The influence of form on motion signal processing in the ventral intraparietal area of macaque monkeys.

The visual system relies on both motion and form signals to perceive the direction of self-motion, yet the coordination mechanisms between these two elements in this process remain elusive. In the current study, we employed heading perception as a model to delve into the interaction characteristics between form and motion signals. We recorded the responses of neurons in the ventral intraparietal area (VIP), an area with strong heading selectivity, to motion-only, form-only, and combined stimuli of simulated self-motion. Intriguingly, VIP neurons responded to form-only cues defined by Glass patterns, although they exhibited no tuning selectivity. In combined condition, introducing a small offset between form and motion cues significantly enhanced neuronal sensitivity to motion cues. However, with a larger offset, the enhancement effect on sensitivity became comparatively smaller. Moreover, we observed that the influence of form cues on neuronal response to motion cues is more pronounced in the later stage (1-2 s) of stimulation, with a relatively smaller effect in the early stage (0-1 s). This suggests a dynamic interaction between motion and form cues over time for heading perception. In summary, our study uncovered that in area VIP, form information plays a role in constructing accurate self-motion perception. This adds valuable insights into the complex dynamics of how the brain integrates motion and form cues for the perception of one's own movements.

A Vip3Af mutant confers high resistance to broad lepidopteran insect pests.

BACKGROUND: Vegetative insecticidal proteins (Vip3) from Bacillus thuringiensis (Bt) have been utilized for control of lepidopteran insect pests. The majority of known Vip3 proteins possess exceptional high toxicity against Noctuid insects such as the fall armyworm (FAW, Spodoptera frugiperda), beet armyworm (BAW, Spodoptera exigua) and cotton bollworm (CBW, Helicoverpa armigera), but generally have relatively low or even no activity against some very important pest insects, such as Asian corn borer (ACB, Ostrinia furnacalis), European corn borer (ECB, Ostrinia nubilalis), rice stem borer (RSB, Chilo suppressalis) and oriental armyworm (OAW, Mythimna separata). RESULTS: Here, we report mutant Vip3Af with a single amino acid mutation, Vip3Af-T686R, which gains significantly higher insecticidal activity against ACB, OAW and BAW, while retaining high activity against FAW, CBW and RSB. Protein proteolytic activation in vitro showed that the proteolytic activation efficiency of the mutant protein was greater than the wild-type protein in the midgut juice of ACB, OAW and BAW. Transgenic corn expressing this mutant Vip3Af showed high levels of resistance to ACB, OAW, FAW, BAW and CBW. CONCLUSION: Our results suggest that Vip3Af may be a superior Vip3A mutant for the development of transgenic crops with resistance to a broad range of lepidopteran pest species. © 2024 Society of Chemical Industry.

Vasoactive intestinal peptide-expressing interneurons modulate the effect of behavioral state on cortical activity.

Animals live in a complex and changing environment with various degrees of behavioral demands. Behavioral states affect the activity of cortical neurons and the dynamics of neuronal populations, however not much is known about the cortical circuitry behind the modulation of neuronal activity across behavioral states. Here we show that a class of GABAergic inhibitory interneurons that express vasoactive intestinal peptide-expressing interneurons (VIP), namely VIP interneurons, play a key role in the circuits involved in the modulation of cortical activity by behavioral state, as reflected in the mice facial motion. We show that inhibition of VIP interneurons reduces the correlated activity between the behavioral state of the animal and the spiking of individual neurons. We also show that VIP inhibition during the quiet state decreases the synchronous spiking of the neurons but increases delta power and phase locking of spiking to the delta-band activity. Taken together our data show that VIP interneurons modulate the behavioral state-dependency of cortical activity across different time scales.

Testing the Pauli Exclusion Principle across the Periodic Table with the VIP-3 Experiment.

The Pauli exclusion principle (PEP), a cornerstone of quantum mechanics and whole science, states that in a system, two fermions can not simultaneously occupy the same quantum state. Several experimental tests have been performed to place increasingly stringent bounds on the validity of PEP. Among these, the series of VIP experiments, performed at the Gran Sasso Underground National Laboratory of INFN, is searching for PEP-violating atomic X-ray transitions in copper. In this paper, the upgraded VIP-3 setup is described, designed to extend these investigations to higher-Z elements such as zirconium, silver, palladium, and tin. We detail the enhanced design of this setup, including the implementation of cutting-edge, 1 mm thick, silicon drift detectors, which significantly improve the measurement sensitivity at higher energies. Additionally, we present calculations of expected PEP-violating energy shifts in the characteristic lines of these elements, performed using the multi-configurational Dirac-Fock method from first principles. The VIP-3 realization will contribute to ongoing research into PEP violation for different elements, offering new insights and directions for future studies.

Unraveling the abundance of vip3-type genes in Indian Bacillus thuringiensis across the agroclimatic landscape and impact of amino acid substitutions for safer agriculture.

Vegetative insecticidal protein (vip) genes of Bacillus thuringiensis (Bt) are candidates for gene pyramiding in the resistance management of pests. The prevalence of vip genes in Bt isolates is relatively under-explored. Bt isolates recovered from 29 diverse sources in nine agro-climatic zones of India were screened for the presence of vip3-type genes by PCR with 4 sets of oligonucleotide primers. Out of 155 Bt isolates, 70.32 % (109) and 44.52 % (69) isolates were positive for amplification of partial vip3-type genes with primer sets 1 and 4, respectively. The primer set-2 was found to be more efficient for amplifying full-length genes (29.03 % /45 isolates) as compared with primer set-3 (3.23 %/ 5 isolates), also corroborated in the amplification of full-length vip3 genes in ten Bt BGSC strains used as reference. Frequency analysis revealed presence of vip3 genes in Bt isolates across all agro-climatic zones. Thus, Indian Bt isolates from diverse sources have a rich repertoire of vip3-type genes. Our study reports the highest number (45) of full-length vip3-type genes detected in a native Bt isolates collection, demonstrating enrichment of Indian Bt isolates for vip3 genes. Twelve of these genes have been cloned, sequenced, and out of these, six were found to be effective against Helicoverpa armigera in our laboratory previously. Comparison of substitutions in deduced amino acids sequence of these genes and expression of Vip3 proteins in SDS-PAGE analysis of selected native Bt isolates positive for full-length vip3-type genes indicated their biopesticidal potential.

The short-term plasticity of VIP interneurons in motor cortex.

Short-term plasticity is an important feature in the brain for shaping neural dynamics and for information processing. Short-term plasticity is known to depend on many factors including brain region, cortical layer, and cell type. Here we focus on vasoactive-intestinal peptide (VIP) interneurons (INs). VIP INs play a key disinhibitory role in cortical circuits by inhibiting other IN types, including Martinotti cells (MCs) and basket cells (BCs). Despite this prominent role, short-term plasticity at synapses to and from VIP INs is not well described. In this study, we therefore characterized the short-term plasticity at inputs and outputs of genetically targeted VIP INs in mouse motor cortex. To explore inhibitory to inhibitory (I → I) short-term plasticity at layer 2/3 (L2/3) VIP IN outputs onto L5 MCs and BCs, we relied on a combination of whole-cell recording, 2-photon microscopy, and optogenetics, which revealed that VIP IN→MC/BC synapses were consistently short-term depressing. To explore excitatory (E) → I short-term plasticity at inputs to VIP INs, we used extracellular stimulation. Surprisingly, unlike VIP IN outputs, E → VIP IN synapses exhibited heterogeneous short-term dynamics, which we attributed to the target VIP IN cell rather than the input. Computational modeling furthermore linked the diversity in short-term dynamics at VIP IN inputs to a wide variability in probability of release. Taken together, our findings highlight how short-term plasticity at VIP IN inputs and outputs is specific to synapse type. We propose that the broad diversity in short-term plasticity of VIP IN inputs forms a basis to code for a broad range of contrasting signal dynamics.

Increased Expression of the Neuropeptides PACAP/VIP in the Brain of Mice with CNS Targeted Production of IL-6 Is Mediated in Part by Trans-Signalling.

Inflammation with expression of interleukin 6 (IL-6) in the central nervous system (CNS) occurs in several neurodegenerative/neuroinflammatory conditions and may cause neurochemical changes to endogenous neuroprotective systems. Pituitary adenylate cyclase-activating polypeptide (PACAP) and vasoactive intestinal polypeptide (VIP) are two neuropeptides with well-established protective and anti-inflammatory properties. Yet, whether PACAP and VIP levels are altered in mice with CNS-restricted, astrocyte-targeted production of IL-6 (GFAP-IL6) remains unknown. In this study, PACAP/VIP levels were assessed in the brain of GFAP-IL6 mice. In addition, we utilised bi-genic GFAP-IL6 mice carrying the human sgp130-Fc transgene (termed GFAP-IL6/sgp130Fc mice) to determine whether trans-signalling inhibition rescued PACAP/VIP changes in the CNS. Transcripts and protein levels of PACAP and VIP, as well as their receptors PAC1, VPAC1 and VPAC2, were significantly increased in the cerebrum and cerebellum of GFAP-IL6 mice vs. wild type (WT) littermates. These results were paralleled by a robust activation of the JAK/STAT3, NF-κB and ERK1/2MAPK pathways in GFAP-IL6 mice. In contrast, co-expression of sgp130Fc in GFAP-IL6/sgp130Fc mice reduced VIP expression and activation of STAT3 and NF-κB pathways, but it failed to rescue PACAP, PACAP/VIP receptors and Erk1/2MAPK phosphorylation. We conclude that forced expression of IL-6 in astrocytes induces the activation of the PACAP/VIP neuropeptide system in the brain, which is only partly modulated upon IL-6 trans-signalling inhibition. Increased expression of PACAP/VIP neuropeptides and receptors may represent a homeostatic response of the CNS to an uncontrolled IL-6 synthesis and its neuroinflammatory consequences.

Probing PAC1 receptor activation across species with an engineered sensor.

Class-B1 G-protein-coupled receptors (GPCRs) are an important family of clinically relevant drug targets that remain difficult to investigate via high-throughput screening and in animal models. Here, we engineered PAClight1P78A, a novel genetically encoded sensor based on a class-B1 GPCR (the human PAC1 receptor, hmPAC1R) endowed with high dynamic range (ΔF/F0 = 1100%), excellent ligand selectivity, and rapid activation kinetics (τON = 1.15 s). To showcase the utility of this tool for in vitro applications, we thoroughly characterized and compared its expression, brightness and performance between PAClight1P78A-transfected and stably expressing cells. Demonstrating its use in animal models, we show robust expression and fluorescence responses upon exogenous ligand application ex vivo and in vivo in mice, as well as in living zebrafish larvae. Thus, the new GPCR-based sensor can be used for a wide range of applications across the life sciences empowering both basic research and drug development efforts.

Transcriptional profiling identifies IL-33-expressing intestinal stromal cells as a signaling hub poised to interact with enteric neurons.

Recent advancements in mucosal immunology have unveiled a complex network of intercellular connections within diverse tissues, shedding light on the unique properties of different cell types. Central to this intricate network is the cytokine IL-33, which has gained significant attention for its critical role in various diseases, from allergy to cancer, triggering type 2 immune responses, among others. Recent research has challenged the prior assumptions attributing IL-33 expression to epithelial cells, highlighting stromal cells as the predominant source in adipose tissue and the lungs. However, in the complex landscape of the intestine, where IL-33 plays a crucial role in mediating immune surveillance and tolerance and is implicated in many gut-related disorders, its primary source, regulation, and main characteristics need more exploration. This study identifies stromal cells as the primary IL-33-expressing cell type in the small intestine. By investigating their transcriptome and intrinsic signaling pathways, we have uncovered a possible role of IL-33+ stromal cells in maintaining the stem cell niche and their potential crosstalk with neurons relevant to the regulation of axonogenesis. Importantly, our experiments have demonstrated that vasoactive intestinal peptide stimulation of a primary intestinal stromal cell culture significantly amplifies IL-33 expression on mRNA and protein level. Therefore, our study represents a significant leap forward in understanding the plethora of interactions IL-33+ intestinal stromal cells maintain in the intestine, paving the way for future investigations into stromal-neuro crosstalk in the gut. These findings hold great promise for developing targeted therapeutic strategies aimed at harnessing the potential of IL-33 across a spectrum of diseases.

Variant Impact Predictor database (VIPdb), version 2: trends from three decades of genetic variant impact predictors.

BACKGROUND: Variant interpretation is essential for identifying patients' disease-causing genetic variants amongst the millions detected in their genomes. Hundreds of Variant Impact Predictors (VIPs), also known as Variant Effect Predictors (VEPs), have been developed for this purpose, with a variety of methodologies and goals. To facilitate the exploration of available VIP options, we have created the Variant Impact Predictor database (VIPdb). RESULTS: The Variant Impact Predictor database (VIPdb) version 2 presents a collection of VIPs developed over the past three decades, summarizing their characteristics, ClinGen calibrated scores, CAGI assessment results, publication details, access information, and citation patterns. We previously summarized 217 VIPs and their features in VIPdb in 2019. Building upon this foundation, we identified and categorized an additional 190 VIPs, resulting in a total of 407 VIPs in VIPdb version 2. The majority of the VIPs have the capacity to predict the impacts of single nucleotide variants and nonsynonymous variants. More VIPs tailored to predict the impacts of insertions and deletions have been developed since the 2010s. In contrast, relatively few VIPs are dedicated to the prediction of splicing, structural, synonymous, and regulatory variants. The increasing rate of citations to VIPs reflects the ongoing growth in their use, and the evolving trends in citations reveal development in the field and individual methods. CONCLUSIONS: VIPdb version 2 summarizes 407 VIPs and their features, potentially facilitating VIP exploration for various variant interpretation applications. VIPdb is available at  https://genomeinterpretation.org/vipdb.

Reward history guides focal attention in whisker somatosensory cortex.

Prior reward is a potent cue for attentional capture, but the underlying neurobiology is largely unknown. In a novel whisker touch detection task, we show that mice flexibly shift attention between specific whiskers on a trial-by-trial timescale, guided by the recent history of stimulus-reward association. Two-photon calcium imaging and spike recordings revealed a robust neurobiological correlate of attention in the somatosensory cortex (S1), boosting sensory responses to the attended whisker in L2/3 and L5, but not L4. Attentional boosting in L2/3 pyramidal cells was topographically precise and whisker-specific, and shifted receptive fields toward the attended whisker. L2/3 VIP interneurons were broadly activated by whisker stimuli, motion, and arousal but did not carry a whisker-specific attentional signal, and thus did not mediate spatially focused tactile attention. Together, these findings establish a new model of focal attention in the mouse whisker tactile system, showing that the history of stimuli and rewards in the recent past can dynamically engage local modulation in cortical sensory maps to guide flexible shifts in ongoing behavior.

Genome-wide DNA methylation profile and its function in regulating Vip3Aa tolerance in fall armyworm (Spodoptera frugiperda).

BACKGROUND: Vegetative insecticidal proteins (Vips) are widely used in pest management, but Vip tolerance poses a significant threat. DNA methylation plays important roles in regulating the response of biological organisms to environmental stress, and it may also regulate fall armyworm (FAW, Spodoptera frugiperda) Vip3Aa tolerance. RESULTS: In this study, a DNA methylation map was developed for FAW, and its function in regulating FAW Vip3Aa tolerance was explored. The FAW genome-wide DNA methylation map showed that exons were preferred regions for DNA methylation and housekeeping genes were highly methylated. FAW was screened using Vip3Aa for ten generations, and bioassays indicated that Vip3Aa tolerance increased trans-generationally. A comparison of DNA methylation maps between Vip3Aa-tolerant and -susceptible strains showed that gene body methylation was positively correlated with gene expression level. FAW exhibits significant variation in DNA methylation among individuals, and Vip3Aa screening induces epigenetic variation based on DNA methylation. Moreover, the study demonstrated that a reduction in methylation density within the gene body of a 3'5'-cyclic nucleotide phosphodiesterase gene resulted in decreased expression and increased tolerance of FAW to Vip3Aa, which was validated through RNA interference experiments. CONCLUSION: The DNA methylation map and mechanism of Vip3Aa tolerance improve our understanding of DNA methylation and its function in Lepidoptera and provide a new perspective for developing pest management strategies. © 2024 Society of Chemical Industry.

Loss of Function of Vasoactive-intestinal Peptide Alters Sex Ratio and Reduces Male Reproductive Fitness in Zebrafish.

Vasoactive-intestinal peptide (Vip) is a pleiotropic peptide with a wide range of distribution and functions. Zebrafish possess 2 isoforms of Vip (a and b), in which Vipa is most homologous to the mammalian form. In female zebrafish, Vipa can stimulate LH secretion from the pituitary but is not essential for female reproduction, as vipa-/- females display normal reproduction. In contrast, we have found that vipa-/- males are severely subfertile and sex ratio of offspring is female-biased. By analyzing all aspects of male reproduction with wild-type (WT) males, we show that the testes of vipa-/- are underdeveloped and contain ∼70% less spermatids compared to WT counterparts. The sperm of vipa-/- males displayed reduced potency in terms of fertilization (by ∼80%) and motility span and duration (by ∼50%). In addition, vipa-/- male attraction to WT females was largely nonexistent, indicating decreased sexual motivation. We show that vipa mRNA and protein is present in Leydig cells and in developing germ cells in the testis of WT, raising the possibility that endogenous Vipa contributes to testicular function. Absence of Vipa in vipa-/- males resulted in downregulation of 3 key genes in the androgen synthesis chain in the testis, 3ß-hsd, 17ß-hsd1, and cyp11c1 (11ß-hydrogenase), associated with a pronounced decrease in 11-ketotestosterone production and, in turn, compromised reproductive fitness. Altogether, this study establishes a crucial role for Vipa in the regulation of male reproduction in zebrafish, like in mammals, with the exception that Vipa is also expressed in zebrafish testis.

Compliance of private ventilated improved pit latrines to odour and fly control guidelines: A technical audit in selected regions of Ghana.

The ventilated improved pit (VIP) latrine offers a promising route to safely managed sanitation to many households in developing countries. However, some technical guidelines must be followed in order to realise the technology's advantage of odour and fly nuisance control. This study sought to audit private VIP latrines in selected regions of Ghana to assess their compliance to conventional technical guidelines and to understand the major factors that influence the latrine designs. An inspection checklist was developed to assess 296 private VIP latrines in the Central, Ashanti and Northern Regions of Ghana while semi-structured interviews were conducted among the latrine owners to enquire the factors that influenced the designs of their latrines. The results show that provision of a window in the superstructure (86 %), and the avoidance of an insect screen in the window(s) (77 %) were the most complied guidelines. The use of 150 mm diameter vent pipe was the least satisfied guideline (5 %). On the average, a latrine satisfied about half (3.6) of the technical guidelines that were assessed. The decision or advice of local artisans is the most influential factor in the design of the latrines. Cost was the least mentioned factor cited by the latrine owners. There is the need to establish information desks at the various Metropolitan, Municipal and District Assemblies (MMDAs) to guide prospective owners on the proper design and construction of the VIP latrine. In addition, toilet construction should be incorporated in the curriculum for the basic training of building and construction students in Technical and Vocational Education and Training (TVET) institutions in Ghana. Further research is required to ascertain the basis of the decisions of local artisans and the potential impact of the use of accessories that are 'borrowed' from the WC toilet on odour and fly control in the latrine.

Extracellular vesicles from primary human macrophages stimulated with VIP or PACAP mediate anti-SARS-CoV-2 activities in monocytes through NF-κB signaling pathway.

Infection by SARS-CoV-2 is associated with uncontrolled inflammatory response during COVID-19 severe disease, in which monocytes are one of the main sources of pro-inflammatory mediators leading to acute respiratory distress syndrome. Extracellular vesicles (EVs) from different cells play important roles during SARS-CoV-2 infection, but investigations describing the involvement of EVs from primary human monocyte-derived macrophages (MDM) on the regulation of this infection are not available. Here, we describe the effects of EVs released by MDM stimulated with the neuropeptides VIP and PACAP on SARS-CoV-2-infected monocytes. MDM-derived EVs were isolated by differential centrifugation of medium collected from cells cultured for 24 h in serum-reduced conditions. Based on morphological properties, we distinguished two subpopulations of MDM-EVs, namely large (LEV) and small EVs (SEV). We found that MDM-derived EVs stimulated with the neuropeptides inhibited SARS-CoV-2 RNA synthesis/replication in monocytes, protected these cells from virus-induced cytopathic effects and reduced the production of pro-inflammatory mediators. In addition, EVs derived from VIP- and PACAP-treated MDM prevented the SARS-CoV-2-induced NF-κB activation. Overall, our findings suggest that MDM-EVs are endowed with immunoregulatory properties that might contribute to the antiviral and anti-inflammatory responses in SARS-CoV-2-infected monocytes and expand our knowledge of EV effects during COVID-19 pathogenesis.

Primary auditory thalamus relays directly to cortical layer 1 interneurons.

Inhibitory interneurons within cortical layer 1 (L1-INs) integrate inputs from diverse brain regions to modulate sensory processing and plasticity, but the sensory inputs that recruit these interneurons have not been identified. Here we used monosynaptic retrograde tracing and whole-cell electrophysiology to characterize the thalamic inputs onto two major subpopulations of L1-INs in the mouse auditory cortex. We find that the vast majority of auditory thalamic inputs to these L1-INs unexpectedly arise from the ventral subdivision of the medial geniculate body (MGBv), the tonotopically-organized primary auditory thalamus. Moreover, these interneurons receive robust functional monosynaptic MGBv inputs that are comparable to those recorded in the L4 excitatory pyramidal neurons. Our findings identify a direct pathway from the primary auditory thalamus to the L1-INs, suggesting that these interneurons are uniquely positioned to integrate thalamic inputs conveying precise sensory information with top-down inputs carrying information about brain states and learned associations.

PACAP/VIP in the prefrontal cortex mediates the rapid antidepressant effects of zhizichi decoction.

ETHNOPHARMACOLOGICAL RELEVANCE: Zhizichi decoction (ZZCD) is a traditional Chinese medicine formula that consists of Gardenia jasminoides J.Ellis (GJ) and Semen Sojae Praeparatum. It is used to treat insomnia and emotion-related disorders, such as irritability. Previous studies have found that GJ has a rapid antidepressant effect. The study found that ZZCD is safer than GJ at the same dosage. Consequently, ZZCD is a superior drug with quicker antidepressant effects than GJ. The rapid antidepressant effects of ZZCD were examined in this study, along with the components that make up this effect. It was determined that the activation of prefrontal Pituitary Adenylate Cyclase Activating Polypeptide (PACAP)/Vasoactive Intestinal Polypeptide (VIP) is essential for ZZCD's rapid antidepressant effects. AIM: This study identified and discussed the rapid antidepressant effects and biological mechanisms of ZZCD. MATERIALS AND METHODS: The tail suspension test (TST) and the forced swimming test (FST) were used to screen the effective dosage of ZZCD (0.67 g/kg, 1 g/kg, 4 g/kg). The effective dosage of ZZCD (1 g/kg) was tested in the TST conducted on Institute of Cancer Research (ICR) mice that were treated with lipopolysaccharide (LPS) at a concentration of 0.1 mg/mL. To confirm the expression of c-Fos, PACAP, and VIP in the prefrontal cortex (PFC), immunohistochemistry tests were conducted on mice following intragastric injection of ZZCD. Chemical characterization analysis and HPLC quality control analysis were conducted using UHPLC-Q-Obitrap-HRMS and chromatographic analysis. RESULTS: The results showed that an acute administration of ZZCD (1 g/kg) decreased the immobility time of Kunming (KM) mice in TST and FST. Depressive behaviors in TST-induced ICR mice treated with LPS (0.1 mg/mL) were reversed by ZZCD (1 g/kg). The results of immunohistochemical experiments showed that ZZCD (1 g/kg) activated neurons in the PFC and PACAP/VIP in the PFC. In this study, 22 substances in ZZCD were identified. Five primary distinctive fingerprint peaks-geniposide, genistin, genipin-1-ß-D-gentiobioside, glycitin, and daidzin-were found among the ten common peaks. CONCLUSION: ZZCD (1 g/kg) had significant rapid antidepressant effects. PACAP/VIP in the PFC was found to mediate the rapid antidepressant effects of ZZCD.

Variant Impact Predictor database (VIPdb), version 2: Trends from 25 years of genetic variant impact predictors.

Background: Variant interpretation is essential for identifying patients' disease-causing genetic variants amongst the millions detected in their genomes. Hundreds of Variant Impact Predictors (VIPs), also known as Variant Effect Predictors (VEPs), have been developed for this purpose, with a variety of methodologies and goals. To facilitate the exploration of available VIP options, we have created the Variant Impact Predictor database (VIPdb). Results: The Variant Impact Predictor database (VIPdb) version 2 presents a collection of VIPs developed over the past 25 years, summarizing their characteristics, ClinGen calibrated scores, CAGI assessment results, publication details, access information, and citation patterns. We previously summarized 217 VIPs and their features in VIPdb in 2019. Building upon this foundation, we identified and categorized an additional 186 VIPs, resulting in a total of 403 VIPs in VIPdb version 2. The majority of the VIPs have the capacity to predict the impacts of single nucleotide variants and nonsynonymous variants. More VIPs tailored to predict the impacts of insertions and deletions have been developed since the 2010s. In contrast, relatively few VIPs are dedicated to the prediction of splicing, structural, synonymous, and regulatory variants. The increasing rate of citations to VIPs reflects the ongoing growth in their use, and the evolving trends in citations reveal development in the field and individual methods. Conclusions: VIPdb version 2 summarizes 403 VIPs and their features, potentially facilitating VIP exploration for various variant interpretation applications. Availability: VIPdb version 2 is available at https://genomeinterpretation.org/vipdb.

Genetic Variability of CYP4F2, CYP2D6, CYP2E1, and ACE in the Chinese Yi Population.

Genetic polymorphisms of very important pharmacogenes (VIP) are a significant factor contributing to inter-individual variability in drug therapy. The purpose of this study was to identify significantly different loci in the Yi population and to enrich their pharmacogenomic information. 54 VIP variants were selected from the Pharmacogenomics Knowledge Base (PharmGKB) and genotyped in 200 Yi individuals. Then, we compared their genotype distribution between the Yi population and the other 26 populations using the χ2 test. Compared with the other 26 populations, the genotype frequencies of 4 single nucleotide polymorphisms (SNPs), rs2108622 (CYP4F2), rs1065852 (CYP2D6), rs2070676 (CYP2E1), and rs4291 (ACE), had significant differences in the Yi population. For example, the TT genotype frequency of rs2108622 (8.1%) was higher than that of African populations, and the AA genotype frequency of rs1065852 (27.3%) was higher than that of other populations except East Asians. We also found that the Yi populations differed the least from East Asians and the most from Africans. Furthermore, the differences in these variants might be related to the effectiveness and toxicity risk of using warfarin, iloperidone, cisplatin cyclophosphamide, and other drugs in the Yi population. Our data complement the pharmacogenomic information of the Yi population and provide theoretical guidance for their personalized treatment.

Binding Analysis of Sf-SR-C MAM Domain and Sf-FGFR Ectodomain to Vip3Aa.

Bacillus thuringiensis Vip3Aa has been widely used in transgenic crops to resist the erosion of insects. The Scavenger Receptor-C (SR-C) and Fibroblast Growth Factor Receptor (FGFR) of Spodoptera frugiperda (Sf-SR-C and Sf-FGFR) have formerly been identified as the cell receptors of Vip3Aa. However, the interaction mechanism of Vip3Aa binding to Sf-SR-C or Sf-FGFR is still unknown. Here, we purified the MAM domain of Sf-SR-C (Sf-MAM) and the Sf-FGFR ectodomain expressed extracellularly by Sf9 cells. We then solved the crystal structure of the Sf-MAM domain. Structure docking analysis of the Sf-MAM and Vip3Aa C-terminal domain (CTD) excluded the possibility of the two proteins binding. A further surface plasmon resonance (SPR) assay also revealed that the Sf-MAM and Sf-FGFR ectodomain could not bind to the Vip3Aa protein. Our results have raised the urgency of determining the authentic cell receptor for Vip3Aa.