Biology subjects

Ai, H.

Publications and source records attributed to Ai, H..

45 records · Page 3Linked to original sources

bioRxiv2020

Seesaw Conformations of Npl4 in the Human p97 Complex and the Inhibitory Mechanism of a Disulfiram Derivative

p97, also known as valosin-containing protein (VCP) or Cdc48, plays a central role in cellular protein homeostasis1. Human p97 mutations are associated with several neurodegenerative diseases2,3. Targeting p97 and its cofactors is a strategy for cancer drug development4. Despite significant structural insights into the fungal homolog Cdc485-7, little is known about how human p97 interacts with its cofactors. Recently, the anti-alcohol abuse drug disulfiram was found to target cancer through Npl4, a cofactor of p978, but the molecular mechanism remains elusive. Here, using single-particle cryo-electron microscopy (cryo-EM), we uncovered three Npl4 conformational states in complex with human p97 before ATP hydrolysis. The motion of Npl4 results from its zinc finger motifs interacting with the N domain of p97, which is essential for the unfolding activity of p97. In vitro and cell-based assays showed that under oxidative conditions, the disulfiram derivative bis-(diethyldithiocarbamate)-copper (CuET) inhibits p97 function by releasing cupric ions, which disrupt the zinc finger motifs of Npl4, locking the essential conformational switch of the complex.

biophysics↗

bioRxiv2020

A Fast High-Affinity Fluorescent Serotonin Biosensor Engineered from a Tick Lipocalin

The authors have withdrawn their manuscript whilst they perform additional experiments to test some of their conclusions. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author. DetailsRegrettably, we, and several other researchers in the corresponding authors lab and not involved in the original study, have been unable to reproduce some of the reported key results under conditions originally described. We recently used the pDisplay-G-GESS-M plasmid to transfect HEK 293T cells and observed that the membrane localization of the biosensor was sensitive to FBS batches. By using an FBS batch from Gibco (Cat# 16000-044 and Lot #2103017RP), we were able to replicate the membrane localization similar to what was reported in Fig. 1e. However, the cells required the addition of several hundred micromolar of serotonin for robust fluorescence increase. These new results suggest that the affinity of G-GESS to serotonin is worse than that claimed in the initial article. We further used liquid chromatography-mass spectrometry (LC-MS) to analyze the serotonin stock solutions identified in our -80{degrees}C lab freezer and observed MS peaks suggesting a glutamate contamination in some of the analyzed samples. In addition, we used polymerase chain reaction (PCR) or reverse transcription-PCR (RT-PCR) to amplify gene fragments from our viral stocks and the sequencing results indicate that the viral stocks were contaminated with a glutamate biosensor. While we are still performing further investigation, in light of the existing findings, all authors agree to retract this paper. In the initial article, the sensor was tested in several cell culture systems, brain slices and behaving mice. We are presently unable to fully explain the observed sensor responses described in the initial article, but it is highly possible that these responses could be caused by the contaminated chemical or viral stocks. We deeply apologize to the scientific community for not detecting these problems sooner.

neuroscience↗

bioRxiv2020

Connectome-based predictive modeling of individual anxiety

Anxiety-related illnesses are highly prevalent in human society. Being able to identify neurobiological markers signaling high trait anxiety could aid the assessment of individuals with high risk for mental illness. Here, we applied connectome-based predictive modeling (CPM) to whole-brain resting-state functional connectivity (rsFC) data to predict the degree of anxiety in 76 healthy participants. Using a computational "lesion" method in CPM, we then examined the weights of the identified main brain areas as well as their connectivity. Results showed that the CPM could predict individual anxiety from whole-brain rsFC, especially from limbic areas-whole brain and prefrontal cortex-whole brain. The prediction power of the model significantly decreased from (simulated) lesions of limbic areas, lesions of the connectivity within the limbic system, and lesions of the connectivity between limbic regions and the prefrontal cortex. Although the same model also predicted depression, anxiety-specific networks could be identified independently, centered at the prefrontal cortex. These findings highlight the important role of the limbic system and the prefrontal cortex in the prediction of anxiety. Our work provides evidence for the usefulness of connectome-based modeling of rsFC in predicting individual personality differences and indicates its potential for identifying personality structures at risk of developing psychopathology.

neuroscience↗

bioRxiv2019

Identification of Factors Complicating Bioluminescence Imaging

In vivo bioluminescence imaging (BLI) has become a standard, non-invasive imaging modality for following gene expression or the fate of proteins and cells in living animals. Currently, bioluminescent reporters used in laboratories are mostly derivatives of two major luciferase families: ATP-dependent insect luciferases and ATP-independent marine luciferases. Inconsistent results have been reported for experiments using different bio-luminescent reporters and users are often confused when trying to choose an optimal bioluminescent reporter for a given research purpose. Herein, we re-examined inconsistency in several experimental settings and identified factors, such as ATP dependency, serum stability, and molecular size, which significantly affected BLI results. We expect this study will make the research community aware of these factors and facilitate more accurate interpretation of BLI data by considering the nature of each bioluminescent reporter.

biochemistry↗

bioRxiv2018

Adaptations during maturation in an identified honeybee interneuron responsive to waggle dance vibration signals

Honeybees are social insects, and individual bees take on different social roles as they mature, performing a multitude of tasks that involve multi-modal sensory integration. Several activities vital for foraging, like flight and waggle dance communication, involve sensing air vibrations using antennae. We investigated changes in the identified vibration-sensitive interneuron DL-Int-1 in the honeybee Apis mellifera during maturation by comparing properties of neurons from newly emerged and forager honeybees. Comparison of morphological reconstructions of the neurons revealed minor changes in gross dendritic features and consistent, region dependent and spatially localized changes in dendritic density. Comparison of electrophysiological properties showed an increase in the firing rate differences between stimulus and non-stimulus periods in foragers compared to newly emerged adult bees. The observed differences in neurons of foragers as compared to newly emerged adult honeybees indicate refined connectivity, improved signal propagation, and enhancement of response features important for the network processing of air vibration signals relevant for the waggle-dance communication of honeybees.

neuroscience↗

bioRxiv2018

A segmentation scheme for complex neuronal arbors and application to vibration sensitive neurons in the honeybee brain

The morphology of a neuron is strongly related to its physiological properties, and thus to information processing functions. Optical microscope images are widely used for extracting the structure of neurons. Although several approaches have been proposed to trace and extract complex neuronal structures from microscopy images, available methods remain prone to errors. In this study, we present a practical scheme for processing confocal microscope images and reconstructing neuronal structures. We evaluated this scheme using image data samples and associated gold standard reconstructions from the BigNeuron Project. In these samples, dendritic arbors belonging to multiple projection branches of the same neuron overlapped in space, making it difficult to automatically and accurately trace their structural connectivity. Our proposed scheme, which combines several software tools for image masking and filtering with an existing tool for dendritic segmentation and tracing, outperformed state-of-the-art automatic methods in reconstructing such neuron structures. For evaluating our scheme, we applied it to a honeybee local interneuron, DL-Int-1, which has complex arbors and is considered to be a critical neuron for encoding the information indicated in the waggle dance of the honeybee.

bioinformatics↗

bioRxiv2017

Development of honeybee waggle dance and its differences between recruits and scouts

The lifetime development of the waggle dance of 14 honeybees was automatically recorded just after the imaginal molt using high-definition camera modules connected with a Raspberry Pi computer and numbered radio-frequency identification tags fitted to the back of each bee. For most honeybees, waggle dance follow preceded the appearance of the first waggle dance from 1 week after the imaginal molt. The duration per trip increased just after waggle dance follow. Before the appearance of the first waggle dance, the honeybee repeatedly follows waggle dances that indicate a limited number (2-6) of food source locations. We discriminated between two types of foragers with different roles, recruits and novice scouts, by comparing the vectors indicated by the bees first waggle dance (sending vectors) with dances they had previously followed (received vectors). Of 14 tagged honeybees, 11 were categorized as recruits and 2 as novice scouts. For recruits (but not for novice scouts), the duration per trip increased significantly after waggle dances follow and substantially increased just before the appearance of the first waggle dance. Moreover, recruits increased the number of times they followed waggle dances indicating the same location, and their first waggle dance indicated this location. These results suggest that the differentiation of these two types of foragers is partly related to behavioral differences after waggle dance follows: whether trip is activated or not by follows a waggle dance.\n\nSummary statementBecause of technological difficulties, there are no studies comparing the development of recruit and scout waggle dances. Using miniature radio frequency identification tags, we observed and clarified these developmental processes.\n\nList of Abbreviations

animal behavior and cognition↗

bioRxiv2017

Network simulations of interneuron circuits in the honeybee primary auditory center

Processing of airborne vibration signals in the auditory system is essential for honeybee communication through the waggle dance language. Properties of neurons in the honeybee primary auditory center suggest a circuitry of excitatory and inhibitory neurons encoding these communication signals. To test this assumption, we simulated this network and analyzed the predicted responses for different types of inputs. In particular, we investigated the effect of specific inhibitory connections in the network. The results indicate that the experimentally observed responses of certain interneuron types are compatible with an inhibitory network of vibration processing in the primary auditory center of the honeybee.

bioinformatics↗

bioRxiv2017

The Y-Chromosome Clarifies The Evolutionary History Of Sus scrofa By Large-Scale Deep Genome Sequencing

The genetics and evolution of sex chromosomes are largely distinct from autosomes and mitochondrial DNA (mtDNA). The Y chromosome offers unique genetic perspective on male-line inheritance. Here, we uncover novel evolutionary history of Sus scrofa based on 205 high-quality genomes from worldwide-distributed different wild boars and domestic pig breeds. We find that only two haplotypes exist in the distal and proximal blocks of at least 7.7 Mb on chromosome Y in pigs across European and Asian continents. And the times of most recent common ancestors (TMRCA) within both haplotypes, approximately 0.14 and 0.10 million years, are far smaller than their divergence time of around 1.07 million years. Whats more, the relationship between Sumatran and Eurasian continent Sus scrofa is much closer than that we knew before. And surprisingly, European pigs share the same haplotype with many Chinese pigs, which is not consistent with their deep splitting status on autosome and mtDNA. Further analyses show that the haplotype in Chinese pigs was likely introduced from European wild boars via ancient gene flow before pig domestication about 24k years ago. Low mutation rates and no recombination in the distal and proximal blocks on chromosome Y help us detect this male-driven ancient gene flow. Taken together, our results update the knowledge of pig demography and evolution, and might shed insight into the genetics and evolution studies on chromosome Y in other mammals.

evolutionary biology↗