Category representation in primary visual cortex after visual perceptual learning.

The visual perceptual learning (VPL) leads to long-term enhancement of visual task performance. The subjects are often trained to link different visual stimuli to several options, such as the widely used two-alternative forced choice (2AFC) task, which involves an implicit categorical decision. The enhancement of performance has been related to the specific changes of neural activities, but few studies investigate the effects of categorical responding on the changes of neural activities. Here we investigated whether the neural activities would exhibit the categorical characteristics if the subjects are requested to respond visual stimuli in a categorical manner during VPL. We analyzed the neural activities of two monkeys in a contour detection VPL. We found that the neural activities in primary visual cortex (V1) converge to one pattern if the contour can be detected by monkey and another pattern if the contour cannot be detected, exhibiting a kind of category learning that the neural representations of detectable contour become less selective for number of bars forming contour and diverge from the representations of undetectable contour. Supplementary Information: The online version contains supplementary material available at 10.1007/s11571-022-09926-8.

γ And ß Band Oscillation in Working Memory Given Sequential or Concurrent Multiple Items: A Spiking Network Model.

Working memory (WM) can maintain sequential and concurrent information, and the load enhances the γ band oscillation during the delay period. To provide a unified account for these phenomena in working memory, we investigated a continuous network model consisting of pyramidal cells, high-threshold fast-spiking interneurons (FS), and low-threshold nonfast-spiking interneurons (nFS) for working memory of sequential and concurrent directional cues. Our model exhibits the γ (30-100 Hz) and ß (10-30 Hz) band oscillation during the retention of both concurrent cues and sequential cues. We found that the ß oscillation results from the interaction between pyramidal cells and nFS, whereas the γ oscillation emerges from the interaction between pyramidal cells and FS because of the strong excitation elicited by cue presentation, shedding light on the mechanism underlying the enhancement of γ power in many cognitive executions.

Functional Autapses Form in Striatal Parvalbumin Interneurons but not Medium Spiny Projection Neurons.

Autapses selectively form in specific cell types in many brain regions. Previous studies have also found putative autapses in principal spiny projection neurons (SPNs) in the striatum. However, it remains unclear whether these neurons indeed form physiologically functional autapses. We applied whole-cell recording in striatal slices and identified autaptic cells by the occurrence of prolonged asynchronous release (AR) of neurotransmitters after bursts of high-frequency action potentials (APs). Surprisingly, we found no autaptic AR in SPNs, even in the presence of Sr2+. However, robust autaptic AR was recorded in parvalbumin (PV)-expressing neurons. The autaptic responses were mediated by GABAA receptors and their strength was dependent on AP frequency and number. Further computer simulations suggest that autapses regulate spiking activity in PV cells by providing self-inhibition and thus shape network oscillations. Together, our results indicate that PV neurons, but not SPNs, form functional autapses, which may play important roles in striatal functions.

MAL31, a sugar transporter involved in pullulan biosynthesis in Aureobasidium pullulans.

To investigate the role of the sugar transporter MAL31 on pullulan biosynthesis, the coding gene mal31 was respectively disrupted and overexpressed in the parental strain A. pullulans CCTCC M 2012259 to construct mutants of A. pullulans Δmal31 and A. pullulans Mal31. Batch pullulan production significantly decreased by 69.1 % in A. pullulans Δmal31 but increased by 15.9 % in A. pullulans Mal31, as compared to the parental strain. We performed kinetics analysis, assays of key enzymes, determination of intracellular UDPG, NADH, and ATP contents, and measurement of transcriptional levels of genes associated with pullulan biosynthesis and excretion. The results confirmed that the mal31 disruption decreased the glucose consumption rate, decreased the formation rate and titer of pullulan, but increased the intracellular UDPG supply for ß-glucan accumulation. In contrast, the mal31 overexpression increased the transcriptional levels of genes associated with pullulan biosynthesis, and accelerated the rates of glucose consumption and pullulan formation, thereby increased pullulan production. Our findings revealed that MAL31 is involved in the transport of precursors for pullulan biosynthesis. This study provides an accurate operating site for genetic modification of A. pullulans for improving pullulan production and also presents a feasible technique route for the overproduction of other polysaccharides.

A spiking network model for clustering report in a visual working memory task.

Introduction: Working memory (WM) plays a key role in many cognitive processes, and great interest has been attracted by WM for many decades. Recently, it has been observed that the reports of the memorized color sampled from a uniform distribution are clustered, and the report error for the stimulus follows a Gaussian distribution. Methods: Based on the well-established ring model for visuospatial WM, we constructed a spiking network model with heterogeneous connectivity and embedded short-term plasticity (STP) to investigate the neurodynamic mechanisms behind this interesting phenomenon. Results: As a result, our model reproduced the clustering report given stimuli sampled from a uniform distribution and the error of the report following a Gaussian distribution. Perturbation studies showed that the heterogeneity of connectivity and STP are necessary to explain experimental observations. Conclusion: Our model provides a new perspective on the phenomenon of visual WM in experiments.

Degeneracy and stability in neural circuits of dopamine and serotonin neuromodulators: A theoretical consideration.

Degenerate neural circuits perform the same function despite being structurally different. However, it is unclear whether neural circuits with interacting neuromodulator sources can themselves degenerate while maintaining the same neuromodulatory function. Here, we address this by computationally modeling the neural circuits of neuromodulators serotonin and dopamine, local glutamatergic and GABAergic interneurons, and their possible interactions, under reward/punishment-based conditioning tasks. The neural modeling is constrained by relevant experimental studies of the VTA or DRN system using, e.g., electrophysiology, optogenetics, and voltammetry. We first show that a single parsimonious, sparsely connected neural circuit model can recapitulate several separate experimental findings that indicated diverse, heterogeneous, distributed, and mixed DRNVTA neuronal signaling in reward and punishment tasks. The inability of this model to recapitulate all observed neuronal signaling suggests potentially multiple circuits acting in parallel. Then using computational simulations and dynamical systems analysis, we demonstrate that several different stable circuit architectures can produce the same observed network activity profile, hence demonstrating degeneracy. Due to the extensive D2-mediated connections in the investigated circuits, we simulate the D2 receptor agonist by increasing the connection strengths emanating from the VTA DA neurons. We found that the simulated D2 agonist can distinguish among sub-groups of the degenerate neural circuits based on substantial deviations in specific neural populations' activities in reward and punishment conditions. This forms a testable model prediction using pharmacological means. Overall, this theoretical work suggests the plausibility of degeneracy within neuromodulator circuitry and has important implications for the stable and robust maintenance of neuromodulatory functions.

Improved production of ß-glucan by a T-DNA-based mutant of Aureobasidium pullulans.

To improve ß-1,3-1,6-D-glucan (ß-glucan) production by Aureobasidium pullulans, an Agrobacterium tumefaciens-mediated transformation method was developed to screen a mutant A. pullulans CGMCC 19650. Based on thermal asymmetric-interlaced PCR detection, DNA sequencing, BLAST analysis, and quantitative real-time PCR assay, the T-DNA was identified to be inserted in the coding region of mal31 gene, which encodes a sugar transporter involved in pullulan biosynthesis in the mutant. The maximal biomass and ß-glucan production under batch fermentation were significantly increased by 47.6% and 78.6%, respectively, while pullulan production was decreased by 41.7% in the mutant, as compared to the parental strain A. pullulans CCTCC M 2012259. Analysis of the physiological mechanism of these changes revealed that mal31 gene disruption increased the transcriptional levels of pgm2, ugp, fks1, and kre6 genes; increased the amounts of key enzymes associated with UDPG and ß-glucan biosynthesis; and improved intracellular UDPG contents and energy supply, all of which favored ß-glucan production. However, the T-DNA insertion decreased the transcriptional levels of ags2 genes, and reduced the biosynthetic capability to form pullulan, resulting in the decrease in pullulan production. This study not only provides an effective approach for improved ß-glucan production by A. pullulans, but also presents an accurate and useful gene for metabolic engineering of the producer for efficient polysaccharide production. KEY POINTS: • A mutant A. pullulans CGMCC 19650 was screened by using the ATMT method. • The mal31 gene encoding a sugar transporter was disrupted in the mutant. • ß-Glucan produced by the mutant was significantly improved.

An Early Stage Researcher's Primer on Systems Medicine Terminology.

Background: Systems Medicine is a novel approach to medicine, that is, an interdisciplinary field that considers the human body as a system, composed of multiple parts and of complex relationships at multiple levels, and further integrated into an environment. Exploring Systems Medicine implies understanding and combining concepts coming from diametral different fields, including medicine, biology, statistics, modeling and simulation, and data science. Such heterogeneity leads to semantic issues, which may slow down implementation and fruitful interaction between these highly diverse fields. Methods: In this review, we collect and explain more than100 terms related to Systems Medicine. These include both modeling and data science terms and basic systems medicine terms, along with some synthetic definitions, examples of applications, and lists of relevant references. Results: This glossary aims at being a first aid kit for the Systems Medicine researcher facing an unfamiliar term, where he/she can get a first understanding of them, and, more importantly, examples and references for digging into the topic.

Triton X-100 improves co-production of ß-1,3-D-glucan and pullulan by Aureobasidium pullulans.

The effects of several surfactants on the biosynthesis of ß-1,3-D-glucan (ß-glucan) and pullulan by Aureobasidium pullulans CCTCC M 2012259 were investigated, and Triton X-100 was found to decrease biomass formation but increase ß-glucan and pullulan production. The addition of 5 g/L Triton X-100 to the fermentation medium and bioconversion broth significantly increased ß-glucan production by 76.6% and 69.9%, respectively, when compared to the control without surfactant addition. To reveal the physiological mechanism underlying the effect of Triton X-100 on polysaccharides production, the cell morphology and viability, membrane permeability, key enzyme activities, and intracellular levels of UDPG, NADH, and ATP were determined. The results indicated that Triton X-100 increased the activities of key enzymes involved in ß-glucan and pullulan biosynthesis, improved intracellular UDPG and energy supply, and accelerated the transportation rate of precursors across the cell membrane, all of which contributed to the enhanced production of ß-glucan and pullulan. Moreover, a two-stage culture strategy with combined processes of batch fermentation and bioconversion was applied, and co-production of ß-glucan and pullulan in the presence of 5 g/L Triton X-100 additions was further improved. The present study not only provides insights into the effect of surfactant on ß-glucan and pullulan production but also presents a feasible approach for efficient production of analogue exopolysaccharides. KEY POINTS: • Triton X-100 increased ß-glucan and pullulan production under either batch fermentation or bioconversion. • Triton X-100 increased the permeability of cell membrane and accelerated the transportation rate of precursors across cell membrane. • Activities of key enzymes involved in ß-glucan and pullulan biosynthesis were increased in the presence of Triton X-100. • Intracellular UDPG levels and energy supply were improved by Triton X-100 addition.

Communication speeds up but impairs the consensus decision in a dyadic colour estimation task.

Communication plays an important role in consensus decision-making which pervades our daily life. However, the exact role of communication in consensus formation is not clear. Here, to study the effects of communication on consensus formation, we designed a dyadic colour estimation task, where a pair of isolated participants repeatedly estimated the colours of discs until they reached a consensus or completed eight estimations, either with or without communication. We show that participants' estimates gradually approach each other, reaching towards a consensus, and these are enhanced with communication. We also show that dyadic consensus estimation is on average better than individual estimation. Surprisingly, consensus estimation without communication generally outperforms that with communication, indicating that communication impairs the improvement of consensus estimation. However, without communication, it takes longer to reach a consensus. Moreover, participants who partially cooperate with each other tend to result in better overall consensus. Taken together, we have identified the effect of communication on the dynamics of consensus formation, and the results may have implications on group decision-making in general.

Opportunities for multiscale computational modelling of serotonergic drug effects in Alzheimer's disease.

Alzheimer's disease (AD) is an age-specific neurodegenerative disease that compromises cognitive functioning and impacts the quality of life of an individual. Pathologically, AD is characterised by abnormal accumulation of beta-amyloid (Aß) and hyperphosphorylated tau protein. Despite research advances over the last few decades, there is currently still no cure for AD. Although, medications are available to control some behavioural symptoms and slow the disease's progression, most prescribed medications are based on cholinesterase inhibitors. Over the last decade, there has been increased attention towards novel drugs, targeting alternative neurotransmitter pathways, particularly those targeting serotonergic (5-HT) system. In this review, we focused on 5-HT receptor (5-HTR) mediated signalling and drugs that target these receptors. These pathways regulate key proteins and kinases such as GSK-3 that are associated with abnormal levels of Aß and tau in AD. We then review computational studies related to 5-HT signalling pathways with the potential for providing deeper understanding of AD pathologies. In particular, we suggest that multiscale and multilevel modelling approaches could potentially provide new insights into AD mechanisms, and towards discovering novel 5-HTR based therapeutic targets.

Environmental exposure to lead and cadmium and hearing loss in Chinese adults: A case-control study.

Hearing loss is the second most common nonfatal problem affecting the Chinese population. Historical studies have suggested an association between exposure to heavy metals, such as cadmium and lead, and hearing loss. Few studies have investigated this relationship in the general population in China. We conducted a case-control study with 1008 pairs of participants from a cross-sectional epidemiological survey conducted in Zhejiang Province. A self-designed questionnaire was adopted to collect information on demographics, chronic diseases, lifestyles and environmental noise. Pure-tone averages of hearing thresholds at frequencies of 0.5, 1, 2, and 4 kHz were computed. Blood lead and cadmium levels were analyzed with an atomic absorption spectrometer. After adjusting for all other potential confounding factors, compared with the lowest blood cadmium quartile (0.00-0.53 µg/L), blood cadmium quartile 2 (0.54-0.92 µg/L), quartile 3 (0.93-1.62 µg/L) and quartile 4 (1.63-57.81 µg/L) exhibited significantly elevated risks for hearing loss, with odds ratios of 1.932 (95% CI: 1.356-2.751), 2.036 (95% CI: 1.423-2.914) and 1.495 (95% CI: 1.048-2.133), respectively (P-trend<0.001). However, an association of lead with hearing loss was not found. Young age (less than 60 years), male sex and current smoking were associated with increased blood cadmium concentration. Additionally, a positive association between blood cadmium and lead concentrations was found. Therefore, we conclude that exposure to environmental cadmium may be a risk factor for hearing loss among the general population in China.

Distribution and association study in copy number variation of KCNJ12 gene across four Chinese cattle populations.

Copy number variation is a large genome variation which usually happens in the noncoding-region, and it may occur at the locus associated with the functional gene to further influence the phenotype. Potassium inwardly-rectifying channel, subfamily J 12 (KCNJ12) gene expressed widely in cardiomyocytes and neurons, plays an important role in tumor therapy and muscle movement regulation. In this study, we detected the distribution of CNVs for KCNJ12 gene in 404 individuals belonging to four Chinese cattle breeds (NY, JX, JA and GF). We also investigated the KCNJ12 gene expression in different tissues of JX cattle. Additionally, we examined the association of two CNV regions (CNV1: 1,600 bp, intron 1; CNV2: 4,800 bp, intergenic) with growth traits. The statistical analyses indicated that the CNV1 is associated with the body length, rump length and weight in JX cattle population (P < 0.05); and there has a significant association with the body length, chest circumference, and body weight in GF cattle (P < 0.05).The CNV2 had a significant effect on the body length and body weight in JX cattle (P < 0.05); the body length, chest circumference, rump length and body weight in GF cattle (P < 0.01 or P < 0.05). The copy numbers of KCNJ12 gene presented the negative correlations with the transcript level of gene in skeletal muscles (P < 0.05). Our results provide evidence that CNV1 and CNV 2 in KCNJ12 are associated with growth traits in two cattle populations and may be used as candidates for marker-assisted selection and breeding management in cattle.

An ensemble-based likelihood ratio approach for family-based genomic risk prediction.

OBJECTIVE: As one of the most popular designs used in genetic research, family-based design has been well recognized for its advantages, such as robustness against population stratification and admixture. With vast amounts of genetic data collected from family-based studies, there is a great interest in studying the role of genetic markers from the aspect of risk prediction. This study aims to develop a new statistical approach for family-based risk prediction analysis with an improved prediction accuracy compared with existing methods based on family history. METHODS: In this study, we propose an ensemble-based likelihood ratio (ELR) approach, Fam-ELR, for family-based genomic risk prediction. Fam-ELR incorporates a clustered receiver operating characteristic (ROC) curve method to consider correlations among family samples, and uses a computationally efficient tree-assembling procedure for variable selection and model building. RESULTS: Through simulations, Fam-ELR shows its robustness in various underlying disease models and pedigree structures, and attains better performance than two existing family-based risk prediction methods. In a real-data application to a family-based genome-wide dataset of conduct disorder, Fam-ELR demonstrates its ability to integrate potential risk predictors and interactions into the model for improved accuracy, especially on a genome-wide level. CONCLUSIONS: By comparing existing approaches, such as genetic risk-score approach, Fam-ELR has the capacity of incorporating genetic variants with small or moderate marginal effects and their interactions into an improved risk prediction model. Therefore, it is a robust and useful approach for high-dimensional family-based risk prediction, especially on complex disease with unknown or less known disease etiology.

Sodium chloride improves pullulan production by Aureobasidium pullulans but reduces the molecular weight of pullulan.

The effect of sodium chloride (NaCl) on pullulan production by batch culture of Aureobasidium pullulans CCTCC M 2012259 was investigated. NaCl at 3 g/L improved the pullulan titer by 26.7% but reduced the molecular weight of pullulan to only 46.8% of that obtained in the control without NaCl. In order to elucidate the physiological mechanism underlying the effect of NaCl on pullulan production, assays of key enzyme activity, gene expression, energy metabolism, and intracellular uridine diphosphate glucose (UDP-glucose) content were performed. Results indicated that NaCl increased the activities of α-phosphoglucose mutase and glucosyltransferase involved in pullulan biosynthesis, increased the activities of α-amylase being responsible for pullulan degradation, upregulated the transcriptional levels of pgm1, fks, and amy2 genes, enhanced the driving force for ATP supply, and helped to maintain intracellular UDP-glucose at a high level in A. pullulans CCTCC M 2012259. All these results illuminate the reason by which NaCl increases pullulan titer but reduces the molecular weight of pullulan.

Dynamic Information Encoding With Dynamic Synapses in Neural Adaptation.

Adaptation refers to the general phenomenon that the neural system dynamically adjusts its response property according to the statistics of external inputs. In response to an invariant stimulation, neuronal firing rates first increase dramatically and then decrease gradually to a low level close to the background activity. This prompts a question: during the adaptation, how does the neural system encode the repeated stimulation with attenuated firing rates? It has been suggested that the neural system may employ a dynamical encoding strategy during the adaptation, the information of stimulus is mainly encoded by the strong independent spiking of neurons at the early stage of the adaptation; while the weak but synchronized activity of neurons encodes the stimulus information at the later stage of the adaptation. The previous study demonstrated that short-term facilitation (STF) of electrical synapses, which increases the synchronization between neurons, can provide a mechanism to realize dynamical encoding. In the present study, we further explore whether short-term plasticity (STP) of chemical synapses, an interaction form more common than electrical synapse in the cortex, can support dynamical encoding. We build a large-size network with chemical synapses between neurons. Notably, facilitation of chemical synapses only enhances pair-wise correlations between neurons mildly, but its effect on increasing synchronization of the network can be significant, and hence it can serve as a mechanism to convey the stimulus information. To read-out the stimulus information, we consider that a downstream neuron receives balanced excitatory and inhibitory inputs from the network, so that the downstream neuron only responds to synchronized firings of the network. Therefore, the response of the downstream neuron indicates the presence of the repeated stimulation. Overall, our study demonstrates that STP of chemical synapse can serve as a mechanism to realize dynamical neural encoding. We believe that our study shed lights on the mechanism underlying the efficient neural information processing via adaptation.

Toward a multiscale modeling framework for understanding serotonergic function.

Despite its importance in regulating emotion and mental wellbeing, the complex structure and function of the serotonergic system present formidable challenges toward understanding its mechanisms. In this paper, we review studies investigating the interactions between serotonergic and related brain systems and their behavior at multiple scales, with a focus on biologically-based computational modeling. We first discuss serotonergic intracellular signaling and neuronal excitability, followed by neuronal circuit and systems levels. At each level of organization, we will discuss the experimental work accompanied by related computational modeling work. We then suggest that a multiscale modeling approach that integrates the various levels of neurobiological organization could potentially transform the way we understand the complex functions associated with serotonin.

Kinesins in spermatogenesis.

Kinesins are essential for the proper function of many types of polar cells, including epithelial cells, neurons, and sperm. Spermatogenesis is closely associated with many different kinesins. These kinesins participate in several fundamental processes, including mitotic and meiotic division, essential organelle transport, and the biogenesis of peculiar structures for the formation of mature sperm. Kinesin-13, kinesin-8, and the chromokinesin families cooperate to ensure normal sister chromatid congression and segregation. The kinesin-8 family motor KIF18A, kinesin-12 motors PAKRP/kinesin12A and PAKRP1L/kinesin12B, and other kinesin-like motors are essential in the process of homologous chromosome pairing and in the separation to create haploid gametes. During spermiogenesis, the responsibility of a handful of kinesin members lies in the maturation of spermatids into mature, motile, and intact spermatozoa. Such roles are completed upon the release of viable and functional sperm into the lumen of seminiferous tubules. In this process, KIFC1, KIF5C, KRP3A, and KRP3B may be involved in acrosome biogenesis; KIFC1, KIFC5, CHO2, KIF17b, and KIF3A probably contribute to nuclear shaping; KIF17b, KIF3A, and KLC3 are implicated in the tail formation process; and KIF20 and KRP3 likely participate in sperm translocation. KIF17b also exhibited postmeiosis transcriptional activities that are critical for the dramatic alterations observed in nuclear and cytoplasmic structures. This review summarizes the roles of kinesins during mitosis, meiosis, and spermiogenesis, and proposes several important issues for further investigation.