantic memory, provides perceptual representations that can serve recognition, visual thought, planning and memory offline. In recent years, this interpretation, initially based chiefly on studies of non-human primates and human neurological patients, has been well supported by functional MRI studies in humans. This perspective presents empirical evidence for the contention that the dorsal stream governs the visual control of movement without the intervention of visual awareness.     

Crucial role of the Rcl1p–Bms1p interaction for yeast pre-ribosomal RNA processing

The essential Rcl1p and Bms1p proteins form a complex required for 40S ribosomal subunit maturation. Bms1p is a GTPase and Rcl1p has been proposed to catalyse the endonucleolytic cleavage at site A₂ separating the pre-40S and pre-60S maturation pathways. We determined the 2.0 Å crystal structure of Bms1p associated with Rcl1p. We demonstrate that Rcl1p nuclear import depends on Bms1p and that the two proteins are loaded into pre-ribosomes at a similar stage of the maturation pathway and remain present within pre-ribosomes after cleavage at A₂. Importantly, GTP binding to Bms1p is not required for the import in the nucleus nor for the incorporation of Rcl1p into pre-ribosomes, but is essential for early pre-rRNA processing. We propose that GTP binding to Bms1p and/or GTP hydrolysis may induce conformational rearrangements within the Bms1p-Rcl1p complex allowing the interaction of Rcl1p with its RNA substrate.     

Prognostic impact of Metadherin–SND1 interaction in colon cancer

The interaction between Metadherin (MTDH) and Staphylococcal nuclease homology domain containing 1 (SND1) is involved in tumorigenesis and tumor progression of several human malignancies. However, its roles in colon cancer are still unclear. To investigate the clinical value of MTDH and SND1 expression in colon cancer. Immunohistochemical staining was performed to detect the expression of MTDH and SND1 using human colon cancer and their corresponding non-cancerous colon tissues from 196 patients’ biopsies. Positive expression of MTDH and SND1 were both increased in colon cancer tissues compared to paired non-cancerous colon tissues. There was a positive correlation between MTDH and SND1 expression in colon cancer tissues (r?=?0.86, p?<?0.001). In addition, their positive expression were both significantly associated with nodal status (both p?=?0.02), pathological stage (p?=?0.006 and 0.008, respectively) and differentiation (both p?=?0.03). Moreover, the overall survival in colon cancer patients with positive expression of MTDH and SND1 were significantly shorter than those without their expression (both p?=?0.01). Furthermore, multivariate Cox regression analysis suggested that positive expression of MTDH and SND1 was an independent poor prognostic predictor in colon cancer. Our data suggest that the increased expression of MTDH and/or SND1 is closely related to carcinogenesis, progression, and prognosis of colon cancer. The co-expression of MTDH/SND1 may be a novel distinctive marker to benefit us in prediction of the prognosis in colon cancer.     

Engineering-approach accelerates computational understanding of V1–V2 neural properties

We present two computational models (i) long-range horizontal connections and the nonlinear effect in V1 and (ii) the filling-in process at the blind spot. Both models are obtained deductively from standard regularization theory to show that physiological evidence of V1 and V2 neural properties is essential for efficient image processing. We stress that the engineering approach should be imported to understand visual systems computationally, even though this approach usually ignores physiological evidence and the target is neither neurons nor the brain.

III–V dry processing from R&D to production

Issues relating to the use of III–V dry processing for device fabrication in R&D and production are critically important. Of particular concern are current process and equipment limits which can prevent scaling to full device production.     

Mutators in SACCHAROMYCES CEREVISIAE: MUT1–1, MUT1–2 and MUT2–1

The purpose of this study was to characterize two mutator stocks of yeast which were induced and selected on the basis of high spontaneous reversion rates of the suppressible "ochre" nonsense allele lys1-1. In the mutator stock VA-3, a single mutation, designated mut1-1, is responsible for the increase in the reversion rate of the ochre alleles lys1-1 and arg4-17. In stock VA-105, there are two separate mutator mutations. Tetrad analysis data showed these two loci are loosely linked. Based on complementation data, one of these mutations is at the same locus as mut1-1 and designated mut1-2. The second mutator of stock VA-105 was designated mut2-1. All three mutators are recessive. Both mut1-1 and mut1-2 give a high mutation rate for ochre nonsense suppressor (SUP) loci, but not for the ochre nonsense alleles. On the contrary, the mutation rates of the ochre alleles are greatly reduced. With the mutant mut2-1 there were mutations at both the lys1-1 site and its suppressors; mut2-1 is as effective as mut1-2 but not as effective as mut1-1 in inducing reversions of a missense mutant, his1-7. Neither mut1-1, mut1-2 nor mut2-1 were effective in inducing reversions of a putative frameshift mutation, hom3-10, or in inducing forward mutations to canavanine resistance.     

Gut microbiome–immune system interaction in reptiles

Reptiles are ectothermic amniotes in a world dominated by endotherms. Reptiles originated more than 300 million years ago and they often dwell in polluted environments which may expose them to pathogenic micro-organisms, radiation and/or heavy metals. Reptiles also possess greater longevity and may live much longer than similar-sized land mammals, for example, turtles, tortoises, crocodiles and tuatara are long-lived reptiles living up to 100 years or more. Many recent studies have emphasized the pivotal role of the gut microbiome on its host; thus, we postulated that reptilian gut microbiome and/or its metabolites and the interplay with their robust immune system may contribute to their longevity and overall hardiness. Herein, we discuss the composition of the reptilian gut microbiome, immune system–gut microbiome cross-talk, antimicrobial peptides, reptilian resistance to infectious diseases and cancer, ageing, as well the current knowledge of the genome and epigenome of these remarkable species. Preliminary studies have demonstrated that microbial gut flora of reptiles such as crocodiles, tortoises, water monitor lizard and python exhibit remarkable anticancer and antibacterial properties, as well as comprise novel gut bacterial metabolites and antimicrobial peptides. The underlying mechanisms between the gut microbiome and the immune system may hold clues to developing new therapies overall for health, and possible extrapolation to exploit the ancient defence systems of reptiles for Homo sapiens benefit.     

Cell–cell communication in Arabidopsis early embryogenesis

The basic body plan of the adult plant is established during embryogenesis, resulting in the juvenile form of the seedling. Arabidopsis embryogenesis is distinguished by a highly regular pattern of cell divisions. Some of these divisions are asymmetric, generating daughter cells with different fates. However, their subsequent differentiation might still depend on cell–cell communication to be fully accomplished or maintained. In some cases, cell fate specification solely depends on cell–cell communication that in general plays an important role in the generation of positional information within the embryo. Although auxin-dependent signalling has received much attention, other ways of cell–cell communication have also been demonstrated or suggested. This review focuses on aspects of pattern formation and cell–cell communication during Arabidopsis embryogenesis up to the mid-globular stage of development.     

Olfactory learning and behaviour are ‘insulated’ against visual processing in larval Drosophila

We investigate the organization of behaviour across sensory modalities, using larval Drosophila melanogaster. We ask whether olfactory learning and behaviour are affected by visual processing. We find that: (1) Visual choice does not affect concomitant odour choice. (2) Visual context does not influence odour learning, nor do changes of visual context between training and test affect retrieval of odour memory. (3) Larvae cannot solve a biconditional discrimination task, despite generally permissive conditions. In this task, larvae are required to establish conditional associations: in light, one odour is rewarded and the other one is not, whereas in dark the opposite contingency is established. After such training, choice between the two odours is equal under light and dark testing conditions, suggesting that larvae do not establish odour memories specifically for one visual context only. Together, these data suggest that, in larval Drosophila, olfactory learning and behaviour are ‘insulated’ against visual processing.     

Spike-induced interference in auditory sensory processing in Landau–Kleffner syndrome

Objectives: Landau–Kleffner Syndrome (LKS) is an epileptic syndrome characterised by a deficit in language comprehension and production, paroxysmal epileptiform activity in the posterior temporal leads, and by the inconsistent presence of epileptic fits. Its interest lies in the fact that it stands as a model for the study of interference of epileptiform activity on cognitive function, although the pathophysiology of the decline in language skills that follows its onset has not yet been clarified.Methods: We have recorded spike-triggered auditory evoked responses in a group of 6 children with LKS, to investigate whether the occurrence of individual EEG paroxysms is able per se to induce a decline in the response of the auditory cortex.Results: Results have indicated that left hemisphere spikes are associated with a greater reduction in amplitude and an increase in latency of the N1, than spikes occurring in the right hemisphere. No stable change in the evoked response has been detected outside of the EEG paroxysm.Conclusions: We postulate EEG interictal activity is able to induce impairment in processing auditory information and that this may play a role in the pathogenesis of language deficit (deficiency?) in LKS.     

Signal molecules in the peanut–bradyrhizobia interaction

Main nodulation signal molecules in the peanut–bradyrhizobia interaction were examined. Flavonoids exuded by Arachis hypogaea L. cultivar Tegua were genistein, daidzein and chrysin, the latest being released in lower quantities. Thin layer chromatography analysis from genistein-induced bacterial cultures of three peanut bradyrhizobia resulted in an identical Nod factor pattern, suggesting low variability in genes involved in the synthesis of these molecules. Structural study of Nod factor by mass spectrometry and NMR analysis revealed that it shares a variety of substituents with the broad-host-range Rhizobium sp. NGR234 and Bradyrhizobium spp. Nodulation assays in legumes nodulated by these rhizobia demonstrated differences between them and the three peanut bradyrhizobia. The three isolates were classified as Bradyrhizobium sp. Their fixation gene nifD and the common nodulation genes nodD and nodA were also analyzed. Accession numbers: AY427207, EF202193, EF158295 (16S rRNA gene of strains NLH25, NOD31 and NDEHE, respectively); DQ295199, DQ295200, DQ295201 (Partial nifD gene sequences of strains NLH25, NOD31 and NDEHE, respectively).     

Zooplankton in Svalbard fjords on the Atlantic–Arctic boundary

Zooplankton abundance and community structures were studied in three west Spitsbergen fjords at the beginning of the warm phase, which seem to have entered in 2006. Sampling was conducted in summer 2007 at stations distributed along transects in Hornsund, Isfjorden and Kongsfjorden. Variations in zooplankton standing stocks and community structures (assessing taxonomic diversity and zoogeographical affiliations) were analysed in relation to the environmental variables using multivariate techniques. The hydrographic conditions in Hornsund were influenced by the cold Arctic Water, whereas those in Isfjorden and especially in Kongsfjorden were, to a greater extent, under the influence of the warm Atlantic Water. High abundances of both meroplankton and holoplankton organisms were observed in Kongsfjorden, with high contributions of boreal and ubiquitous species (Calanus finmarchicus and Oithona similis, respectively). In Hornsund at the same time, the zooplankton consisted mainly of boreo-Arctic and Arctic species, the abundances of which were comparable along the West Spitsbergen Shelf. Our results indicate that the difference in hydrography had measurable effects on the zooplankton community in the study area. Furthermore, by comparing regions of contrasting oceanographic conditions, we present evidence as to how the zooplankton structure will change in the Arctic ecosystems if the warming trends continue to operate with the same dynamics. The advection of Atlantic waters to the Arctic seas may lead to changes in zooplankton structure, with increased abundance and contributions of boreal and small ubiquitous species. The ‘warmer Arctic fjords’ scenarios may also induce more rapid development of both holoplankton and meroplankton populations and, consequently, modify the trophic interactions in plankton communities.     

The epidermal lipid barrier in microbiome–skin interaction

The corneocyte layers forming the upper surface of mammalian skin are embedded in a lamellar-membrane matrix which repels harmful molecules while retaining solutes from subcutaneous tissues. Only certain bacterial and fungal taxa colonize skin surfaces. They have ways to use epidermal lipids as nutrients while resisting antimicrobial fatty acids. Skin microorganisms release lipophilic microbe-associated molecular pattern (MAMP) molecules which are largely retained by the epidermal lipid barrier. Skin barrier defects, as in atopic dermatitis, impair lamellar-membrane integrity, resulting in altered skin microbiomes, which then include the pathogen Staphylococcus aureus. The resulting increased penetration of MAMPs and toxins promotes skin inflammation. Elucidating how microorganisms manipulate the epidermal lipid barrier will be key for better ways of preventing inflammatory skin disorders.     

Advances in the study of protein–DNA interaction

Protein-DNA interaction plays an important role in many biological processes. The classical methods and the novel technologies advanced have been developed for the interaction of protein-DNA. Recent developments of these methods and research achievements have been reviewed in this paper.     

Research advances in the Pyrenophora teres–barley interaction

Pyrenophora teres f. teres and P. teres f. maculata are significant pathogens that cause net blotch of barley. An increased number of loci involved in P. teres resistance or susceptibility responses of barley as well as interacting P. teres virulence effector loci have recently been identified through biparental and association mapping studies of both the pathogen and host. Characterization of the resistance/susceptibility loci in the host and the interacting effector loci in the pathogen will provide a path for targeted gene validation for better-informed release of resistant barley cultivars. This review assembles concise consensus maps for all loci published for both the host and pathogen, providing a useful resource for the community to be used in pathogen characterization and barley breeding for resistance to both forms of P. teres.     

The role of stratifin in fibroblast–keratinocyte interaction

Stratifin is a member of 14-3-3 protein family, a highly conserved group of proteins constituted by seven isoforms. They are involved in numerous crucial intracellular functions such as cell cycle and apoptosis, regulation of signal transduction pathways, cellular trafficking, cell proliferation and differentiation, cell survival, and protein folding and processing, among others. At epidermal level, stratifin (also called 14-3-3 sigma) has been described as molecule with relevant functions. For instance, this isoform is a marker associated with keratinocyte differentiation. In this maturation process, the presence of dominant negative molecules of p53 induces a “stemness condition” of keratinocyte precursor cells and suppression of stratifin expression. In addition, the recently described keratinocyte-releasable form of stratifin is involved in dermal fibroblast MMP-1 over-expression through c-Fos and c-Jun activity. This effect is mediated, at least in part, by p38 mitogen-activated protein kinase (MAPK). Other MMP family members such as stromelysin-1 (MMP-3), stromelysin-2 (MMP-10), neutrophil collagenase (MMP-8), and membrane-type MMP-24 (MT5-MMP) are also up-regulated by stratifin. Within fibroproliferative disorder of skin, hypertrophic scar and keloids exhibit a high content of collagen, proteoglycans, and fibronectin. Thus, the MMP profile induced by stratifin is an interesting starting point to establish new therapeutic tools to control the process of wound healing. In this review, we will focus on site of synthesis and mode of action of stratifin in skin and wound healing.     

Mechanical filtering by the boundary layer and fluid–structure interaction in the superficial neuromast of the fish lateral line system

A great diversity of aquatic animals detects water flow with ciliated mechanoreceptors on the body's surface. In order to understand how these receptors mechanically filter signals, we developed a theoretical model of the superficial neuromast in the fish lateral line system. The cupula of the neuromast was modeled as a cylindrical beam that deflects in response to an oscillating flow field. Its accuracy was verified by comparison with prior measurements of cupular deflection in larval zebrafish (Danio rerio). The model predicts that the boundary layer of flow over the body attenuates low-frequency stimuli. The fluid-structure interaction between this flow and the cupula attenuates high-frequency stimuli. The number and height of hair cell kinocilia and the dimensions of the cupular matrix determine the range of intermediate frequencies to which a neuromast is sensitive. By articulating the individual mechanical contributions of the boundary layer and the components of cupular morphology, this model provides the theoretical framework for understanding how a hydrodynamic receptor filters flow signals.     

Identification of structural motifs in the E2 glycoprotein of Chikungunya involved in virus–host interaction

Chikungunya fever is one of the reemerging vector-borne diseases. It has become a major global health problem especially in the developing countries. There are no vaccines or specific antiviral drugs available to date. This study reports small molecule inhibitors of envelope glycoprotein 2 (E2 glycoprotein) which are predicted based on Chikungunya virus–host interactions. E2 glycoprotein of Chikungunya virus interacts at 216 residue of the host receptor protein which plays a vital role in initiating infection. Understanding the structural aspects of E2 glycoprotein is crucial to develop specific inhibitors to prevent the virus binding from host receptors. In silico method was adopted to predict the sequence motifs of envelope protein, as the method like yeast two hybrid system is laborious, time consuming, and costly. The E2 glycoprotein structure of the Indian isolate was modeled using two templates (2XFC and 3JOC) and then validated. The class III PDZ domain binding motif was found to be identified at 213–216 amino acids. The corresponding peptide structures which recognize the PDZ domain binding motif were identified by the literature search and were used for generating five point pharmacophore model (ADDDR) containing acceptor, donor and aromatic ring features. Databases such as Asinex, TosLab and Maybridge were searched for the matches for the predicted pharmacophore model. Two compounds were identified as lead molecules as their glide score is?>?5?kcal/mol. Since the pharmacophore model is developed based on Chikungunya virus–host interaction, it can be used for designing promising antiviral lead compounds for the treatment of Chikungunya fever.An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:21