Biology subjects

Lin, Y.-S.

Publications and source records attributed to Lin, Y.-S..

At least 19 recordsLinked to original sources

bioRxiv2026

Minimal N-methylated and stapled peptide ligands for the autophagy protein GABARAP

The LC3/GABARAP protein family is a promising target for selective inhibition of autophagy. Further, LC3/GABARAP ligands have been used as targeted degraders of soluble proteins, protein aggregates, mitochondria, lipid droplets, and RNA. However, the small molecules used for such applications have poor binding affinity and known off-target effects. LC3/GABARAP proteins are challenging targets for small-molecule drug development due to their long, shallow binding grooves. In this work, we evaluate multiple approaches to stabilizing the extended structure of the native binding motif, producing N-methylated peptides and stapled peptides with low nanomolar affinity. A crystal structure and molecular dynamics simulations support a model where the N-methylation pre-organizes the motif into an extended, strand-like structure. N-methylation allowed minimization of the binding motif to a tetrapeptide that retained sub-micromolar affinity while minimizing charge and overall molecular weight. The truncated, N-methylated tetrapeptide showed passive permeability in artificial membrane and cell-based transwell assays. These results highlight new drug-like space for LC3/GABARAP ligands with high affinity and subfamily selectivity. Table of Contents GraphicDrawn and developed by Mollie McGibbon and Joshua Kritzer O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/710535v2_ufig1.gif" ALT="Figure 1"> View larger version (68K): org.highwire.dtl.DTLVardef@1b74a1org.highwire.dtl.DTLVardef@861c09org.highwire.dtl.DTLVardef@9abc2corg.highwire.dtl.DTLVardef@b7f745_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Tractor Workflow Pipeline: A Scalable Nextflow Framework for Local Ancestry-Aware Genome-Wide Association Studies

The routine exclusion of admixed individuals from traditional Genome-Wide Association Studies (GWAS) due to concerns about spurious associations has hindered genetic analyses involving multiple ancestries. Tractor GWAS addresses this issue by incorporating local ancestry into its analysis, empowering identification of ancestry-enriched hits and generating ancestry-specific summary statistics. However, Tractor requires accurate genomic phasing and local ancestry inference as prerequisite steps, which requires additional bioinformatics expertise and decision points regarding reference panel setup. To streamline, harmonize, and automate this process, we present a scalable Nextflow workflow that integrates all necessary steps, minimizing the need for manual intervention while remaining modular and customizable. The workflow supports multiple commonly used tools and offers flexibility in how Tractor is implemented. To demonstrate its utility, we applied this pipeline to analyze 32 blood biomarkers in 6,245 two-way AFR-EUR admixed individuals from the UK Biobank. This pipeline ran efficiently at scale, replicated known associations, and identified novel ancestry-specific loci. These novel associations were largely driven by variants present on African ancestral tracts but absent from European tracts, underscoring the value of local ancestry-aware methods in uncovering previously missed genetic signals. By enabling the efficient analysis of admixed individuals, our workflow facilitates Tractor use, paving the way for more broader genetic discovery.

genomics↗

bioRxiv2025

Predictable modulation of a spontaneous post-translational modification in living cells

Glycation is a non-enzymatic post-translational modification associated with aging and disease. Because it occurs spontaneously, it is extremely difficult to control the extent of glycation at distinct sites within target proteins, especially in cellular systems. Here we report a chemical approach, referred to as dialAGE, that enables the site-specific control of protein glycation. This unique tool requires the introduction of just a single point mutation that modulates the glycation susceptibility of a nearby arginine. As proof-of-concept, extensive mass spectrometry analysis was performed to confirm that dialAGE can modulate site-specific glycation levels at multiple arginine residues in ubiquitin in vitro, enabling both enhanced and diminished glycation. Introduction of dialAGE point mutations and/or glycation with the biologically relevant glycating agent methylglyoxal did not affect polyubiquitin chain formation using in vitro ubiquitination assays. Furthermore, we show that dialAGE can be used to modulate ubiquitin glycation levels in living mammalian cells. We therefore anticipate that this method will be particularly useful for enabling the study of glycation as a genuine, functional, post-translational modification.

biochemistry↗

bioRxiv2025

Differential performance of polygenic prediction across traits and populations depending on genotype discovery approach

Polygenic scores (PGS) are widely used to estimate genetic predisposition to complex traits by aggregating the effects of common variants into a single measure. They hold promise in identifying individuals at increased risk for diseases, allowing earlier screening and interventions. Genotyping arrays, commonly used for PGS computation, are affordable and computationally efficient, while whole-genome sequencing (WGS) offers a more comprehensive view of genetic variation. In this study, we compared PGS derived from arrays and WGS across multiple traits to evaluate differences in predictive performance, portability across populations, and computational efficiency. We computed PGS for 10 traits, representing a range of heritability and polygenicity, in the three largest genetic ancestry groups in All of Us (European, African American, Admixed American), trained on multi-ancestry meta-analyses from the Pan-UK Biobank. Using the clumping and thresholding (C+T) method, we found that WGS-based PGS outperformed array-based PRS for highly polygenic traits but showed differentially reduced accuracy for sparse traits in certain populations. With the LD-informed PRS-CS method, we observed overall improved prediction performance compared to C+T, with WGS outperforming arrays across most non-cancer traits. The results obtained using PRS-CS closely align with those derived from pre-trained models in the PGS Catalog, with prediction achieving better performance using WGS than array genotypes for non-sparse traits. To further investigate factors influencing differential prediction performance between array and WGS, we ran simulations varying the proportions of causal SNPs directly captured by the technologies. These demonstrated that the proportion of causal variants genotyped dramatically affects prediction accuracy. Fine-mapping of empirical data supported this concept but also highlighted the importance of reducing non-informative variants for optimal prediction accuracy. In conclusion, while WGS-based PGS generally offer superior predictive power with PRS-CS, the advantage over arrays is context-dependent, varying by trait, population, and the PGS method. The ability to capture causal variants through these technologies largely drives the prediction accuracy. This study provides insights into the complexities and potential advantages of using different genotype discovery approaches for polygenic predictions across populations and informs on strategies to enhance accuracy.

genetics↗

bioRxiv2024

Dominant-negative TP53 mutations potentiated by the HSF1-regulatedproteostasis network

Protein mutational landscapes are shaped by how amino acid substitutions affect stability and folding or aggregation kinetics. These properties are modulated by cellular proteostasis networks. Heat shock factor 1 (HSF1) is the master regulator of cytosolic and nuclear proteostasis. Chronic HSF1 ac-tivity upregulation is a hallmark of cancer cells, potentially because upregulated proteostasis factors fa-cilitate the acquisition and maintenance of oncogenic mutations. Here, we assess how HSF1 activation influences mutational trajectories by which p53 can escape cytotoxic pressure from nutlin-3, an inhibitor of the p53 regulator MDM2. HSF1 activation broadly increases the fitness of dominant-negative p53 substitutions, particularly non-conservative, biophysically unfavorable amino acid changes within buried regions of the p53 DNA-binding domain. These findings demonstrate that HSF1 activation reshapes the oncogenic mutational landscape by preferentially supporting the emergence and persistence of bio-physically disruptive, cancer-associated p53 substitutions, linking proteostasis network activity directly to oncogenic evolution.

molecular biology↗

bioRxiv2023

Repeated Caffeine Intake Suppresses Cerebral Grey Matter Responses to Chronic Sleep Restriction in an A1 Adenosine Receptor-Dependent Manner.

Evidence has shown that both sleep loss and daily caffeine intake can induce changes in grey matter (GM). Caffeine is frequently used to combat sleepiness and impaired performance caused by insufficient sleep. It is unclear 1) whether daily use of caffeine could prevent or exacerbate the GM alterations induced by chronic sleep restriction, and 2) whether the potential impact on GM plasticity depends on individual differences in the availability of adenosine receptors, which are involved in mediating effects of caffeine on sleep and waking function. In this double-blind, randomized, controlled study, 36 healthy adults (aged 28.9 {+/-} 5.2 y/o; 15 females; habitual daily caffeine intake < 450 mg; 29 homozygous C/C allele carriers of the A2A adenosine receptor (A2AR) gene variant rs5751876 of ADORA2A) underwent a 9-day laboratory visit consisting of one adaption day, 2 baseline days (BL), 5-day sleep restriction (CSR, 5 h time-in-bed), and a recovery day (REC) after an 8-h sleep opportunity. Nineteen participants received 300 mg caffeine in coffee through the 5 days of CSR (CAFF group), while 17 matched participants received decaffeinated coffee (DECAF group). We measured the GM morphology on the 2nd BL Day, 5th CSR Day, and REC Day. Moreover, we used [18F]-CPFPX PET to quantify the baseline availability of A1 adenosine receptors (A1R) and their relation to GM plasticity. The voxel-wise multimodal whole-brain analysis on T1-weighted images controlled for variances of cerebral blood flow indicated a significant interaction between caffeine and CSR in four brain regions: 1) right temporal-occipital region, 2) right thalamus, 3) left dorsolateral, and 4) dorsomedial prefrontal region. The post-hoc analyses indicated increased GM intensity in the DECAF group in all four regions but decreased GM in the thalamus as well as dorsolateral and dorsomedial prefrontal regions in the CAFF group after sleep restriction. Furthermore, lower baseline subcortical A1R availability predicted larger reduction in the CAFF group after CSR of all brain regions except for the caffeine-associated thalamic reduction. In conclusion, our data suggest an adaptive upregulation in GM after 5-day CSR, while concomitant use of caffeine instead leads to a GM reduction. The lack of consistent association with individual A1R availability may suggest that CSR and caffeine affect GM plasticity predominantly by a different mechanism. Future studies on the role of adenosine A2A receptors (ADORA2A) in CSR-induced GM plasticity are warranted.

neuroscience↗

bioRxiv2022

The evolution and structure of snake venom phosphodiesterase (svPDE) highlight its importance in venom actions

For decades, studies of snake venoms focused on the venom-ome-specific toxins (VSTs). VSTs are dominant soluble proteins believed to contribute to the main venomous effects and emerged into gene clusters for fast adaptation and diversification of snake venoms. However, the conserved minor venom components, such as snake venom phosphodiesterase (svPDE), remain largely unexplored. Here, we focus on svPDE by genomic and transcriptomic analysis across snake clades and demonstrate that soluble svPDE is co-opted from the ancestral membrane-attached ENPP3 (ectonucleotide pyrophosphatase/phosphodiesterase 3) gene by replacing the original 5 exon with the exon encoding a signal peptide. Notably, the exons, promoters and transcription/translation starts have been replaced multiple times during snake evolution, suggesting the evolutionary necessity of svPDE. The structural and biochemical analyses also show that svPDE shares the similar functions with ENPP family, suggesting its perturbation to the purinergic signaling and insulin transduction in venomous effects. Significance StatementWe provided a case of the evolutionary co-option strategy in which the secretory svPDE, one of the minor venom components, is generated from the ancestral membrane-anchored ENPP3 gene by using an alternative 5 exon. The first exon of the svPDE transcript encodes a signal peptide instead of the transmembrane domain of the ENPP3. Multiple replacement events of genomic elements during snake evolution maintain the expression of the svPDE transcripts, suggesting the crucial function of svPDE. Also, the structures and biochemical analyses indicate that svPDE reuse the original functions of ENPP3 in the bitten tissues and may interfere with normal cell signaling. Together, our study reveals the evolution of svPDE and suggests the importance of minor venom components.

evolutionary biology↗

bioRxiv2022

Genetically-Encoded Discovery of Perfluoroaryl-Macrocycles that Bind to Albumin and Exhibit Extended Circulation in-vivo

In this paper, we report selection of albumin-binding macrocyclic peptides from genetically encoded libraries of peptides modified by perfluoroaryl-cysteine SNAr chemistry. Modification of phage-displayed libraries SXCXnC-phage, n=3-5, where X is any amino acid except for cysteine by decafluoro-diphenylsulfone (DFS), yields genetically-encoded library of octafluoro-diphen-ylsulfone-crosslinked macrocycles (OFS-SXCXnC-phage). Selection from these libraries using albumin as a bait identified a family of significantly enriched perfluoroaryl-macrocycles. Synthesis of perfluoroaryl-macrocycles predicted by phage display and testing their binding properties by 19F NMR and fluorescent polarization identified OFS-macrocycle with SICRFFC sequence as the most potent albumin binder. We observed that OFS-macrocycles slowly react with biological nucleophiles such as glutathione. Replacing decafluoro-diphenylsulfone by nearly isosteric pentafluorophenyl sulfide yielded perfluorophenylsulfide (PFS)-crosslinked macrocycles devoid of undesired reactivity. The augmented lead PFS-macrocycle with SICRFFC sequence exhibited KD = 4-6 M towards human serum albumin and similar affinities towards rat and mouse albumins. When injected in mouse, the PFS-SICRFFCGGG compound was significantly retained in circulation in vivo when compared to control PFS-macrocyclic peptide. The perfluoroaryl-macrocycles with SICRFFC motif are the smallest known peptide macrocycle with significant affinity for human albumin and they are a productive starting point for future development of compact macrocycles with predictable circulation half-life in vivo. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=67 SRC="FIGDIR/small/504611v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@cd54d2org.highwire.dtl.DTLVardef@7bd9aborg.highwire.dtl.DTLVardef@10f7515org.highwire.dtl.DTLVardef@1cfc49a_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2022

Omicron-specific mRNA vaccine induced potent neutralizing antibody against Omicron but not other SARS-CoV-2 variants

The emerging SARS-CoV-2 variants of concern (VOC) harbor mutations associated with increasing transmission and immune escape, hence undermine the effectiveness of current COVID-19 vaccines. In late November of 2021, the Omicron (B.1.1.529) variant was identified in South Africa and rapidly spread across the globe. It was shown to exhibit significant resistance to neutralization by serum not only from convalescent patients, but also from individuals receiving currently used COVID-19 vaccines with multiple booster shots. Therefore, there is an urgent need to develop next generation vaccines against VOCs like Omicron. In this study, we develop a panel of mRNA-LNP-based vaccines using the receptor binding domain (RBD) of Omicron and Delta variants, which are dominant in the current wave of COVID-19. In addition to the Omicron- and Delta-specific vaccines, the panel also includes a "Hybrid" vaccine that uses the RBD containing all 16 point-mutations shown in Omicron and Delta RBD, as well as a bivalent vaccine composed of both Omicron and Delta RBD-LNP in half dose. Interestingly, both Omicron-specific and Hybrid RBD-LNP elicited extremely high titer of neutralizing antibody against Omicron itself, but few to none neutralizing antibody against other SARS-CoV-2 variants. The bivalent RBD-LNP, on the other hand, generated antibody with broadly neutralizing activity against the wild-type virus and all variants. Surprisingly, similar cross-protection was also shown by the Delta-specific RBD-LNP. Taken together, our data demonstrated that Omicron-specific mRNA vaccine can induce potent neutralizing antibody response against Omicron, but the inclusion of epitopes from other variants may be required for eliciting cross-protection. This study would lay a foundation for rational development of the next generation vaccines against SARS-CoV-2 VOCs.

microbiology↗

bioRxiv2021

Vaccinia virus-based vaccines confer protective immunity against SARS-CoV-2 virus in Syrian hamsters

COVID-19 in humans is caused by Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) that belongs to the beta family of coronaviruses. SARS-CoV-2 causes severe respiratory illness in 10-15% of infected individuals and mortality in 2-3%. Vaccines are urgently needed to prevent infection and to contain viral spread. Although several mRNA- and adenovirus-based vaccines are highly effective, their dependence on the "cold chain" transportation makes global vaccination a difficult task. In this context, a stable lyophilized vaccine may present certain advantages. Accordingly, establishing additional vaccine platforms remains vital to tackle SARS- CoV-2 and any future variants that may arise. Vaccinia virus (VACV) has been used to eradicate smallpox disease, and several attenuated viral strains with enhanced safety for human applications have been developed. We have generated two candidate SARS-CoV-2 vaccines based on two vaccinia viral strains, MVA and v-NY, that express full-length SARS-CoV-2 spike protein. Whereas MVA is growth-restricted in mammalian cells, the v-NY strain is replication-competent. We demonstrate that both candidate recombinant vaccines induce high titers of neutralizing antibodies in C57BL/6 mice vaccinated according to prime-boost regimens. Furthermore, our vaccination regimens generated TH1-biased immune responses in mice. Most importantly, prime-boost vaccination of a Syrian hamster infection model with MVA-S and v-NY-S protected the hamsters against SARS-CoV-2 infection, supporting that these two vaccines are promising candidates for future development. Finally, our vaccination regimens generated neutralizing antibodies that partially cross-neutralized SARS-CoV-2 variants of concern.

immunology↗

bioRxiv2021

Time to recover from daily caffeine intake.

Caffeine elicits widespread effects in the central nervous system and is the most frequently consumed psychostimulant worldwide. First evidence indicates that, during daily intake, the elimination of caffeine may slow down and the primary metabolite, paraxanthine, may accumulate. The neural impact of such adaptions is virtually unexplored. In this report, we leveraged the data of a laboratory study with N= 20 participants and three within-subject conditions: caffeine (150 mg caffeine x 3/day x 10 days), placebo (150 mg mannitol x 3/day x 10 days), and withdrawal (caffeine x 9 days, afterwards placebo x 1 day). Using liquid chromatography-mass spectrometry coupled with tandem mass spectrometry, we determined the course of salivary caffeine and paraxanthine, measured regularly at day 10. We assessed grey matter (GM) intensity and cerebral blood flow (CBF) in the withdrawal condition as compared to their changes in caffeine in our previous report. The results indicate high remaining levels of paraxanthine and of caffeine carried overnight during daily intake, and the levels of paraxanthine remained higher than in placebo during withdrawal. After 36 h of withdrawal, the previously reported caffeine-induced GM reduction was partially mitigated, while CBF was elevated compared to placebo. Our findings unveil that conventional daily caffeine intake does not provide sufficient time to clear up psychoactive compounds and restore cerebral responses, even after 36 hours of abstinence. They also suggest investigating consequences of a paraxanthine accumulation during daily caffeine intake.

pharmacology and toxicology↗

bioRxiv2021

The Host Cell's Endoplasmic Reticulum Proteostasis Network Profoundly Shapes the Protein Sequence Space Accessible to HIV Envelope

The sequence space accessible to evolving proteins can be enhanced by cellular chaperones that assist biophysically defective clients in navigating complex folding landscapes. It is also possible, however, for proteostasis mechanisms that promote strict quality control to greatly constrain accessible protein sequence space. Unfortunately, most efforts to understand how proteostasis mechanisms influence evolution rely on artificial inhibition or genetic knockdown of specific chaperones. The few experiments that perturb quality control pathways also generally modulate the levels of only individual quality control factors. Here, we use chemical genetic strategies to tune proteostasis networks via natural stress response pathways that regulate levels of entire suites of chaperones and quality control mechanisms. Specifically, we upregulate the unfolded protein response (UPR) to test the hypothesis that the host endoplasmic reticulum (ER) proteostasis network shapes the sequence space accessible to human immunodeficiency virus-1 (HIV) envelope (Env) protein. Elucidating factors that enhance or constrain Env sequence space is critical because Env evolves extremely rapidly, yielding HIV strains with antibody and drug escape mutations. We find that UPR-mediated upregulation of ER proteostasis factors, particularly those controlled by the IRE1-XBP1s UPR arm, globally reduces Env mutational tolerance. Conserved, functionally important Env regions exhibit the largest decreases in mutational tolerance upon XBP1s activation. This phenomenon likely reflects strict quality control endowed by XBP1s-mediated remodeling of the ER proteostasis environment. Intriguingly and in contrast, specific regions of Env, including regions targeted by broadly neutralizing antibodies, display enhanced mutational tolerance when XBP1s is activated, hinting at a role for host proteostasis network hijacking in potentiating antibody escape. These observations reveal a key function for proteostasis networks in decreasing instead of expanding the sequence space accessible to client proteins, while also demonstrating that the host ER proteostasis network profoundly shapes the mutational tolerance of Env in ways that could have important consequences for HIV adaptation.

biochemistry↗

bioRxiv2021

Working Memory Performance after Daily Caffeine Intake: Compromised Performance and Reduced Hippocampal Activity.

Neuroprotective effects of caffeine have been frequently reported in the context of disease and cognitive dysfunction as well as in epidemiological studies in humans. However, evidence on caffeine effects on neural and memory functions during daily intake in a healthy cognitive state remains scarce. This randomized double-blind placebo-controlled crossover study investigated working memory functions by N-back tasks and functional magnetic resonance imaging (fMRI) after daily caffeine intake compared to a placebo baseline and to acute caffeine withdrawal in 20 young healthy volunteers. Each volunteer was given 3 times 150 mg caffeine for 10 days in the daily caffeine condition, 3 times 150 mg mannitol for 10 days in the placebo condition, and 9-day caffeine plus 1-day mannitol in the acute withdrawal condition. During the 10th day, participants performed 4 N-back sessions (two loads each: 0- and 3-back) under controlled laboratory conditions. During the 4th session of N-Back (i.e. at 5.5 h, 36.5 h and > 10 days after the last caffeine intake in the caffeine, withdrawal, and placebo condition, respectively) we assessed blood-oxygen-level-dependent (BOLD) activity. During the entire 10th day, in 0-back tasks, we observed longer reaction times (RTs) in the withdrawal compared to the placebo (Cohens d = 0.7) and caffeine condition (Cohens d = 0.6), but no significant effects of conditions on error rates. In contrast, in 3-back tasks (controlled for 0-back), the RTs in the caffeine condition were longer compared to placebo (Cohens d = 0.6) and withdrawal (Cohens d = 0.5). Error rates were higher during both caffeine and withdrawal conditions compared to placebo (Cohens d of both contrasts = 0.4). Whole-brain analyses on fMRI data did not reveal significant condition-dependent differences in activities between task loads. Across task loads, however, we observed a reduced hippocampal activation (Cohens d = -1.3) during the caffeine condition compared to placebo, while no significant difference in brain activities between withdrawal and placebo conditions. Taken together, the worse working memory function and the hippocampal hypoactivation implicate a potential detrimental effect of daily caffeine intake on neurocognitive functions of healthy adults. Moreover, they echo the hippocampal volumetric reduction reported previously in the same volunteers. Lastly, acute withdrawal from daily caffeine intake impairs both low-order cognitive processes and working memory performance. Taking earlier studies on acute caffeine effects into account, our findings indicate that daily caffeine intake elicits a dynamic change in cerebral activities during the course of repeated consumption, with unknown consequences in the long run.

neuroscience↗

bioRxiv2021

CpG-adjuvanted stable prefusion SARS-CoV-2 spike protein protected hamsters from SARS-CoV-2 challenge

The COVID-19 pandemic presents an unprecedented challenge to global public health. Rapid development and deployment of safe and effective vaccines are imperative to control the pandemic. In the current study, we applied our adjuvanted stable prefusion SARS-CoV-2 spike (S-2P)-based vaccine, MVC-COV1901, to hamster models to demonstrate immunogenicity and protection from virus challenge. Golden Syrian hamsters immunized intramuscularly with two injections of 1 {micro}g or 5 {micro}g of S-2P adjuvanted with CpG 1018 and aluminum hydroxide (alum) were challenged intranasally with SARS-CoV-2. Prior to virus challenge, the vaccine induced high levels of neutralizing antibodies with 10,000-fold higher IgG level and an average of 50-fold higher pseudovirus neutralizing titers in either dose groups than vehicle or adjuvant control groups. Six days after infection, vaccinated hamsters did not display any weight loss associated with infection and had significantly reduced lung pathology and most importantly, lung viral load levels were reduced to lower than detection limit compared to unvaccinated animals. Vaccination with either 1 g or 5 g of adjuvanted S-2P produced comparable immunogenicity and protection from infection. This study builds upon our previous results to support the clinical development of MVC-COV1901 as a safe, highly immunogenic, and protective COVID-19 vaccine.

microbiology↗

bioRxiv2020

Regular caffeine intake attenuates REM sleep promotion and sleep quality in healthy men

Acute caffeine intake can attenuate homeostatic sleep pressure and worsen sleep quality. Besides, caffeine intake - particularly in high doses and close to bedtime - may also affect circadian-regulated REM sleep promotion, an important determinant of subjective sleep quality. However, it is not known whether such changes persist under chronic caffeine consumption during daytime. Twenty male caffeine consumers (26.4 {+/-} 4 years old, habitual caffeine intake 478.1 {+/-} 102.8 mg/day) participated in a double-blind crossover study. Each volunteer completed a caffeine (3 x 150 mg caffeine daily), a withdrawal (3 x 150 mg caffeine for eight days then placebo), and a placebo condition. After ten days of controlled intake and a fixed sleep-wake cycle, we recorded 8 h of electroencephalography starting 5 h after habitual bedtime (i.e., start on average at 04:22 am which is around the peak of circadian REM sleep promotion). A 60 min evening nap preceded each sleep episode and reduced high sleep pressure levels. While total sleep time and sleep architecture did not significantly differ between the three conditions, REM latency was longer after daily caffeine intake compared to both placebo and withdrawal. Moreover, the accumulation of REM sleep proportion was slower, and volunteers reported more difficulties at awakening after sleep and feeling more tired upon wake-up in the caffeine condition compared to placebo. Our data indicate that besides acute also regular daytime caffeine intake affects REM sleep regulation in men. We have evidence that regular caffeine intake during daytime weakens circadian sleep promotion when compared to placebo. Moreover, the observed caffeine-induced deterioration in the quality of awakening may suggest a potential motive to reinstate caffeine intake after sleep.

neuroscience↗

bioRxiv2020

The impact of daily caffeine intake on nighttime sleep: signs of overnight withdrawal?

Acute caffeine intake can delay sleep initiation and reduce sleep intensity, particularly when consumed in the evening. However, it is not clear whether these sleep disturbances disappear when caffeine is continuously consumed during daytime, which is common for most coffee drinkers. To address this question, we investigated the sleep of twenty male young habitual caffeine consumers during a double-blind, randomized, crossover study including three 10-day conditions: caffeine (3 x 150 mg caffeine daily), withdrawal (3 x 150 mg caffeine for eight days, then switch to placebo), and placebo (3 x placebo daily). After nine days of continuous treatment, electroencephalographically (EEG)-derived sleep structure and intensity were recorded during a scheduled 8-h nighttime sleep episode starting 8 (caffeine condition) and 15 h (withdrawal condition) after the last caffeine intake. Upon scheduled wake up time, subjective sleep quality and caffeine withdrawal symptoms were assessed. Unexpectedly, neither polysomnography-derived total sleep time, sleep latency, sleep architecture, nor subjective sleep quality differed among placebo, caffeine, and withdrawal conditions. Nevertheless, EEG power density in the sigma frequencies (12-16 Hz) during non-rapid eye movement (NREM) sleep was reduced in both caffeine and withdrawal conditions when compared to placebo. These results indicate that daily caffeine intake in the morning and afternoon hours does not strongly impair nighttime sleep structure or subjective sleep quality in healthy good sleepers who regularly consume caffeine. The reduced EEG power density in the sigma range might represent early signs of overnight withdrawal from the continuous presence of the stimulant during the day. Statement of SignificanceCaffeine consumption is highly prevalent worldwide and has been repeatedly shown to acutely disrupt sleep, particularly when consumed after several days of abstinence or close to bedtime. However, commonly, caffeine is consumed daily and during daytime. Our well-controlled laboratory study revealed that this common pattern of intake affects nighttime sleep differently: While slow-wave sleep duration or slow-wave activity were rather similar compared to placebo, caffeine intake surprisingly reduced EEG power density in the sigma frequencies. In the light of earlier studies, this might present early signs of caffeine withdrawal which occurs due to overnight caffeine abstinence. The present findings provide novel insights into the impact of daily presence and nightly abstinence of caffeine on nighttime sleep in regular consumers.

neuroscience↗

bioRxiv2020

Geographic and subsequent biotic isolations led to a diversity anomaly of Heterotropa (Aristolochiaceae) in insular versus continental regions of the Sino-Japanese Floristic Region

The Sino-Japanese Floristic Region is highly diverse with respect to temperate plants. However, the reasons for this diversity are poorly understood because most studies have only considered geographic isolation caused by climatic oscillations. Heterotropa (genus Asarum; Aristolochiaceae) diverges here and shows high species diversity in insular systems (63 species) compared to continental areas (25 species). Heterotropa shows low dispersal ability with small distribution ranges, implying diversification by geographic events, and high floral diversity, implying pollinator-mediated diversification. To reveal how abiotic and biotic factors have shaped the diversity anomaly of Heterotropa, we conducted phylogenetic analysis using ddRAD-seq and chloroplast genome datasets including 79 species, estimation of floral trait evolution, and comparison of isolation factors within clades based on distribution range and floral trait analysis. Phylogenetic analysis indicates that Heterotropa originated in mainland China and expanded to the Japanese Archipelago in the Miocene, and the major clades almost correspond to geographic distributions. Floral traits evolved repeatedly in the tip nodes within the clades. Although the major clades include a high proportion of species pairs showing isolation by floral traits, there are no conditional relationships between two isolation factors, indicating that most species pairs with floral trait isolation are distributed allopatrically. The repeated exposure and submergence of land-bridges caused by climatic oscillations would have led to significant population fragmentation in insular systems. Thus, the diversity anomaly of Heterotropa would have resulted from geographic and climatic events during the Miocene, while subsequent repeated floral trait evolution would have followed geographic isolation during the Pleistocene.

plant biology↗

bioRxiv2020

The potential SARS-CoV-2 entry inhibitor

Outbreak of coronavirus disease 2019 (COVID-19) occurred in Wuhan and has rapidly spread to almost all parts of world. In coronaviruses, the receptor binding domain (RBD) in the distal part of S1 subunit of SARS-CoV-2 spike protein can directly bind to angiotensin converting enzyme 2 (ACE2). RBD promote viral entry into the host cells and is an important therapeutic target. In this study, we discovered that theaflavin showed the lower idock score (idock score: -7.95 kcal/mol). To confirm the result, we discovered that theaflavin showed FullFitness score of -991.21 kcal/mol and estimated {Delta}G of -8.53 kcal/mol for the most favorable interaction with contact area of SARS-CoV-2 RBD by SwissDock service. Regarding contact modes, hydrophobic interactions contribute significantly in binding and additional hydrogen bonds were formed between theaflavin and Arg454, Phe456, Asn460, Cys480, Gln493, Asn501 and Val503 of SARS-CoV-2 RBD, near the direct contact area with ACE2. Our results suggest that theaflavin could be the candidate of SARS-CoV-2 entry inhibitor for further study.

bioinformatics↗