Biology subjects

Guo, J.

Publications and source records attributed to Guo, J..

At least 289 records · Page 16Linked to original sources

bioRxiv2021

Hippocampus-striatum wiring diagram revealed by directed stepwise polysynaptic tracing

The hippocampus and the striatum represent two major systems in the brain for learning, memory and navigation. Although they were traditionally considered as two parallel systems responsible for distinct types of learning or navigation, increasing evidence indicates a close synergetic or competitive interaction between them. Both the hippocampus and the striatum consist of multiple anatomical and functional domains. Besides the limited direct projection from the hippocampus to the ventral striatum, most of the functional interaction between them may be mediated by polysynaptic projections. Polysynaptic connectivity has been difficult to examine due to a lack of methods to continuously track the pathways in a controlled manner. Here we developed a novel approach for directed stepwise polysynaptic tracing by reconstituting a replication-deficient retrograde transneuronal virus - pseudorabies virus lacking gene IE180 (PRV{Delta}IE). We minimized PRV neurotoxicity by temporally restricting viral replication; and enabled both anatomical tracing and functional analysis of the circuits. With these tools, we delineated a hippocampus-striatum wiring diagram, which consists of pathways from specific functional domains in the hippocampus to corresponding domains in the striatum via distinct intermediate regions. This polysynaptic wring diagram provides a structural foundation for further elucidation of the interaction between the hippocampus and the stratum in multiple brain functions. Significance StatementWe created a new method for controlled stepwise tracing of polysynaptic neuronal circuits which also enables functional analysis of the circuits. With this method, we revealed the polysynaptic wiring diagram between the hippocampus and the striatum, two major brain structures centrally involved in learning, memory and spatial navigation. This wiring diagram demonstrates how specific anatomical domains in the hippocampus are connected to the specific domains in the striatum via distinct intermediate brain regions; thus it will help to elucidate the functional interaction between these two major memory and navigation systems. Our new method can be broadly applied to many other brain circuits for anatomical and functional analysis.

neuroscience↗

bioRxiv2021

Boundary domain genes were recruited to suppress bract growth and promote branching in maize

Grass inflorescence development is diverse and complex and involves sophisticated but poorly understood interactions of genes regulating branch determinacy and leaf growth. Here, we use a combination of transcript profiling, genetic and phylogenetic analyses to investigate tasselsheath1 (tsh1) and tsh4, two maize genes that simultaneously suppress inflorescence leaf growth and inhibit branching. We identify a regulatory network of inflorescence leaf suppression that involves the phase change gene tsh4 upstream of tsh1 and the ligule identity gene liguleless2 (lg2). We also find that a series of duplications in the tsh1 gene lineage facilitated its shift from boundary domain in non-grasses to suppressed inflorescence leaves of grasses. Collectively, these results suggest that the boundary domain genes tsh1 and lg2 were recruited to inflorescence leaves where they suppress growth and regulate a non-autonomous signaling center that promotes inflorescence branching, an important component of yield in cereal grasses.

plant biology↗

bioRxiv2021

Performance Comparison of Computational Prediction Methods for the Function and Pathogenicity of Non-coding Variants

Non-coding variants in the human genome greatly influence some traits and complex diseases by their own regulation and modification effects. Hence, an increasing number of computational methods are developed to predict the effects of variants in the human non-coding sequences. However, it is difficult for users with insufficient knowledge about the performances of computational methods to select appropriate computational methods from dozens of methods. In order to solve this problem, we assessed 12 performance measures of 24 methods on four independent non-coding variant benchmark datasets: (I) rare germline variant from ClinVar, (II) rare somatic variant from COSMIC, (III) common regulatory variant dataset, and (IV) disease associated common variant dataset. All 24 tested methods performed differently under various conditions, indicating that these methods have varying strengths and weaknesses under different scenarios. Importantly, the performance of existing methods was acceptable in the rare germline variant from ClinVar with area under curves (AUCs) of 0.4481 - 0.8033 and poor in the rare somatic variant from COSMIC (AUCs: 0.4984 - 0.7131), common regulatory variant dataset (AUCs: 0.4837 - 0.6472), and disease associated common variant dataset (AUCs: 0.4766 -0.5188). We also compared the prediction performance among 24 methods for non-coding de novo mutations in autism spectrum disorder and found that the CADD and CDTS methods showed better performance. Summarily, we assessed the performances of 24 computational methods under diverse scenarios, providing preliminary advice for proper tool selection and new method development in interpreting non-coding variants.

bioinformatics↗

bioRxiv2021

Enhancement of alphavirus replication in mammalian cells at sub-physiological temperatures

Chikungunya virus (CHIKV) is an alphavirus transmitted by Aedes mosquitoes, causing fever, rash and arthralgia in mammals. The function of the CHIKV non-structural protein 3 (nsP3) remains enigmatic. Building on previous studies (Gao et al, 2019) [1], we generated a panel of mutants in a conserved and surface-exposed cluster in the nsP3 alphavirus unique domain (AUD) and tested their replication using a sub-genomic replicon (SGR). Three of these SGR mutants replicated well in mosquito cells but poorly in mammalian cells. We observed that this difference was due to culture temperature (mosquito cells: 28{degrees}C; mammalian cells: 37{degrees}C), as the mutants exhibited no replication defect in mammalian cells grown at a sub-physiological temperature (28{degrees}C). Similar phenotypes were observed for infectious CHIKV and the closely related ONyong Nyong virus. Intriguingly, the wildtype SGR replicated more efficiently in mammalian cells at 28{degrees}C compared to 37{degrees}C. To explore the mechanism behind this difference, we focused on two known antiviral pathways: interferon-stimulated genes (ISGs) and stress granules (SGs). SGR replication was concomitant with increased expression of ISGs at 37{degrees}C, but this response was impaired at 28{degrees}C. We also observed enhanced recruitment of the SG component G3BP1 into cytoplasmic sites of viral genome replication at 28{degrees}C. These findings may have real-world implications as when a mosquito bites a mammal, the virus first infects cells in peripheral tissues which are often at sub-physiological temperatures. We propose that alphaviruses such as CHIKV have evolved mechanisms to both promote viral genome replication and concomitantly limit antiviral responses in these cells. Significance statementChikungunya virus (CHIKV) is a re-emerging arbovirus that is transmitted by Aedes mosquitos and poses epidemic threats. Arboviruses must be able to grow efficiently in both the mosquito vector and the mammalian host, which have different body temperatures. Following a mosquito bite, the first cells infected are typically in the skin and are at sub-physiological temperatures, ie lower than the internal body temperature (37{degrees}C). Here we show that CHIKV grows more efficiently in mammalian cells cultured at 28{degrees}C, compared to 37{degrees}C. We investigated the mechanism behind this increase in growth efficiency and demonstrated that at the lower temperature the production of antiviral genes was impaired. Additionally, proteins that respond to cellular stress and are needed for virus replication were more abundantly recruited to sites in the cell where the virus was replicating. We propose that CHIKV has evolved mechanisms to promote its replication in mammalian cells at sub-physiological temperatures to facilitate infection of mammals via a mosquito bite.

microbiology↗

bioRxiv2021

Inhibitory hippocampo-septal projection controls locomotion and exploratory behavior

Although the hippocampus is generally considered a cognitive center for spatial representation, learning and memory, increasing evidence supports its roles in regulation of locomotion. However, the neuronal mechanisms of hippocampal regulation of locomotion and exploratory behavior remain unclear. Here we found that the inhibitory hippocampo-septal projection bi-directionally controls locomotion speed of mice. Pharmacogenetic activation of these septum-projecting interneurons decreased locomotion and exploratory behavior. Similarly, activation of the hippocampus-originated inhibitory terminal in the medial septum reduced locomotion. On the other hand, inhibition of the hippocampus-originated inhibitory terminal increased locomotion. The locomotion-regulative roles were specific to the septal projecting interneurons as activation of hippocampal interneurons projecting to the retrosplenial cortex did not change animal locomotion. Therefore, this study reveals a specific long-range inhibitory output from the hippocampus in the regulation of animal locomotion.

neuroscience↗

bioRxiv2021

A G-lectin Receptor Kinase is a Negative Regulator of Arabidopsis Immunity Against Root-Knot Nematode Meloidogyne incognita

Root-knot nematodes (Meloidogyne spp., RKN) are responsible for extensive crop losses worldwide. For infection, they penetrate plant roots, migrate between plant cells, and establish feeding sites, known as giant cells, in the root pericycle. Previously, we found that nematode perception and early plant responses were similar to those for microbial pathogens and require the BAK1 co-receptor in Arabidopsis thaliana and tomato. To identify additional receptors involved in this process, we implemented a reverse genetic screen for resistance or sensitivity to RKN using Arabidopsis T-DNA alleles of genes encoding transmembrane receptor-like kinases. This screen identified a pair of allelic mutations with enhanced resistance to RKN in a gene we named ENHANCED RESISTANCE TO NEMATODES 1 (ERN1). ERN1 encodes a G-type lectin receptor kinase (G-LecRK) with a single pass transmembrane domain. Further characterization showed that ern1 mutants displayed stronger activation of MAP kinases, elevated levels of the defense marker MYB51, and enhanced H202 accumulation in roots upon RKN elicitor treatments. Elevated MYB51 expression and ROS burst were also observed in leaves of ern1 mutants upon flg22 treatment. Complementation of ern1.1 with 35S- or native promotor-driven ERN1 rescued the RKN infection and enhanced defense phenotypes. Taken together, our results indicate that ERN1 is an important negative regulator of immunity. One sentence summaryA plasma membrane localized G-lectin receptor kinase acts as a negative immune regulator by interfering with defense responses activated by nematode and microbial elicitors.

plant biology↗

bioRxiv2021

Iron promotes Slc7a11-deficient valvular interstitial cell osteogenic differentiation: A possible mechanism by which ferroptosis participates in intraleaflet hemorrhage-induced calcification.

BackgroundCalcific aortic valve disease (CAVD) is the most frequent pathogeny of aortic valve replacement in developed countries. Iron deposits are found in the intraleaflet hemorrhage (IH) areas of calcific aortic valves. Ferroptosis is a form of regulated cell death that involves metabolic dysfunction resulting from iron overload-dependent excessive lipid peroxidation. In this research, we attempted to clarify the role of ferroptosis in CAVD. MethodsThe level of ferroptosis in tissue and valvular interstitial cells (VICs) was assessed by the contents of 4-HNE, NADPH, ROS, and GSH, lipid peroxidation and mitochondrial morphology. The levels of calcification, iron accumulation and Slc7a11 expression in surgical aortic valve specimens were detected by Alizarin red or Von Kossa, Perls blue and immunohistochemical staining. The osteogenic differentiation of VICs was assessed by PCR and western blot analyses. Furthermore, RNA sequencing was used to detect potential differentially expressed genes between normal and osteogenic medium-treated (OM-treated) VICs. ResultsOur experiments demonstrated that ferroptosis occurred in the IH areas of calcific aortic valves. We also found that Slc7a11 was expressed at low levels in OM-treated VICs and IH areas. Finally, we demonstrated that iron promoted Slc7a11-deficient VICs osteogenic differentiation by aggravating ferroptosis in vitro. ConclusionIn conclusion, iron promotes Slc7a11-deficient VIC osteogenic differentiation by aggravating ferroptosis in vitro, thereby accelerating the progression of aortic valve calcification. StatementStatements and opinions expressed in the articles and communications herein are those of the author(s) and not necessarily those of the Editor(s), Society, or publisher, and the Editor(s), Society, and publisher disclaim any responsibility or liability for such material. Brief SummaryIn this work, two novel notions have been proposed. First, we reported that ferroptosis participated in the progression of CAVD. Second, this is the first cytology experiment of valvular interstitial cells (VICs) to clarify the mechanism by which intraleaflet hemorrhage aggravates calve calcification. This research provides new ideas and targets for alleviating the progression of CAVD, especially in patients who have calcified aortic valves without severe stenosis.

molecular biology↗

bioRxiv2021

Screening and Identification of Lujo Virus Entry Inhibitors from an FDA-Approved Drugs Library

The Lujo virus (LUJV) belongs to the Old World (OW) genus Mammarenavirus (family Arenaviridae); it is categorized as a biosafety level (BSL) 4 agent. Currently, there are no U.S. Food and Drug Administration (FDA)-approved drugs or vaccines specifically for LUJV or other pathogenic OW mammarenaviruses. Here, a high-throughput screening of an FDA-approved drug library was conducted using pseudotype viruses bearing LUJV envelope glycoprotein (GPC) to identify inhibitors of LUJV entry. Three hit compounds, trametinib, manidipine, and lercanidipine, were identified as LUJV entry inhibitors in the micromolar range. Mechanistic studies revealed that trametinib inhibited LUJV GPC-mediated membrane fusion by targeting C410 (located in the transmembrane (TM) domain), while manidipine and lercanidipine inhibited LUJV entry by acting as calcium channel blockers. Meanwhile, all three hits extended their antiviral spectra to the entry of other pathogenic mammarenaviruses. Furthermore, all three could inhibit the authentic prototype mammarenavirus, lymphocytic choriomeningitis virus (LCMV), and could prevent infection at the micromolar level. This study shows that trametinib, manidipine, and lercanidipine are candidates for LUJV therapy, and highlights the critical role of calcium in LUJV infection. The presented findings reinforce the notion that the key residue(s) located in the TM domain of GPC provide an entry-targeted platform for designing mammarenavirus inhibitors. IMPORTANCETo date, only one LUJV outbreak has been recorded; it occurred in 2008 and resulted in a fatality rate of 80% (4/5 cases). Pathogenesis studies and therapeutic strategies are therefore urgently needed. Repurposing approved drugs can accelerate the development of drug design and facilitate the understanding of infectious mechanisms. Here, three compounds, trametinib, manidipine, and lercanidipine, were identified as entry inhibitors against LUJV. Studying the underling mechanisms revealed that a key residue (C410) in LUJV GPC modulates its sensitivity/resistance to trametinib and demonstrated the critical role of calcium in LUJV infection.

microbiology↗

bioRxiv2021

The northern gene flow into southeastern East Asians inferred from genome-wide array genotyping

The population history of Southeast China remains poorly understood due to the sparse sampling of present-day populations and far less modeling with ancient genomic data. We here newly reported genome-wide genotyping data from 207 present-day Han Chinese and Hmong-Mien-speaking She people from Fujian and Taiwan, southeast China. We co-analyzed with 66 early-Neolithic to Iron-Age ancient Fujian and Taiwan individuals obtained from literature to explore the genetic continuity and admixture based on the genetic variations of high-resolution time transect. We found the genetic differentiation between northern and southern East Asians defined by a north-south East Asian genetic cline and the studied southern East Asians were clustered in the southern end of this cline. We also found that southeastern coastal continental modern East Asians harbored the genetic differentiation with other southern Tai-Kadai, Hmong-Mien, Austronesian and Austroasiatic speakers, as well as geographically close Neolithic-to-Iron Age populations, but relatedly close to post-Neolithic Yellow River ancients, which suggested the influence of southward gene flow on the modern southern coastal gene pool. Besides, we also identified one new Hmong-Mien genetic cline in East Asia with the coastal Fujian She localizing at the intersection position between Hmong-Mien and Han clines in the principal component analysis. She people show stronger genetic affinity with southern East Asian indigenous populations with the main ancestry deriving from Hanben-related populations. The southeastern Han Chinese could be modeled with the primary ancestry deriving from the group related to the Yellow River Basin millet farmers and the remaining from groups related to southeastern ancient indigenous rice farmers, which was consistent with the northern China origin of modern southeastern Han Chinese and in line with the historically and archaeologically attested southward migrations of Han people and their ancestors. Interestingly, f4-statistics and three-way admixture model results showed both coastal ancient sources related to Austronesian speakers and inland ancient sources related to Austroasiatic speakers complexed the modern observed fine-scale genetic structure here. Our estimated north-south admixture time ranges based on the decay of the linkage disequilibrium spanned from the Bronze age to historic periods, suggesting the recent large-scale population migrations and subsequent admixture participated in the formation of modern Han in Southeast Asia.

genetics↗

bioRxiv2021

Genomic insights into the differentiated population admixture structure and demographic history of North East Asians

North China and South Siberia, mainly populated by Altaic-speaking populations, possess extensive ethnolinguistic diversity and serve as the crossroad for the initial peopling of America and western-eastern trans-continental communication. Yet, the complex scenarios of genetic origin, population structure, and admixture history of North-East Asia remain to be fully characterized, especially for Mongolic people in China with a genome-wide perspective. Thus, we genotyped genome-wide SNPs for 510 individuals from 38 Chinese Mongolic, Tungusic, and Sinitic populations to explore the sharing alleles and haplotypes within the studied groups and following merged it with 3508 modern and ancient Eurasian individuals to reconstruct the deep evolutionary and natural selection history of northern East Asians. We identified significant substructures within Altaic-speaking populations with the primary common ancestry linked to the Neolithic northern East Asians: Western Turkic people harbored more western Eurasian ancestry; Northern Mongolic people in Siberia and eastern Tungusic people in Amur River Basin (ARB) possessed dominant Neolithic Mongolian Plateau (MP) or ARB ancestry; Southern Mongolic people in China owned obvious genetic impact from Neolithic Yellow River Basin (YRB) farmers. Additionally, we found the differentiated admixture history between western and eastern Mongolians and geographically close Northeast Hans: the former received a genetic impact from western Eurasians and the latter retained the dominant YRB and ARB Neolithic ancestry. Moreover, we demonstrated that Kalmyk people from the northern Caucasus Mountain possessed a strong genetic affinity with Neolithic MP people, supporting the hypothesis of their eastern Eurasian origin and long-distance migration history. We also illuminated that historic pastoral empires in the MP contributed considerably to the gene pool of northern Mongolic people but rarely to southern ones. We finally found natural signatures in Mongolians associated with alcohol metabolism. Generally, our results not only illuminated that complex population migration and admixture of Neolithic ancestral sources from the MP or ARB played an important role in the spread of Altaic-speaking populations and Proto-Altaic language, which partly supported the Northeast Asia-origin hypothesis, but also demonstrated that the observed multi-sources of genetic diversity contributed significantly to the modern existing extensive ethnolinguistic diversity in North-East Asia.

genomics↗

bioRxiv2021

The genomic formation of Tanka people, an isolated 'Gypsies in water' in the coastal region of Southeast China

ObjectivesThree different hypotheses proposed via the controversial evidence from cultural, anthropological and uniparental genetic analysis respectively stated that Tanka people probably originated from Han Chinese, ancient Baiyue tribe, or the admixture of them. Therefore, the genetic origin and admixture history of the Tanka people, an isolated "Gypsies in water" in the coastal region of Southeast China, are needed to be genetically clarified. Materials and methodsTo elucidate the genetic origin of the Southeast Tanka people and explore their genetic relationship with surrounding indigenous Tai-Kadai and Austronesian people and Neolithic-to-historic ancients from the Yellow River Basin (YRB) and Fujian, we conducted a large-scale population genomic study among 1498 modern and ancient Eurasians, in which 73 Tanka and 4 Han people were first reported here. Both allele-shared and haplotype-based statistical methods were used here, including PCA, ADMIXTURE, f-statistics, ALDER, qpGraph-/TreeMix and qpAdm/qpWave, ChromoPainter and FineSTRUCTURE ResultsWe found a specific genetic cline in PCA plots and detected the Tanka-specific homogeneous ancestry in model-based ADMIXTURE results, suggesting differentiated demographic history between Tanka and surrounding Hans. Formal tests based on sharing allele patterns showed a close relationship between Tanka people and Han Chinese, but the Tanka population harbored more southern East Asian ancestry related to Austronesian and Tai-Kadai people compared with southern Hans. Besides, the reconstructed differentiated demographic history revealed that southern Xinshizhou Tanka harbored more ancestry related to the Tai-Kadai or coastal ancient Neolithic to Bronze Age East Asians compared with northern Shacheng Tanka. The qpGraph-/TreeMix-based phylogenetic framework, qpAdm/qpWave-based admixture modeling and FineSTRUCTURE-based dendrogram among ancient northern and southern East Asians further demonstrated that the primary ancestry of modern Tanka derived from ancient millet farmers in the YRB with additional admixture from multiple southern East Asian sources. DiscussionSharing ancestry estimated from the f-statistics and sharing haplotypic landscape inferred from the ChromoPainter and FineSTRUCTURE showed that Southeast Tanka people not only had a close genetic relationship with both Northern Hans and YRB millet farmers but also possessed more southern East Asian ancestry related to Austronesian, Tai-Kadai and Hmong-Mien people. Our genomic data and fitted admixture models supported modern Tanka originated from ancient North China and obtained additional gene flow from ancient southern East Asians in the processes of southward migrations.

genetics↗

bioRxiv2021

Inactivation effects of plasma-activated water on Fusarium graminearum

The continuous usage of fungicides poses a potential threat to the environment, ranging from mere irritation to being very toxic to human beings and organisms. Plasma-activated water (PAW) has recently gained much interest as a promising candidate to inactivate fungi. However, the inactivation mechanisms of PAW are still not well understood. In this study, the effect of PAW on the viability and the cellular responses of Fusarium graminearum in PAW inactivation were investigated. The results showed that microbial activity of spores was significantly inhibited by PAW treatment (P < 0.05). The symptoms caused by F. graminearum were significantly reduced on the spikelets. Our data indicated that PAW could induce cell wall sculpturing, membrane permeability changes, and mitochondrial dysfunction. Differential gene expression analysis also confirmed that the cell membrane, the cell wall and the mitochondria were the organelles most affected by PAW. The results from this study facilitate the understanding of the mechanisms underlying the responses of F. graminearum to PAW and the development of PAW as a potential fungicidal agent or an effective supplement to fungicides. HighlightsO_LIThe viability of F. graminearum is notably inhibited by PAW C_LIO_LIThe symptoms caused by F. graminearum were significantly reduced on the spikelets C_LIO_LIOxidative stress induce cell wall sculpturing, membrane permeability change C_LIO_LIPAW can cause the mitochondrial dysfunction C_LIO_LICell wall, membrane and mitochondria are the most affected organelles by PAW C_LI

microbiology↗

bioRxiv2021

Novel insights into pulmonary phosphate homeostasis and osteoclastogenesis emerge from the study of pulmonary alveolar microlithiasis.

Pulmonary alveolar microlithiasis (PAM) is an autosomal recessive lung disease caused by a deficiency in the pulmonary epithelial Npt2b sodium-phosphate co-transporter that results in accumulation of phosphate and formation of hydroxyapatite microliths in the alveolar space. The single cell transcriptomic analysis of a PAM lung explant showing a robust osteoclast gene signature in alveolar monocytes and the finding that calcium phosphate microliths contain a rich protein and lipid matrix that includes bone resorbing osteoclast enzymes suggested a role for osteoclast-like cells in the defense against microliths. While investigating the mechanisms of microlith clearance, we found that Npt2b modulates pulmonary phosphate homeostasis through effects on alternative phosphate transporter activity and alveolar osteoprotegerin, and that microliths induce osteoclast formation and activity in a receptor activator of nuclear factor-{kappa}B ligand (RANKL) and dietary phosphate dependent manner. This work reveals that Npt2b and pulmonary osteoclast-like cells play key roles in pulmonary homeostasis and suggest potential new therapeutic targets for the treatment of lung disease.

molecular biology↗

bioRxiv2021

Cell adhesion factors during adolescence support amygdalo-cortical connections and flexible action later in life

Adolescent brain development is characterized by dramatic neuronal remodeling in the prefrontal cortex. This plasticity is presumed to act in part to "set the stage" for prefrontal cortical function in adulthood, but causal relationships have largely not been verified. Integrins are cell adhesion factors that provide a link between the extracellular matrix and the intracellular actin cytoskeleton. We find that {beta}1-integrin presence in the prelimbic subregion of the prefrontal cortex (PL) during adolescence, but not adulthood, is necessary for adult mice to select actions based on reward likelihood and value. These behaviors require coordinated limbic-frontal-striatal circuits. We identified projections from the basolateral amygdala (BLA) to PL as being necessary for mice to express learned response strategies. We then visualized adolescent PL neurons receiving input from the BLA and projecting to the dorsomedial striatum (DMS), a primary striatal output by which the PL controls reward-related behavior. These projection-defined neurons had a more "adult-like" morphology relative to a general population of layer V PL neurons. {beta}1-integrin loss caused the overexpression of stubby-type dendritic spines at the expense of more mature spines, a phenotype not observed when {beta}1-integrins were silenced before or after adolescence. Together, these experiments localize {beta}1-integrin-mediated cell adhesion activity within a developing di-synaptic circuit that coordinates flexible action.

neuroscience↗

bioRxiv2021

Screening and Identification of Lassa Virus Endonuclease-targeting Inhibitors from a Fragment-based Drug Development Library

Lassa virus (LASV) belongs to the Old World genus Mammarenavirus, family Arenaviridae, and order Bunyavirales. Arenavirus contains a segmented negative-sense RNA genome, which is in line with the bunyavirus and orthomyxoviruses. The segmented negative-sense RNA viruses utilize a cap-snatching strategy to provide primers cleavaged from the host capped mRNA for viral mRNA transcription. As a similar strategy and the conformational conservation shared with these viruses, the endonuclease (EN) would serve as an attractive target for developing broad-spectrum inhibitors. Using the LASV minigenome (MG) system, we screened a fragment-based drug development library and found three candidates (F1204, F1781, and F1597) inhibited MG activity. All three candidates also inhibited the prototype arenavirus Lymphocytic choriomeningitis virus (LCMV) MG activity. Furthermore, the investigation revealed that two benzotriazole compounds (F1204 and F1781) effectively inhibited authentic LCMV and severe fever with thrombocytopenia syndrome virus (SFTSV) infections. The combination of either compound with an arenavirus entry inhibitor had significant synergistic antiviral effects. Moreover, both F1204 and F1781 were found to exert the binding ability of LASV EN with binding affinity at the micromolar level. These findings provide a basis for developing benzotriazole compounds as potential candidates for the treatment of segmented negative-sense RNA virus infections. ImportanceCap-snatching is the mRNA transcription strategy shared by all the segmented, negative-sense RNA viruses. Using a fragment-based drug development (FBDD) library, we tried to screen out the backbone compound to inhibit the endonuclease activity and thus block this kind of virus infection. Two benzotriazole compounds, F1204 and F1781, were identified to inhibit the Lassa virus (LASV) minigenome activity by targeting the LASV EN.

microbiology↗

bioRxiv2021

Mutation in Abl kinase with altered drug binding kinetics indicates a novel mechanism of imatinib resistance

Protein kinase inhibitors are potent anti-cancer therapeutics (1). For example, the Bcr-Abl kinase inhibitor imatinib decreases mortality for Chronic Myeloid Leukemia (CML) by 80% (2, 3), but 22-41% of patients acquire resistance to imatinib (4). About 70% of relapsed patients harbor mutations in the Bcr-Abl kinase domain (5), in which more than a hundred different mutations have been identified (6-8). Some mutations are located near the imatinib binding site and cause resistance through altered interactions with the drug. However, many resistance mutations are located far from the drug binding site (9) and it remains unclear how these mutations confer resistance. Additionally, earlier studies on small sets of patient-derived imatinib resistance mutations indicated that some of these mutant proteins were in fact sensitive to imatinib in cellular and biochemical studies (10). Here, we surveyed the resistance of 94 patient-derived Abl kinase domain mutations annotated as disease-relevant or resistance-causing using an engagement assay in live cells. We found that only two-thirds of mutations weaken imatinib affinity by more than two-fold compared to Abl wild type. Surprisingly, one-third of mutations in Abl kinase domain still remain sensitive to imatinib and bind with similar or higher affinity than wild type. Intriguingly, we identified a clinical Abl mutation that binds imatinib with wild type-like affinity but dissociates from imatinib three times faster. Given the relevance of residence time for drug efficacy (11-14), mutations that alter binding kinetics could cause resistance in the non-equilibrium environment of the body where drug export and clearance play critical roles. SignificanceWe performed the first in cell screen of imatinib binding against a library of Abl kinase mutants derived from patients with imatinib-resistant CML. The majority of mutations readily bind imatinib, posing the question of how these mutations cause resistance in patients. We identified a kinetic mutant that binds imatinib with wild type affinity but dissociates considerably faster from the mutant kinase. Using NMR and molecular dynamics, we found that this mutation increases the conformational dynamics of the mutant protein, linking conformational dynamics of the protein to drug dissociation. The results underline the importance of drug dissociation kinetics for drug efficacy and propose a novel kinetic resistance mechanism that may be targetable by altering drug treatment schedules.

biochemistry↗

bioRxiv2021

Distinct Hippocampal Neuronal Reactions Reveal Different Neuronal Codes for Memory Generalization

To survive in an ever-changing world we need to learn and memorize associations of environmental stimuli and generalize them to new situations. Both memory and generalization critically rely on the hippocampus, but it is unclear how hippocampal neuronal activities represent memory and generalization, and if a conserved hippocampal mechanism serves these functions. Here we compared neuronal activities in hippocampal CA1 region of two sub-strains of the widely used C57BL/6 mice, C57BL/6J (B6J) and C57BL/6NCrl (B6NCrl), in contextual fear conditioning. Both sub-strains learnt well but differed in freezing and generalization. They displayed distinct early-late bi-phasic reactions to the unconditioned stimulus. While in both sub-strains the neurons showing late-phase reactions were preferentially engaged in memory representation, the neuronal activity feature that correlated with generalization level differed in the two sub-strains: in B6NCrl, these neurons activity level during learning negatively correlated with the generalization level; in B6J, functional coupling of these late-phase neurons with other neurons positively correlated with the generalization level. We further found that the distinct neuronal reactions were accompanied by distinct GABAb receptor-mediated inhibition but not by differences in the major synaptic inputs or neuronal excitability of the CA1. Therefore, this comparative study reveals two signature neuronal activity features in learning that can predict generalization levels. The results also demonstrate that differences in hippocampal network properties lead to diverse hippocampal mechanisms in memory encoding and generalization.

neuroscience↗

bioRxiv2021

Genomic history and forensic characteristics of Sherpa highlanders on the Tibetan Plateau inferred from high-resolution genome-wide InDels and SNPs

Sherpa people, one of the high-altitude hypoxic adaptive populations, mainly reside in Nepal and the southern Tibet Autonomous Region. The genetic origin and detailed evolutionary profiles of Sherpas remain to be further explored and comprehensively characterized. Here we analyzed the newly-generated InDel genotype data from 628 Dingjie Sherpa people by merging with 4222 worldwide InDel profiles and collected genome-wide SNP data (approximately 600K SNPs) from 3324 individuals in 382 modern and ancient populations to explore and reconstruct the fine-scale genetic structure of Sherpas and their relationships with nearby modern and ancient East Asians based on the shared alleles and haplotypes. The forensic parameters of 57 autosomal InDels (A-InDels) included in our used new-generation InDel amplification system showed that this updated InDel panel is informative and polymorphic in Sherpas, suggesting that it can be used as the supplementary tool for forensic personal identification and parentage testing in the highland East Asians. Descriptive findings from the PCA, ADMIXTURE and TreeMix-based phylogeny suggested that Sherpas showed excess allele sharing with neighboring Tibeto-Burman Tibetans. Furthermore, patterns of allele sharing in f-statistics demonstrated that Sherpa people had a different evolutionary history compared with their neighbors from Nepal (Newar and Gurung) but showed genetic similarity with 2700-year-old Chokhopani and modern Tibet Tibetans. QpAdm/qpGraph-based admixture sources and models further showed that Sherpa, core Tibetans and Chokhopani formed one clade which could be fitted as having the main ancestry from late Neolithic Qijia millet farmers and other deep ancestries from early Asians. Chromosome painting profiles and shared IBD fragments inferred from FineStructure and ChromoPainter not only confirmed the abovementioned genomic affinity patterns but also revealed the fine-scale microstructures among Sino-Tibetan speakers. Finally, natural-selection signals revealed via iHS, nSL, and iHH12 showed signatures associated with disease susceptibility in Sherpa people. Generally, we provided the comprehensive landscape of admixture and evolutionary history of Sherpa people based on the shared alleles and haplotypes from the low-density forensic markers and high-density genome-wide SNP data. The more detailed genetic landscape of Sherpa people should be further confirmed and characterized via ancient genomes or single-molecule real-time sequencing technology.

genetics↗