Data-driven modelling of visual receptive fields: comparison between the generalized quadratic model and the nonlinear input model.

Neurons in primary visual cortex (V1) display a range of sensitivity in their response to translations of their preferred visual features within their receptive field: from high specificity to a precise position through to complete invariance. This visual feature selectivity and invariance is frequently modelled by applying a selection of linear spatial filters to the input image, that define the feature selectivity, followed by a nonlinear function that combines the filter outputs, that defines the invariance, to predict the neural response. We compare two such classes of model, that are both popular and parsimonious, by applying them to data from multielectrode recordings from cat primary visual cortex in response to spatially white Gaussian noise: the Generalized Quadratic Model (GQM) and the Nonlinear Input Model (NIM). These two classes of model differ primarily in that the NIM can accommodate a greater diversity in the form of nonlinearity that is applied to the outputs of the filters. After fitting both classes of model to a database of 342 single units, we analyze the qualitative and quantitative differences in the visual feature processing performed by the two models and their ability to predict neural response. We find that the NIM predicts response rates on a held-out data at least as well as the GQM for 95% of single units. Superior performance occurs predominantly for those units with above average spike rates and is largely due to the NIMs ability to capture aspects of the model's nonlinear function cannot be captured with the GQM rather than differences in the visual features being processed by the two different models. .

Functional changes of OsTrxm from reductase to molecular chaperone under heat shock stress.

Ubiquitous disulfide reductases, thioredoxins (Trxs), function in the redox balance of all living organisms. Although the roles of the rice (Oryza sativa) Trx m-type isoform (OsTrxm) in chloroplast development have been already published, biochemical and molecular functions of OsTrxm remain to be elucidated for decades. The OsTrxm and its two conserved active cysteine mutant (OsTrxm C95S/C98S, referred to as OsTrxmC/S) proteins in Arabidopsis thaliana were overexpressed to characterize in vivo roles of active cysteines of OsTrxm. Interestingly, the OsTrxm overexpressed variant plants were resistant to heat shock treatment. Especially OsTrxmC/S with higher molecular weight (HMW) complexes showed higher heat tolerance than OsTrxm with lower molecular weight (LMW) structure in Arabidopsis thaliana. To confirm the importance of active cysteines on structural changes under heat stress, OsTrxm and OsTrxmC/S proteins were bacterially expressed and isolated. This study found that two proteins have various structures ranging from LMW to HMW complexes and have potential functions as a disulfide reductase and a molecular chaperone, which has never been reported anywhere. The function of molecular chaperone predominated in the HMW complexes, whereas the disulfide reductase function was observed in LMW forms. These results suggest that the active cysteines of OsTrxm play a critical role in protein structural change as well as heat tolerance in plants.

Characterization of extracellular spike waveforms recorded in wallaby primary visual cortex.

Extracellular recordings were made from 642 units in the primary visual cortex (V1) of a highly visual marsupial, the Tammar wallaby. The receptive field (RF) characteristics of the cells were objectively estimated using the non-linear input model (NIM), and these were correlated with spike shapes. We found that wallaby cortical units had 68% regular spiking (RS), 12% fast spiking (FS), 4% triphasic spiking (TS), 5% compound spiking (CS) and 11% positive spiking (PS). RS waveforms are most often associated with recordings from pyramidal or spiny stellate cell bodies, suggesting that recordings from these cell types dominate in the wallaby cortex. In wallaby, 70-80% of FS and RS cells had orientation selective RFs and had evenly distributed linear and nonlinear RFs. We found that 47% of wallaby PS units were non-orientation selective and they were dominated by linear RFs. Previous studies suggest that the PS units represent recordings from the axon terminals of non-orientation selective cells originating in the lateral geniculate nucleus (LGN). If this is also true in wallaby, as strongly suggested by their low response latencies and bursty spiking properties, the results suggest that significantly more neurons in wallaby LGN are already orientation selective. In wallaby, less than 10% of recorded spikes had triphasic (TS) or sluggish compound spiking (CS) waveforms. These units had a mixture of orientation selective and non-oriented properties, and their cellular origins remain difficult to classify.

Potent Antifungal Functions of a Living Modified Organism Protein, CP4-EPSPS, against Pathogenic Fungal Cells.

Various proteins introduced into living modified organism (LMO) crops function in plant defense mechanisms against target insect pests or herbicides. This study analyzed the antifungal effects of an introduced LMO protein, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) from Agrobacterium sp. strain CP4 (CP4-EPSPS). Pure recombinant CP4-EPSPS protein, expressed in Escherichia coli, inhibited the growth of human and plant fungal pathogens (Candida albicans, C. tropicalis, C. krusei, Colletotrichum gloeosporioides, Fusarium solani, F. graminearum, and Trichoderma virens), at minimum inhibitory concentrations (MICs) that ranged from 62.5 to 250 µg/mL. It inhibited fungal spore germination as well as cell proliferation on C. gloeosporioides. Rhodamine-labeled CP4-EPSPS accumulated on the fungal cell wall and within intracellular cytosol. In addition, the protein induced uptake of SYTOX Green into cells, but not into intracellular mitochondrial reactive oxygen species (ROS), indicating that its antifungal action was due to inducing the permeability of the fungal cell wall. Its antifungal action showed cell surface damage, as observed from fungal cell morphology. This study provided information on the effects of the LMO protein, EPSPS, on fungal growth.

Functional characterization of the DNA-binding protein from starved cells (DPS) as a molecular chaperone under heat stress.

The DNA-binding protein from starved cells, known as DPS, has been characterized as a crucial factor in protecting E. coli from external stresses. The DPS functions in various cellular processes, including protein-DNA binding, ferroxidase activity, compaction of chromosome and regulation of stress resistance gene expression. DPS proteins exist as oligomeric complexes; however, the specific biochemical activity of oligomeric DPS in conferring heat shock tolerance has not been fully understood. Therefore, we investigated the novel functional role of DPS under heat shock. To elucidate the functional role of DPS under heat shock conditions, we purified recombinant GST-DPS protein and demonstrated its thermostability and existence in its highly oligomeric form. Furthermore, we discovered that the hydrophobic region of GST-DPS influenced the formation of oligomers, which exhibited molecular chaperone activity, thereby preventing the aggregation of substrate proteins. Collectively, our findings highlight the novel functional role of DPS, as a molecular chaperone and may confer thermotolerance to E. coli.

Orientation pinwheels in primary visual cortex of a highly visual marsupial.

Primary visual cortices in many mammalian species exhibit modular and periodic orientation preference maps arranged in pinwheel-like layouts. The role of inherited traits as opposed to environmental influences in determining this organization remains unclear. Here, we characterize the cortical organization of an Australian marsupial, revealing pinwheel organization resembling that of eutherian carnivores and primates but distinctly different from the simpler salt-and-pepper arrangement of eutherian rodents and rabbits. The divergence of marsupials from eutherians 160 million years ago and the later emergence of rodents and rabbits suggest that the salt-and-pepper structure is not the primitive ancestral form. Rather, the genetic code that enables complex pinwheel formation is likely widespread, perhaps extending back to the common therian ancestors of modern mammals.

Functional Characterization of an Arabidopsis Profilin Protein as a Molecular Chaperone under Heat Shock Stress.

Profilins (PFNs) are actin monomer-binding proteins that function as antimicrobial agents in plant phloem sap. Although the roles of Arabidopsis thaliana profilin protein isoforms (AtPFNs) in regulating actin polymerization have already been described, their biochemical and molecular functions remain to be elucidated. Interestingly, a previous study indicated that AtPFN2 with high molecular weight (HMW) complexes showed lower antifungal activity than AtPFN1 with low molecular weight (LMW). These were bacterially expressed and purified to characterize the unknown functions of AtPFNs with different structures. In this study, we found that AtPFN1 and AtPFN2 proteins have LMW and HMW structures, respectively, but only AtPFN2 has a potential function as a molecular chaperone, which has never been reported elsewhere. AtPFN2 has better protein stability than AtPFN1 due to its higher molecular weight under heat shock conditions. The function of AtPFN2 as a holdase chaperone predominated in the HMW complexes, whereas the chaperone function of AtPFN1 was not observed in the LMW forms. These results suggest that AtPFN2 plays a critical role in plant tolerance by increasing hydrophobicity due to external heat stress.

How Stimulus Statistics Affect the Receptive Fields of Cells in Primary Visual Cortex.

We studied the changes that neuronal receptive field (RF) models undergo when the statistics of the stimulus are changed from those of white Gaussian noise (WGN) to those of natural scenes (NSs), by fitting the models to multielectrode data recorded from primary visual cortex (V1) of female cats. This allowed the estimation of both a cascade of linear filters on the stimulus, as well as the static nonlinearities that map the output of the filters to the neuronal spike rates. We found that cells respond differently to these two classes of stimuli, with mostly higher spike rates and shorter response latencies to NSs than to WGN. The most striking finding was that NSs resulted in RFs that had additional uncovered filters compared with WGN. This finding was not an artifact of the higher spike rates observed for NSs relative to WGN, but rather was related to a change in coding. Our results reveal a greater extent of nonlinear processing in V1 neurons when stimulated using NSs compared with WGN. Our findings indicate the existence of nonlinear mechanisms that endow V1 neurons with context-dependent transmission of visual information.SIGNIFICANCE STATEMENT This study addresses a fundamental question about the concept of the receptive field (RF): does the encoding of information depend on the context or statistical regularities of the stimulus type? We applied state-of-the-art RF modeling techniques to data collected from multielectrode recordings from cat visual cortex in response to two statistically distinct stimulus types: white Gaussian noise and natural scenes. We find significant differences between the RFs that emerge from our data-driven modeling. Natural scenes result in far more complex RFs that combine multiple features in the visual input. Our findings reveal that different regimes or modes of operation are at work in visual cortical processing depending on the information present in the visual input. The complexity of V1 neural coding appears to be dependent on the complexity of the stimulus. We believe this new finding will have interesting implications for our understanding of the efficient transmission of information in sensory systems, which is an integral assumption of many computational theories (e.g., efficient and predictive coding of sensory processing in the brain).

The complete mitochondrial genome of Myzus persicae (Sulzer, 1776; Hemiptera: Aphididae) isolated in Korea.

We de novo assembled the complete mitochondrial genome of the green peach aphid, Myzus persicae, using its genomic DNA isolated from the bell pepper in Korea. The circular mitogenome of M. persicae is 16,936 bp long and contains the standard 37 genes: 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes, as well as a single control region of 798 bp. Given the high AT ratio (84.1%) of the M. persicae mitogenome, we found, through the comparison of the Chinese M. persicae mitogenomes, that approximately 1.6% of the mitogenome is polymorphic, including 30 single nucleotide polymorphisms (SNPs), 12 insertions and deletions (INDELs), and large sequence variations in the control region. To resolve the phylogenetic position of M. persicae, we analyzed all mitochondrial protein-coding genes from 38 species within the Aphidoidea superfamily, with Adelges laricis as an outgroup. Our M. persicae sample was significantly grouped with three existing M. persicae samples, and the species belonging to the family Aphididae formed a monophyletic clade.

Hybrid LPG-FBG Based High-Resolution Micro Bending Strain Sensor.

Sensitivity and reliability are essential factors for the practical implementation of a wearable sensor. This study explores the possibility of using a hybrid high-resolution Bragg grating sensor for achieving a fast response to dynamic, continuous motion and Bragg signal pattern monitoring measurement. The wavelength shift pattern for real-time monitoring in picometer units was derived by using femtosecond laser Bragg grating processing on an optical wave path with long-period grating. The possibility of measuring the demodulation system's Bragg signal pattern on the reflection spectrum of the femtosecond laser precision Bragg process and the long-period grating was confirmed. By demonstrating a practical method of wearing the sensor, the application of wearables was also explored. It is possible to present the applicability of sophisticated micro transformation measurement applications in picometer units.

Novel functional characterization of the insecticidal protein Vip3Aa on DNA binding activity.

The toxicity of Vip3Aa protein on insect pests is known, however, it remains unclear underlying the structure-dependent molecular function of the Vip3Aa protein. To investigate the novel function of the Vip3Aa protein, we isolated recombinant Vip3Aa protein. The recombinant Vip3Aa protein was mostly present as oligomeric form depending on the hydrophobic amino acid residue. We found that the oligomeric Vip3Aa protein specifically binds to nucleic acids, including single-stranded (ssDNA) and double-stranded DNA (dsDNA). The conformational and functional domains of the Vip3Aa protein were confirmed by separating the Vip3Aa full and Vip3Aa active (actVip3Aa) forms using size exclusion chromatography and nucleic acid binding activity. Interestingly, actVip3Aa protein had a conformational change and decreased DNA binding activity compared to that of the Vip3Aa full, suggesting that N-terminal part of the Vip3Aa play an important role in maintaining the conformation and nucleic acid binding activity. These studies highlight novel functional characterization of the insecticidal protein Vip3Aa on DNA binding activity and may be attributed to the protection of DNA from the damage caused by oxidative stress.

Origins of Functional Organization in the Visual Cortex.

How are the complex maps for orientation selectivity (OS) created in the primary visual cortex (V1)? Rodents and rabbits have a random distribution of OS preferences across V1 while in cats, ferrets, and all primates cells with similar OS preferences cluster together into relatively wide cortical columns. Given other clear similarities in the organization of the visual pathways, why is it that maps coding OS preferences are so radically different? Prominent models have been created of cortical OS mapping that incorporate Hebbian plasticity, intracortical interactions, and the properties of growing axons. However, these models suggest that the maps arise primarily through intracortical interactions. Here we focus on several other features of the visual system and brain that may influence V1 structure. These are: eye divergence, the total number of cells in V1, the thalamocortical networks, the topography of the retina and phylogeny. We outline the evidence for and against these factors contributing to map formation. One promising theory is that the central-to-peripheral ratio (CP ratio) of retinal cell density can be used to predict whether or not a species has pinwheel maps. Animals with high CP ratios (>7) have orientation columns while those with low CP ratios (<4) have random OS maps. The CP ratio is related to the total number of cells in cortex, which also appears to be a reasonable contributing factor. However, while these factors correlate with map structure to some extent, there is a gray area where certain species do not fit elegantly into the theory. A problem with the existing literature is that OS maps have been investigated in only a small number of mammals, from a small fraction of the mammalian phylogenetic tree. We suggest four species (agouti, fruit bat, sheep, and wallaby) that have a range of interesting characteristics, which sit at intermediate locations between primates and rodents, that make them good targets for filling in the missing gaps in the literature. We make predictions about the map structures of these species based on the organization of their brains and visual systems and, in doing so, set possible paths for future research.

Hybrid diamond/ carbon fiber microelectrodes enable multimodal electrical/chemical neural interfacing.

Implantable medical devices are now in regular use to treat or ameliorate medical conditions, including movement disorders, chronic pain, cardiac arrhythmias, and hearing or vision loss. Aside from offering alternatives to pharmaceuticals, one major advantage of device therapy is the potential to monitor treatment efficacy, disease progression, and perhaps begin to uncover elusive mechanisms of diseases pathology. In an ideal system, neural stimulation, neural recording, and electrochemical sensing would be conducted by the same electrode in the same anatomical region. Carbon fiber (CF) microelectrodes are the appropriate size to achieve this goal and have shown excellent performance, in vivo. Their electrochemical properties, however, are not suitable for neural stimulation and electrochemical sensing. Here, we present a method to deposit high surface area conducting diamond on CF microelectrodes. This unique hybrid microelectrode is capable of recording single-neuron action potentials, delivering effective electrical stimulation pulses, and exhibits excellent electrochemical dopamine detection. Such electrodes are needed for the next generation of miniaturized, closed-loop implants that can self-tune therapies by monitoring both electrophysiological and biochemical biomarkers.

Functional Mechanisms Underlying the Antimicrobial Activity of the Oryza sativa Trx-like Protein.

Plants are constantly subjected to a variety of environmental stresses and have evolved regulatory responses to overcome unfavorable conditions that might reduce or adversely change a plant's growth or development. Among these, the regulated production of reactive oxygen species (ROS) as a signaling molecule occurs during plant development and pathogen defense. This study demonstrates the possible antifungal activity of Oryza sativa Tetratricopeptide Domain-containing thioredoxin (OsTDX) protein against various fungal pathogens. The transcription of OsTDX was induced by various environmental stresses known to elicit the generation of ROS in plant cells. OsTDX protein showed potent antifungal activity, with minimum inhibitory concentrations (MICs) against yeast and filamentous fungi ranging between 1.56 and 6.25 and 50 and 100 µg/mL, respectively. The uptake of SYTOX-Green into fungal cells and efflux of calcein from artificial fungus-like liposomes suggest that its killing mechanism involves membrane permeabilization and damage. In addition, irregular blebs and holes apparent on the surfaces of OsTDX-treated fungal cells indicate the membranolytic action of this protein. Our results suggest that the OsTDX protein represents a potentially useful lead for the development of pathogen-resistant plants.

Effect of metallic tools on scattered radiation dose during the use of C-arm fluoroscopy in orthopaedic surgery.

This study investigated the effect of metallic tools on the scattered radiation dose delivered to surgeons' radiosensitive organs while simulating hip surgery using C-arm fluoroscopy. Two phantoms, a pelvis and a Rando phantom, were used to simulate a patient and a surgeon in this study. Photoluminescence dosimeters were inserted into the Rando phantom in the positions of the eye, thyroid and gonad. A drill was positioned above the hip of the pelvis phantom or beside the pelvis phantom of the same height. For each drill location, the scattered radiation dose was measured when the angle to the operator phantom was 45°; this was repeated when the angle was 90°. The scattered radiation doses to the eye, thyroid and gonad when the drill was placed beside the pelvis phantom with 90° angulation to the operator phantom were significantly lower than the reference values and those when the drill was placed beside the pelvis phantom at a 45° angulation to the operator phantom. The scattered radiation doses to the eye and thyroid when the drill was placed above the hip were significantly lower than the references values. Of the four different scenarios, the scattered radiation doses to the eye, thyroid and gonad were lowest when the drill was placed beside the pelvis phantom with 90° angulation. This study showed that the scattered radiation doses to radiosensitive organs were affected by the location and angle of the metallic tools in relation to the operator. Therefore, orthopedic surgeons should consider the effect of metallic tools on the scattered radiation dose during intraoperative use of C-arm fluoroscopy.

Molecular mechanism of Arabidopsis thaliana profilins as antifungal proteins.

BACKGROUND: It remains an open question whether plant phloem sap proteins are functionally involved in plant defense mechanisms. METHODS: The antifungal effects of two profilin proteins from Arabidopsis thaliana, AtPFN1 and AtPFN2, were tested against 11 molds and 4 yeast fungal strains. Fluorescence profiling, biophysical, and biochemical analyses were employed to investigate their antifungal mechanism. RESULTS: Recombinant AtPFN1 and AtPFN2 proteins, expressed in Escherichia coli, inhibited the cell growth of various pathogenic fungal strains at concentrations ranging from 10 to 160 µg/mL. The proteins showed significant intracellular accumulation and cell-binding affinity for fungal cells. Interestingly, the AtPFN proteins could penetrate the fungal cell wall and membrane and act as inhibitors of fungal growth via generation of cellular reactive oxygen species and mitochondrial superoxide. This triggered the AtPFN variant-induced cell apoptosis, resulting in morphological changes in the cells. CONCLUSION: PFNs may play a critical role as antifungal proteins in the Arabidopsis defense system against fungal pathogen attacks. GENERAL SIGNIFICANCE: The present study indicates that two profilin proteins, AtPFN1 and AtPFN2, can act as natural antimicrobial agents in the plant defense system.

Functional characterization of the Arabidopsis universal stress protein AtUSP with an antifungal activity.

An antifungal protein, AtUSP protein (At3g53990), was isolated from Arabidopsis thaliana leaves by ion and size chromatography and sequenced by N-terminal sequencing. The AtUSP gene amplified from an Arabidopsis leaf cDNA library was transformed to Escherichia coli to express the AtUSP protein. The recombinant protein inhibited the cell growth of various pathogenic fungal strains. The levels of the AtUSP transcripts were increased by various stresses, including pathogenic infection and salt stress. These results suggest that Arabidopsis AtUSP plays a critical role in the plant tolerance to diverse pathogenic infections. The potent antifungal action, which is a new function of AtUSP, was attributed to fungal reactive oxygen species (ROS) generation and mitochondrial potential alteration.

HY5, a positive regulator of light signaling, negatively controls the unfolded protein response in Arabidopsis.

Light influences essentially all aspects of plant growth and development. Integration of light signaling with different stress response results in improvement of plant survival rates in ever changing environmental conditions. Diverse environmental stresses affect the protein-folding capacity of the endoplasmic reticulum (ER), thus evoking ER stress in plants. Consequently, the unfolded protein response (UPR), in which a set of molecular chaperones is expressed, is initiated in the ER to alleviate this stress. Although its underlying molecular mechanism remains unknown, light is believed to be required for the ER stress response. In this study, we demonstrate that increasing light intensity elevates the ER stress sensitivity of plants. Moreover, mutation of the ELONGATED HYPOCOTYL 5 (HY5), a key component of light signaling, leads to tolerance to ER stress. This enhanced tolerance of hy5 plants can be attributed to higher expression of UPR genes. HY5 negatively regulates the UPR by competing with basic leucine zipper 28 (bZIP28) to bind to the G-box-like element present in the ER stress response element (ERSE). Furthermore, we found that HY5 undergoes 26S proteasome-mediated degradation under ER stress conditions. Conclusively, we propose a molecular mechanism of crosstalk between the UPR and light signaling, mediated by HY5, which positively mediates light signaling, but negatively regulates UPR gene expression.

The membrane-tethered NAC transcription factor, AtNTL7, contributes to ER-stress resistance in Arabidopsis.

We screened for endoplasmic reticulum (ER) stress-resistant mutants among 25 mutants of the Arabidopsis NTL (NAC with Transmembrane motif 1-Like) family. We identified a novel mutant, SALK_044777, showing strong resistance to ER stress. RT-PCR and genomic DNA sequence analyses identified the mutant as atntl7, which harbors a T-DNA insertion in the fourth exon of AtNTL7. Two other atntl7-mutant alleles, in which T-DNA was inserted in the second exon and third intron of AtNTL7, respectively, showed ER-stress sensitive phenotypes, suggesting that SALK_044777 is a gain-of-function mutant. Arabidopsis plants overexpressing AtNTL7 showed strong ER-stress resistance. Our findings suggest that AtNTL7 fragment is cleaved from the ER membrane under ER stress and translocates into the nucleus to induce downstream ER-stress responsive genes.

Orange protein has a role in phytoene synthase stabilization in sweetpotato.

Carotenoids have essential roles in light-harvesting processes and protecting the photosynthetic machinery from photo-oxidative damage. Phytoene synthase (PSY) and Orange (Or) are key plant proteins for carotenoid biosynthesis and accumulation. We previously isolated the sweetpotato (Ipomoea batatas) Or gene (IbOr), which is involved in carotenoid accumulation and salt stress tolerance. The molecular mechanism underlying IbOr regulation of carotenoid accumulation was unknown. Here, we show that IbOr has an essential role in regulating IbPSY stability via its holdase chaperone activity both in vitro and in vivo. This protection results in carotenoid accumulation and abiotic stress tolerance. IbOr transcript levels increase in sweetpotato stem, root, and calli after exposure to heat stress. IbOr is localized in the nucleus and chloroplasts, but interacts with IbPSY only in chloroplasts. After exposure to heat stress, IbOr predominantly localizes in chloroplasts. IbOr overexpression in transgenic sweetpotato and Arabidopsis conferred enhanced tolerance to heat and oxidative stress. These results indicate that IbOr holdase chaperone activity protects IbPSY stability, which leads to carotenoid accumulation, and confers enhanced heat and oxidative stress tolerance in plants. This study provides evidence that IbOr functions as a molecular chaperone, and suggests a novel mechanism regulating carotenoid accumulation and stress tolerance in plants.