Biology subjects

Hong, B.

Publications and source records attributed to Hong, B..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

Exogenous Methylglyoxal Improves Maize Yield by Alleviating Plant Diabetes and leaf senescence under Drought

Drought-induced leaf senescence is related to high sugar levels in leaves, photosynthesis inhibition, and ultimate yield loss. This physiological phenomenon in leaves bears resemblance to the symptom of diabetes in human disease. However, the underlying mechanisms of plant diabetes on carbon imbalance in maize leaf and corresponding detoxification strategy have not been well understood. In this study, we demonstrated that foliar application of exogenous methylglyoxal (MG) delayed leaf senescence and promoted photoassimilation, retrieved 14% yield loss induced by drought stress during grain filling stage. Transcriptome and metabolite analysis revealed that drought increased sugar accumulation in leaf with inhibition of sugar transporters facilitating phloem loading. This further lead to disequilibrium of glycolysis and over-accumulation of endogenous MG. Contrarily, exogenous MG significantly upregulated glycolytic flux and glyoxalase system catabolizing endogenous MG and advanced glycation end products toxicity, ultimately alleviating plant diabetes. Besides, the genes facilitating anabolism and catabolism of trehalose- 6-phosphate were promoted and suppressed by drought, respectively, whereas exogenous MG reversed the effect. Moreover, exogenous MG activated phenylpropanoid biosynthetic pathway, likely promoting cell structural integrity. Collectively, these results suggest that exogenous MG alleviates the toxic effect from drought-induced sugar accumulation and activates the defense-related pathway, thereby maintaining leaf function and yield production. HighlightExogenous methylglyoxal stimulates glycolytic flux and glyoxalase system, providing a potential insight to alleviate plant diabetes under drought condition.

physiology↗

bioRxiv2023

A longitudinal resource for population neuroscience of school-age children and adolescents in China

During the past decade, cognitive neuroscience has been calling for population diversity to address the challenge of validity and generalizability, ushering in a new era of population neuroscience. The developing Chinese Color Nest Project (devCCNP, 2013-2022), a ten-year pilot stage of the lifespan CCNP (2013-2032), is an ongoing project focusing on brain-mind development. The project aims to create and share a large-scale, longitudinal and multimodal dataset of typically developing children and adolescents (ages 6.0-17.9 at enrolment) in the Chinese population. The devCCNP houses not only phenotypes measured by demographic, biophysical, psychological and behavioural, cognitive, affective, and ocular-tracking assessments but also neurotypes measured with magnetic resonance imaging (MRI) of brain morphometry, resting-state function, naturalistic viewing function and diffusion structure. This Data Descriptor introduces the first data release of devCCNP including a total of 864 visits from 479 participants. Herein, we provided details of the experimental design, sampling strategies, and technical validation of the devCCNP resource. We demonstrate and discuss the potential of a multicohort longitudinal design to depict normative brain growth curves from the perspective of developmental population neuroscience. The devCCNP resource is shared as part of the "Chinese Data-sharing Warehouse for In-vivo Imaging Brain" in the Chinese Color Nest Project (CCNP) - Lifespan Brain-Mind Development Data Community (https://www.scidb.cn/en/c/ccnp) at the Science Data Bank. Design TypesO_LIAccelerated longitudinal design C_LIO_LIBrain-mind development C_LIO_LIPopulation imaging C_LIO_LIBrain chart C_LIO_LIRepeated measure C_LI MeasurementsO_LIPsychological behaviours C_LIO_LIBiophysical and physical measures C_LIO_LIIntelligence quotient measure C_LIO_LINeuroimaging C_LI Sample Characteristic - OrganismO_LIHomo sapiens C_LI Sample Characteristic - EnvironmentO_LISchool- and community-based sample C_LI Sample Characteristic - LocationO_LIChongqing and Beijing, China C_LI DurationO_LI10 years (2013-2022) C_LI

neuroscience↗

bioRxiv2022

Strike different neural notes at distinct stages: An integrative process of attention modulation in naturalistic speech

When we pay attention to someone, do we focus only on the sound they make, the word they use, or do we form a mental space shared with the speaker we want to pay attention to? Some would argue that the human language is no other than a simple signal, but others claim that human beings understand each other not only by relying on the words that have been said but also formed a shared ground in the specific conversation. This debate was raised early, but the conclusion remains vague. Our study aimed to investigate how attention modulates the neural coupling between the speaker and the listener in a cocktail party paradigm. The temporal response function (TRF) method was employed to reveal how the listener was coupled to the speaker at the neural level. The results showed that the neural coupling between the listener and the attended speaker peaked 5 seconds before speech onset at the delta band over the left frontal region, and was correlated with speech comprehension performance. In contrast, the attentional processing of speech acoustics and semantics occurred primarily at a later stage after speech onset and was not significantly correlated with comprehension performance. These findings suggest that our human brain might have adopted a predictive mechanism to achieve speaker-listener neural coupling for successful speech comprehension. Three key pointsO_LIListeners EEG signals coupled to the speakers 5 s before the speech onset, which revealed a "beyond the stimulus" attentional modulation. C_LIO_LISpeaker-listener attentional coupling is correlated to the listeners comprehension performance, but the speech-listeners coupling didnt. C_LIO_LIThe implementation of temporal response function methods and the neural language methods yielded novel perspectives to the analysis of the inter-brain studies. C_LI

neuroscience↗

bioRxiv2022

Recycling upstream redox enzymes expands the regioselectivity of cycloaddition in pseudo-aspidosperma alkaloid biosynthesis

Nature uses cycloaddition reactions to generate complex natural product scaffolds. Dehydrosecodine is a highly reactive biosynthetic intermediate that undergoes cycloaddition to generate several alkaloid scaffolds that are the precursors to pharmacologically important compounds such as vinblastine and ibogaine. Here we report how dehydrosecodine can be subjected to redox chemistry, which in turn allows cycloaddition reactions with alternative regioselectivity. By incubating dehydrosecodine with reductase and oxidase biosynthetic enzymes that act upstream in the pathway, we can access the rare pseudo-aspidosperma alkaloids, pseudo-tabersonine and pseudo-vincadifformine, both in vitro and by reconstitution in the plant Nicotiana benthamiana from an upstream intermediate. We propose a stepwise mechanism to explain the formation of the pseudo-tabersonine scaffold by structurally characterizing enzyme intermediates, and by monitoring the incorporation of deuterium labels. This discovery highlights how plants use redox enzymes to enantioselectively generate new scaffolds from common precursors.

biochemistry↗

bioRxiv2022

Expansion of the Catalytic Repertoire of Alcohol Dehydrogenases in Plant Metabolism

Medium-chain alcohol dehydrogenases (ADHs) comprise a highly conserved enzyme family that catalyse the reversible reduction of aldehydes. However, recent discoveries in plant natural product biosynthesis suggest that the catalytic repertoire of ADHs has been expanded. Here we report the crystal structure of dihydroprecondylocarpine acetate synthase (DPAS), an ADH that catalyses the non-canonical 1,4 reduction of an ,{beta}-unsaturated iminium moiety. Comparison with structures of plant-derived ADHs that catalyse 1,2-aldehyde and 1,2-iminium reductions suggest how the canonical ADH active site can be modified to carry out atypical carbonyl reductions, providing insight into how chemical reactions are diversified in plant metabolism.

biochemistry↗

bioRxiv2022

A non-lemniscal thalamic interface connecting alerting sensory cues to internal states in mice

Alterations in internal states, such as elevated arousal level and increased anxiety or fear, triggered by alerting environmental cues are required for behavioral state transitions promoting survival. However, the specific brain region that plays an interfacing role between alerting stimuli and internal states remains to be identified. Here, we report that the medial sector of the auditory thalamus (ATm), which consists of a group of non-lemniscal thalamic nuclei, can fulfill this function. VGluT2-expressing ATm (ATmVGluT2+) neurons receive direct and strong inputs from both visual and auditory midbrain regions, and project to multiple downstream structures critically involved in brain state regulation. Their activity was correlated with, and indispensable for, both blue light- and sound-induced NREM sleep-to-Wake transition, and their arousing effects were mainly mediated by, but not limited to, the temporal association cortices. ATmVGluT2+ neuron activation in awake behaving mice induced pupil dilation and behavioral responses suggestive of anxiety. Blocking the neurotransmitter release of ATmVGluT2+ neurons receiving auditory inputs selectively abolished loud noise-triggered escape behavior but not locomotion. Thus, the ATm is an interface in mouse brain that can transform alerting environmental cues into internal arousal and emotional state alterations that promote survival.

neuroscience↗

bioRxiv2022

Pathogen-Host Adhesion between SARS-CoV-2 S Proteins from Different Variants and Human ACE2 Probed at Single-Molecule and Single-Cell Levels

Pathogen-Host adhesion is considered the first step of infection for many pathogens such as bacteria and virus. The binding of the receptor binding domain (RBD) of SARS-CoV-2 Spike protein (S protein) onto human angiotensin-converting enzyme 2 (ACE2) is considered as the first step for the SARS-CoV-2 to adhere onto the host cells during the infection. Within three years, a number of variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been found all around the world. Here, we investigated the adhesion of S Proteins from different variants and ACE2 using atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) and single-cell force spectroscopy (SCFS). We found that the unbinding force and binding probability of the S protein from Delta variant to the ACE2 was the highest among the variants tested in our study at both single-molecule and single-cell levels. Molecular dynamics simulation showed that ACE2-RBD (Omicron) complex is destabilized by the E484A and Y505H mutations and stabilized by S477N and N501Y mutations, when compared with Delta variant. In addition, a neutralizing antibody, produced by immunization with wild type RBD of S protein, could effectively inhibit the binding of S proteins from wild type, Delta and Omicron variants onto ACE2. Our results provide new insight for the molecular mechanism of the adhesive interactions between S protein and ACE2 and suggest that effective monoclonal antibody can be prepared using wild type S protein against the different variants.

biophysics↗

bioRxiv2022

Neural correlates of perceived emotions in human insula and amygdala

The emotional status of a speaker is an important non-linguistic cue carried by human voice and can be perceived by a listener in vocal communication. Understanding the neural circuits involved in processing emotions carried by human voice is crucial for understanding the neural basis of social interaction. Previous studies have shown that human insula and amygdala responded more selectively to emotional sounds than non-emotional sounds. However, it is not clear whether the neural selectivity to emotional sounds in these brain structures is determined by the emotion presented by a speaker or by the emotion perceived by a listener. In this study, we recorded intracranial electroencephalography (iEEG) responses to emotional human voices while subjects performed emotion recognition tasks. We found that the iEEG responses of Heschls gyrus (HG) and posterior insula were determined by the presented emotion, whereas the iEEG responses of anterior insula and amygdala were driven by the perceived emotion. These results suggest that the anterior insula and amygdala play a crucial role in representing subjectively perceived emotion.

neuroscience↗

bioRxiv2021

Synaptic and mitochondrial plasticity associated with fear memory revealed by deep learning-based 3D reconstruction

Serial section electron microscopy (ssEM) can provide comprehensive 3D ultrastructural information of the brain with exceptional computational cost. Targeted reconstruction of subcellular structures from ssEM datasets is less computationally demanding but still highly informative. We thus developed a Region-CNN-based deep learning method to identify, segment, and reconstruct synapses and mitochondria to explore the structural plasticity of synapses and mitochondria in the auditory cortex of mice subjected to fear conditioning. Upon reconstructing over 135,000 mitochondria and 160,000 synapses, we found that fear conditioning significantly increases the number of mitochondria but decreases their size, and promotes the formation of multi-contact synapses comprising a single axonal bouton and multiple postsynaptic sites from different dendrites. Modeling indicates that such multi-contact configuration increases the information storage capacity of new synapses by over 50%. With high accuracy and speed in reconstruction, our method yields structural and functional insight into cellular plasticity associated with fear learning.

neuroscience↗

bioRxiv2021

Physiological underpinning of default-mode network emergence in the human infant brain

Human infancy is characterized by most rapid cerebral blood flow (rCBF) increases across lifespan and emergence of a fundamental brain system default-mode network (DMN). However, how infant rCBF change spatiotemporally across the brain and how the rCBF dynamics support emergence of vital functional networks such as DMN remains unknown. Here, by acquiring cutting-edge multi-modal MRI including pseudo-continuous arterial-spin-labeled perfusion MRI and resting-state functional MRI of infants aged 0 to 24 months, we elucidated unprecedented 4D spatiotemporal infant rCBF framework and region-specific physiology-function coupling across infancy. We found faster rCBF increases in the DMN than other regions. We also found strongly coupled increases of rCBF and network strength specifically in the DMN, suggesting faster local blood flow increase to meet extra neuronal metabolic demands in the DMN maturation. These results offer insights into physiological mechanism of brain functional network emergence and have important implications in altered network maturation in brain disorders.

neuroscience↗

bioRxiv2021

The Human walking kinematic model combined with upper and lower limb movement

The purpose of this study is to build a relatively complete human walking kinematic model. This model is combined with the rolling-foot model (lower limb) and multi-rod swinging model (upper limb) connected by COM. We calculated the velocity of COM and other critical joints of the upper limb by marker point capture experiment using the high-speed camera. This research shows that the hand joint velocity measured through the experiment can achieve high coincidence with that calculated by the theoretical model given specific inputs. Moreover, the common pattern of upper limb angles is also studied for an accurate description. The proposed kinematic model is expected to forecast desired motion intention for better compliance by the rehabilitation and assistive robots.

biophysics↗

bioRxiv2020

SARS-CoV-2 and Malayan pangolin coronavirus infect human endoderm, ectoderm and induced lung progenitor cells

Since the infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in several somatic cells, little is known about the infection of SASRS-CoV-2 and its related pangolin coronavirus (GX_P2V). Here we present for the first time that SARS-CoV-2 pseudovirus and GX_P2V could infect lung progenitor and even anterior foregut endoderm cells causing these cells death, which differentiated from human embryonic stem cells (hESCs). The infection and replication of SARS-CoV-2 and GX_P2V were inhibited when treated with whey protein of breastmilk and Remdesivir, confirming that these two viruses could infect lung progenitor and even anterior foregut endoderm. Moreover, we found that SARS-CoV-2 pseudovirus could infect endoderm and ectoderm. We found that whey protein blocked SARS-CoV-2 infecting these cells. In line with the SARS-CoV-2 results, GX_P2V could also infected endoderm and ectoderm, and also was inhibited by Remdesivir treatment. Although expressing coronavirus related receptor such as ACE2 and TMPRSS2, mesoderm cells are not permissive for SARS-CoV-2 and GX_P2V infection, which needed further to study the mechanisms. Interestingly, we also found that hESCs, which also express ACE2 and TMPRSS2 markers, are permissive for GX_P2V but not SARS-CoV-2 pseudovirus infection and replication, indicating the widespread cell types for GX_P2V infection. Heparin treatment blocked efficiently viral infection. These results provided insight that these stem cells maybe provided a stable repository of coronavirus function or genome. The potential consequence of SARS-CoV-2 and animal coronavirus such as GX_P2V infection in hESCs, germ layer and induced progenitors should be closely monitored.

microbiology↗

bioRxiv2020

Two bi-functional cytochrome P450 CYP72 enzymes from olive (Olea europaea) catalyze the oxidative C-C bond cleavage in the biosynthesis of secoxy-iridoids - flavor and quality determinants in olive oil

O_LIOlive (Olea europaea) is an important crop in Europe, with high cultural, economic, and nutritional significance. Olive oil flavor and quality depend on phenolic secoiridoids, but the biosynthetic pathway of these iridoids remains largely uncharacterized. C_LIO_LIWe discovered two novel, bi-functional cytochrome P450 enzymes, catalysing the rare oxidative C-C bond cleavage of 7-epi-loganin to produce oleoside methyl ester (OeOMES) and secoxyloganin (OeSXS), both through a ketologanin intermediary. Although these enzymes are homologous to the previously reported Catharanthus roseus Secologanin Synthase (CrSLS), the substrate and product profiles differ. C_LIO_LIBiochemical assays provided mechanistic insights into the two-step OeOMES and CrSLS reactions. Model-guided mutations of OeOMES changed the product profile in a predictable manner, revealing insights into the molecular basis for this change in product specificity. C_LIO_LIOur results suggest that, in contrast to published hypotheses, in planta production of secoxy-iridoids is secologanin independent. Notably, sequence data of cultivated and wild olives, points to a relation between domestication and OeOMES expression. Thus, the discovery of this key biosynthetic gene suggests a link between domestication and secondary metabolism, and could potentially be used as a genetic marker to guide next-generation breeding programs. C_LI

biochemistry↗

bioRxiv2020

The effect of whey protein on viral infection and replication of SARS-CoV-2 and pangolin coronavirus in vitro

Since the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human breastmilk, little is known about the antiviral property of human breastmilk to SARS-CoV-2 and its related pangolin coronavirus (GX_P2V). Here we present for the first time that whey protein from human breastmilk effectively inhibited both SARS-CoV-2 and GX_P2V by blocking viral attachment, entry and even post-entry viral replication. Moreover, human whey protein inhibited infectious virus production proved by the plaque assay. We found that whey protein from different species such as cow and goat also showed anti-coronavirus properties. And commercial bovine milk also showed similar activity. Interestingly, the main antimicrobial components of breastmilk, such as Lactoferrin and IgA antibody, showed limited anti-coronavirus activity, indicating that other factors of breastmilk may play the important anti-coronavirus role. Taken together, we reported that whey protein inhibits SARS-CoV-2 and its related virus of GX_P2V. These results rule out whey protein as a direct-acting inhibitor of SARS-CoV-2 and GX_P2V infection and replication and further investigation of its molecular mechanism of action in the context of COVID-19.

microbiology↗

bioRxiv2020

Snipe: Highly sensitive pathogen detection from metagenomic sequencing data

Metagenomics data provides rich information for the detection of foodborne pathogens from food and environmental samples that are mixed with complex background bacteria strains. While pathogen detection from metagenomic sequencing data has become an activity of increasing interest, shotgun sequencing of uncultured food samples typically produces data that contains reads from many different organisms, making accurate strain typing a challenging task. Particularly, as many pathogens may contain a common set of genes that are highly similar to those from normal bacteria in food samples, traditional strain-level abundance profiling approaches do not perform well at detecting pathogens of very low abundance levels. To overcome this limitation, we propose an abundance correction method based on species-specific genomic regions to achieve high sensitivity and high specificity in target pathogen detection at low abundance.

microbiology↗

bioRxiv2019

Attention-dependent preparatory processing of naturalistic narratives is correlated with speech comprehension

While human speech comprehension is thought to be an active process that involves top-down predictions, it remains unclear how predictive information is used to prepare for the processing of upcoming speech information. We aimed to identify the neural signatures of the preparatory processing of upcoming speech. Participants selectively attended to one of two competing naturalistic, narrative speech streams, and a temporal response function (TRF) method was applied to derive event-related-like neural responses from electroencephalographic data. The phase responses to the attended speech at the delta band (1-4 Hz) were correlated with the comprehension performance of individual participants, with a latency of -200-0 ms before onset over the fronto-central and left-lateralized parietal regions. The phase responses to the attended speech at the alpha band also correlated with comprehension performance, but with a latency of 650-980 ms post-onset over fronto-central regions. Distinct neural signatures were found for the attentional modulation, taking the form of TRF-based amplitude responses at a latency of 240-320 ms post-onset over the left-lateralized fronto-central and occipital regions. Our findings reveal how the brain gets prepared to process an upcoming speech in a continuous, naturalistic speech context.

neuroscience↗

bioRxiv2019

Reconstructing lost BOLD signal in individual participants using deep machine learning

The blood oxygen level-dependent (BOLD) signal in functional neuroimaging suffers from magnetic susceptibility artifacts and interference from metal implants. The resulting signal loss hampers functional neuroimaging studies and can lead to misinterpretation of findings. Here, we reconstructed compromised BOLD signal using deep machine learning. We trained a deep learning model to learn principles governing BOLD activity in one dataset and reconstructed artificially-compromised regions in another dataset, frame by frame. Strikingly, BOLD time series extracted from reconstructed frames were correlated with the original time series, even though the frames did not independently carry information about BOLD fluctuations through time. Moreover, reconstructed functional connectivity (FC) maps exhibited good correspondence with the original FC maps, indicating that the deep learning model recovered functional relationships among brain regions. We replicated this result in patients whose scans suffered signal loss due to intracortical electrodes. Critically, the reconstructions captured individual-specific information rather than group information learned during training. Deep machine learning thus presents a unique opportunity to reconstruct compromised BOLD signal while capturing features of an individuals own functional brain organization.

neuroscience↗

bioRxiv2019

Regularized-Ncut: Robust and homogeneous functional parcellation of neonate and adult brain networks

Brain network parcellation based on resting-state functional MRI (rs-fMRI) is affected by noise, resulting in spurious small patches and decreased functional homogeneity within each network. Robust and homogeneous parcellation of neonate brain is more difficult with neonate rs-fMRI associated with higher level of noise and no functional atlas as spatial constraints. To meet these challenges, we developed a novel data-driven Regularized Normalized-cut (RNcut) method. RNcut is formulated by adding two regularization terms, a smoothing term using Markov random fields and a small-patch removal term, to conventional normalized-cut (Ncut) method. The RNcut and competing methods were tested with simulated datasets with known ground truth and then applied to both adult and neonate rs-fMRI datasets. Based on the parcellated networks generated by RNcut, intra-network connectivity was quantified. The test results from simulated datasets demonstrated that the RNcut method is more robust (p<0.01) to noise and can delineate parcellated functional networks with significantly better (p<0.01) spatial contiguity and significantly higher (p<0.01) functional homogeneity than competing methods. Application of RNcut to neonate and adult rs-fMRI dataset revealed distinctive functional brain organization of neonate brains from that of adult brains. Collectively, we developed a novel data-driven RNcut method by integrating conventional Ncut with two regularization terms, generating robust and homogeneous functional parcellation without imposing spatial constraints. A broad range of brain network applications and analyses, especially exploratory investigations of parcellating neonate and infant brain with noisy dataset, can potentially benefit from this RNcut method.

neuroscience↗