Biology subjects

Lin, H.

Publications and source records attributed to Lin, H..

At least 163 records · Page 9Linked to original sources

bioRxiv2023

ProFAST: a fast and scalable factor analysis for spatially aware dimension reduction of multi-section spatial transcriptomics data

Biological techniques for spatially resolved transcriptomics (SRT) have advanced rapidly in both throughput and spatial resolution for a single spatial location. This progress necessitates the development of efficient and scalable spatial dimension reduction methods that can handle large-scale SRT data from multiple sections. Here, we developed FAST as a fast and efficient generalized probabilistic factor analysis for spatially aware dimension reduction, which simultaneously accounts for the count nature of SRT data and extracts a low-dimensional representation of SRT data across multiple sections, while preserving biological effects with consideration of spatial smoothness among nearby locations. Compared with existing methods, FAST uniquely models the count data across multiple sections while using a local spatial dependence with scalable computational complexity. Using both simulated and real datasets, we demonstrated the improved correlation between FAST estimated embeddings and annotated cell/domain types. Furthermore, FAST exhibits remarkable speed, with only FAST being applicable to analyze a mouse embryo Stereo-seq dataset with >2.3 million locations in only 2 hours. More importantly, FAST identified the differential activities of immune-related transcription factors between tumor and non-tumor clusters and also predicted a carcinogenesis factor CCNH as the upstream regulator of differentially expressed genes in a breast cancer Xenium dataset.

genomics↗

bioRxiv2023

Quantification of glutathione with high throughput live-cell imaging

Reduction oxidation (redox) reactions are central in life and altered redox state is associated with a spectrum of human diseases. Glutathione (GSH) is the most abundant antioxidant in eukaryotic cells and plays critical roles in maintaining redox homeostasis. Thus, measuring intracellular GSH level is an important method to assess the redox state of organism. The currently available GSH probes are based on irreversible chemical reactions with glutathione and cant monitor the real-time glutathione dynamics. Our group developed the first reversible reaction based fluorescent probe for glutathione, which can measure glutathione levels at high resolution using a confocal microscope and in the bulk scale with a flow cytometry. Most importantly it can quantitatively monitor the real-time GSH dynamics in living cells. Using the 2nd generation of GSH probe, RealThiol (RT), this study measured the GSH level in living Hela cells after treatment with varying concentrations of DL-Buthionine sulfoximine (BSO) which inhibits GSH synthesis, using a high throughput imaging system, Cytation 5 cell imaging reader. The results revealed that GSH probe RT at the concentration of 2.0 {micro}M accurately monitored the BSO treatment effect on GSH level in the Hela cells. The present results demonstrated that the GSH probe RT is sensitive and precise in GSH measurement in living cells at a high throughput imaging platform and has the potential to be applied to any cell lines.

biochemistry↗

bioRxiv2023

GIGANTEA accelerates wheat heading time through gene interactions converging on FLOWERING LOCUS T1

Precise regulation of flowering time is critical for cereal crops to synchronize reproductive development with optimum environmental conditions, thereby maximizing grain yield. The plant specific gene GIGANTEA (GI) plays an important role in the control of flowering time, with additional functions on the circadian clock and plant stress responses. In this study, we show that GI loss-of-function mutants in a photoperiod sensitive tetraploid wheat background exhibit significant delays in heading time under both long-day (LD) and short-day (SD) photoperiods, with stronger effects under LD. However, this interaction between GI and photoperiod is no longer observed in isogenic lines carrying either a photoperiod insensitive allele in the PHOTOPERIOD1 (PPD1) gene or a loss-of-function allele in EARLY FLOWERING 3 (ELF3), a known repressor of PPD1. These results suggest that the normal circadian regulation of PPD1 is required for the differential effect of GI on heading time in different photoperiods. Using crosses between mutants or transgenic of GI and those of critical genes in the flowering regulation pathway, we show that GI accelerates wheat heading time by promoting FLOWERING LOCUS T1 (FT1) expression via interactions with ELF3, VERNALIZATION 2 (VRN2), CONSTANS (CO), and the age-dependent microRNA172-APETALA2 (AP2) pathway, at both transcriptional and protein levels. Our study reveals conserved GI mechanisms between wheat and Arabidopsis, but also identifies specific interactions of GI with the distinctive photoperiod and vernalization pathways of the temperate grasses. These results provide valuable knowledge for modulating wheat heading time and engineering new varieties better adapted to a changing environment.

plant biology↗

bioRxiv2023

miR-324 mediates bone homeostasis through the regulation of osteoblast and osteoclast differentiation and activity

microRNAs (miRNAs) are non-coding RNAs which modulate the expression of other RNA molecules. One miRNA can target many transcripts, allowing each miRNA to play key roles in many biological pathways. miR-324 is a miRNA previously implicated in bone and cartilage maintenance, defects of which result in common age-related diseases, such as osteoporosis or osteoarthritis (OA). In global miR-324-null mice cartilage damage was increased in both surgically and ageing-induced OA, despite minimal changes to the cartilage transcriptome, with few predicted miR-324 targets dysregulated. However, micro-computed tomography and histology demonstrated that global miR- 324-null the mice had an increase in bone mineral density, trabecular thickness and cortical thickness, with many parameters increasing with age. The bone marrow of miR-324-null mice also had reduced lipid content while and in vivo TRAP staining revealed a decrease in osteoclasts, with histomorphometry demonstrating an increased rate of bone formation in miR-324-null mice. Ex vivo assays revealed that the high bone mass phenotype of the miR-324-null mice resulted from increased osteoblast activity and decreased osteoclastogenesis. RNA-seq and qRT-PCR followed by miR-324 target prediction and validation in osteoblasts, osteoclasts and bone marrow macrophages identified the osteoclast fusion regulator Pin1 as a miR-324 target in the osteoclast lineage and the master osteogenic regulator Runx2 as a target of miR-324-5p in osteoblasts, the in vitro overexpression of which recapitulated the increased osteogenesis and decreased adipogenesis phenotype observed in vivo. These data point to important roles of miR-324 in skeletal biology with altered bone homeostasis in miR-324-null mice potentially causal for the increased cartilage damage observed during OA and ageing. Elucidation of pathways regulated by miR-324 offer promise for the treatment of bone diseases such as osteoporosis.

cell biology↗

bioRxiv2023

Dissecting components of the Campylobacter jejuni fetMP-fetABCDEF gene cluster in iron scavenging

Campylobacter jejuni is a leading cause of bacterial gastroenteritis worldwide. Acute infection can be antecedent to highly debilitating long-term sequelae. Expression of iron acquisition systems is vital for C. jejuni to survive the low iron availability within the human gut. The C. jejuni fetMP-fetABCDEF gene cluster is known to be upregulated during human infection and under iron limitation. While FetM and FetP have been functionally linked to iron transport in prior work, here we assess the contribution by each of the downstream genes (fetABCDEF) to C. jejuni growth during both iron-depleted and iron-replete conditions. Significant growth impairment was observed upon disruption of fetA, fetB, fetC, and fetD, suggesting a role in iron acquisition for each encoded protein. FetA expression was modulated by iron-availability but not dependent on the presence of FetB, FetC, FetD, FetE or FetF. Functions of the putative thioredoxins FetE and FetF were redundant in iron scavenging, requiring a double deletion ({Delta}fetEF) to exhibit a growth defect. C. jejuni FetE was expressed and the structure solved to 1.50 [A], revealing structural similarity to thiol-disulfide oxidases. Functional characterization in biochemical assays showed that FetE reduced insulin at a slower rate than E. coli Trx and that together, FetEF promoted substrate oxidation in cell extracts, suggesting that FetE (and presumably FetF) are oxidoreductases that can mediate oxidation in vivo. This study advances our understanding of the contributions by the fetMP-fetABCDEF gene cluster to virulence at a genetic and functional level, providing foundational knowledge towards mitigating C. jejuni-related morbidity and mortality.

microbiology↗

bioRxiv2023

The Arabidopsis BUB1/MAD3 family protein BMF3 requires BUB3.3 to recruit CDC20 to kinetochores in spindle assembly checkpoint signaling

Mitosis is monitored by the spindle assembly checkpoint (SAC) which remains active until all chromosomes have their kinetochores attached to microtubules originated from opposite spindle poles. Plants produce both highly conserved and sequence-diverged SAC components, so it has been largely unknown how SAC activation leads to the assembly of these proteins at the unattached kinetochores to prevent anaphase onset in plants. In Arabidopsis thaliana, the noncanonical BUB3.3 protein was detected at kinetochores throughout mitosis, unlike MAD1 and the plant specific BUB1/MAD3 family protein BMF3 that associated with unattached chromosomes only. However, BUB3.3 was required to arrest mitotic progression when one or more chromosomes did not congress at the metaphase plate. Nevertheless, BUB3.3 was not required for the kinetochore localization of other SAC components and vice versa. BUB3.3 specifically interacted with BMF3 in a novel region containing two internal repeats that were not required for the kinetochore localization of BMF3. This interaction was important for BMF3 to recruit the CDC20 protein to the unattached kinetochores. Our results showed that the Arabidopsis BUB3.3 protein functioned in the activation of BMF3 for CDC20 recruitment, rather than the recruitment of BMF proteins as what has been found in fungi and animals, in order to arrest mitosis at prometaphase. Therefore, activated SAC resulted in BUB3.3-independent localization of BMF3 and MAD1 to kinetochores and BUB3.3-dependent licensing of BMF3 for CDC20 recruitment in A. thaliana. SIGNIFICANCE STATEMENTMitotic progression into anaphase is monitored by spindle assembly checkpoint that is poorly understood in plants. Using Arabidopsis thaliana as a reference system, we discovered a novel interaction pattern centered at the BUB1 and MAD3 protein BMF3 at kinetochores. A noncanonical isoform of the evolutionarily conserved BUB3 family protein BUB3.3 interacted with two novel internal repeats in BMF3 for recruiting the CDC20 protein to unattached kinetochores in order to inhibit its function in anaphase onset. Hence, our work sheds light on how spindle assembly checkpoint operates in flowering plants that produce the highly conserved BUB3.3 protein but highly divergent BMF proteins.

plant biology↗

bioRxiv2023

Flagellar switch inverted repeat sequence variation impacts Clostridioides difficile RT027/MLST1 virulence.

Clostridioides difficile RT027 strains cause infections that vary in severity from asymptomatic to lethal, but the molecular basis for this variability is poorly understood. Through comparative analyses of RT027 clinical isolates, we determined that isolates that exhibit greater variability in their flagellar gene expression exhibit greater virulence in vivo. C. difficile flagellar genes are phase-variably expressed due to the site-specific inversion of the flgB 5UTR region, which reversibly generates ON vs. OFF orientations for the flagellar switch. We found that longer inverted repeat (IR) sequences in this switch region correlate with greater disease severity, with RT027 strains carrying 6A/6T IR sequences exhibiting greater phenotypic heterogeneity in flagellar gene expression (60%-75% ON) and causing more severe disease than those with shorter IRs (> 99% ON or OFF). Taken together, our results reveal that phenotypic heterogeneity in flagellar gene expression may contribute to the variable disease severity observed in C. difficile patients.

microbiology↗

bioRxiv2023

Quorum-sensing gene regulates hormetic effects induced by sulfonamides in Comamonadaceae

Hormesis is a toxicological phenomenon whereby exposure to low-dose stress results in stimulation of various biological endpoints. Among these, the induction of cell proliferation by antibiotics is critical, but the underlying molecular mechanisms remain poorly understood. Here, we showed that sulfonyl-containing chemicals (e.g., sulfonamides) can induce cell-proliferation hormesis of Comamonas testosteroni. Investigation of the hormesis mechanism revealed that low-dose sulfonamides bind to the LuxR-type quorum sensing protein LuxR solo, thereby triggering the transcription of 3-ketoacyl-CoA thiolase, a key enzyme of the fatty acid {beta}-oxidation. This provides additional ATP, NADPH, and acetyl-CoA for purine and pyrimidine biosynthesis, allowing cells to synthesize sufficient nucleotides to support rapid cell growth. Our work reports on a previously unknown mechanism for the hormetic effect and highlights its generality in the Comamonadaceae family.

microbiology↗

bioRxiv2023

The vaginal microbiota of pregnant women varies with gestational age, maternal age, and parity

The composition of the vaginal microbiota is heavily influenced by pregnancy and may factor into pregnancy complications, including spontaneous preterm birth. However, results among studies have been inconsistent, due in part to variation in sample sizes and ethnicity. Thus an association between the vaginal microbiota and preterm labor continues to be debated. Yet, before assessing associations between the composition of the vaginal microbiota and preterm labor, a robust and in-depth characterization of the vaginal microbiota throughout pregnancy in the specific study population under investigation is required. Herein, we report a large longitudinal study (N = 474 women, 1862 vaginal samples) of a primarily African-American cohort- which experiences a relatively high rate of pregnancy complications - evaluating associations between individual identity, gestational age, and other maternal characteristics with the composition of the vaginal microbiota throughout gestation resulting in term delivery. The primary factors influencing the composition of the vaginal microbiota in pregnancy are individual identity and gestational age at sampling. Secondary factors are maternal age, parity, obesity, and self-reported Cannabis use. The principal pattern across gestation is for the vaginal microbiota to remain or transition to a state of Lactobacillus dominance. This pattern can be mitigated by maternal parity and obesity. Regardless, network analyses reveal dynamic associations among specific bacterial taxa within the vaginal ecosystem, which shift throughout the course of pregnancy. This study provides a robust foundational understanding of the vaginal microbiota in pregnancy among African-Americans, in particular, and sets the stage for further investigation of this microbiota in obstetrical disease. IMPORTANCEThere is debate regarding links between the vaginal microbiota and pregnancy complications, especially spontaneous preterm birth. Inconsistencies in results among studies are likely due to differences in sample sizes and cohort ethnicity. Ethnicity is a complicating factor because, although all bacterial taxa commonly inhabiting the vagina are present among all ethnicities, the frequencies of these taxa vary among ethnicities. Therefore, an in-depth characterization of the vaginal microbiota throughout pregnancy in the specific study population under investigation is required prior to evaluating associations between the vaginal microbiota and obstetrical disease. This initial investigation is a large longitudinal study of the vaginal microbiota throughout gestation resulting in a term delivery in a primarily African-American cohort, a population that experiences disproportionally negative maternal-fetal health outcomes. It establishes the magnitude of associations between maternal characteristics, such as age, parity, BMI, and self-reported Cannabis use, on the vaginal microbiota in pregnancy.

microbiology↗

bioRxiv2023

Transcription elongation defects link oncogenic splicing factor mutations to targetable alterations in chromatin landscape

Transcription and splicing of pre-messenger RNA are closely coordinated, but how this functional coupling is disrupted in human disease remains unexplored. Here, we investigated the impact of non-synonymous mutations in SF3B1 and U2AF1, two splicing factors commonly mutated in cancer, on transcription. We find that the mutations impair RNA Polymerase II (RNAPII) transcription elongation along gene bodies leading to transcription-replication conflicts, replication stress and altered chromatin organization. This elongation defect is linked to disrupted pre-spliceosome assembly due to impaired protein-protein interactions of mutant SF3B1. Through an unbiased screen, we identified epigenetic factors in the Sin3/HDAC complex, which, when modulated, normalize transcription defects and their downstream effects. Our findings shed light on the mechanisms by which oncogenic mutant spliceosomes impact chromatin organization through their effects on RNAPII transcription elongation and present a rationale for targeting the Sin3/HDAC complex as a potential therapeutic strategy. HIGHLIGHTS- Oncogenic mutations in SF3B1 and U2AF1 cause a gene body RNAPII transcription elongation defect - The elongation defect is linked to impaired assembly of early spliceosome complexes and leads to replication stress and changes to chromatin landscape - RNAPII elongation defects in SF3B1K700E are normalized by modulating epigenetic factors but 3 cryptic splicing events are not reversed - Targeting the Sin3/HDAC pathway to normalize RNAPII elongation defect is a potential therapeutic approach in these disorders GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/530019v3_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@dc6d22org.highwire.dtl.DTLVardef@180f36borg.highwire.dtl.DTLVardef@ed341forg.highwire.dtl.DTLVardef@f8dfb2_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2023

Broadly effective ACE2 decoy proteins protect mice from lethal SARS-CoV-2 infection

As SARS-CoV-2 variants have been causing increasingly serious drug resistance problem, development of broadly effective and hard-to-escape anti-SARS-CoV-2 agents is in urgent need. Here we describe further development and characterization of two SARS-CoV-2 receptor decoy proteins, ACE2-Ig-95 and ACE2-Ig-105/106. We found that both proteins had potent and robust in vitro neutralization activities against diverse SARS-CoV-2 variants including Omicron, with an average IC50 of up to 37 pM. In a stringent lethal SARS-CoV-2 infection mouse model, both proteins lowered lung viral load by up to [~]1000 fold, prevented the emergence of clinical signs in >75% animals, and increased animal survival rate from 0% (untreated) to >87.5% (treated). These results demonstrate that both proteins are good drug candidates for protecting animals from severe COVID-19. In a head-to-head comparison of these two proteins with five previously-described ACE2-Ig constructs, we found that two of these constructs, each carrying five surface mutations in the ACE2 region, had partial loss of neutralization potency against three SARS-CoV-2 variants. These data suggest that extensively mutating ACE2 residues near the RBD-binding interface should be avoided or performed with extra caution. Further, we found that both ACE2-Ig-95 and ACE2-Ig-105/106 could be produced to gram/liter level, demonstrating the developability of them as biologic drug candidates. Stress-condition stability test of them further suggests that more studies are required in the future to improve the stability of these proteins. These studies provide useful insight into critical factors for engineering and preclinical development of ACE2 decoys as broadly effective therapeutics against diverse ACE2-utilizing coronaviruses. Abstract ImportanceEngineering soluble ACE2 proteins that function as a receptor decoy to block SARS-CoV-2 infection is a very attractive approach to broadly effective and hard-to-escape anti-SARS-CoV-2 agents. This study here describes development of two antibody-like soluble ACE2 proteins that broadly block diverse SARS-CoV-2 variants including Omicron. In a stringent COVID-19 mouse model, both proteins successfully protected >87.5% animals from lethal SARS-CoV-2 infection. In addition, a head-to-head comparison of the two constructs developed in this study with five previously-described ACE2 decoy constructs were performed here. Two previously-described constructs with relatively more ACE2-surface mutations were found with less robust neutralization activities against diverse SARS-CoV-2 variants. Further, the developability of the two proteins as biologic drug candidates was also assessed here. This study provides two broadly anti-SARS-CoV-2 drug candidates and useful insight into critical factors for engineering and preclinical development of ACE2 decoy as broadly effective therapeutics against diverse ACE2-utilizing coronaviruses. TweetTwo antibody-like ACE2 decoy proteins could block diverse SARS-CoV-2 variants and prevent animals from severe COVID-19.

microbiology↗

bioRxiv2023

Topological design principle for the robustness of necroptosis biphasic, emergent, and coexistent (BEC) dynamics

Biphasic dynamics, the variable-dependent ability to enhance or restrain biological function, is prevalent in natural systems. Accompanied by biphasic dynamics, necroptosis signaling dominated by RIP1 also appears emergent and coexistent dynamics. Here, we identify the RIP1-RIP3-C8 incoherent feedforward loop embedded with positive feedback of RIP3 to RIP1 is the core topology, and the scale-free feature of RIP3 peak value dictates necroptosis BEC dynamics. Entropy production is introduced to quantify the uncertainty of coexistent dynamics. RIP3 auto-phosphorylation is further determined as a complementary process for robustly attaining necroptosis BEC dynamics. Through screening all possible two- and three-node circuit topologies, a complete atlas of three-node circuit BEC dynamics is generated and only three minimal circuits emerge as robust solutions, proving incoherent feedforward loop is the core topology. Overall, through highlighting a finite set of circuits, this study yields guiding principles for mapping, modulating, and designing circuits for BEC dynamics in biological systems.

systems biology↗

bioRxiv2023

Virulence and genomic diversity among clinical isolates of ST1 (BI/NAP1/027) Clostridioides difficile

Clostridioides difficile (C. difficile), a leading cause of nosocomial infection, produces toxins that damage the colonic epithelium and results in colitis that varies from mild to fulminant. Variation in disease severity is poorly understood and has been attributed to host factors (age, immune competence and intestinal microbiome composition) and/or virulence differences between C. difficile strains, with some, such as the epidemic BI/NAP1/027 (MLST1) strain, being associated with greater virulence. We tested 23 MLST1(ST1) C. difficile clinical isolates for virulence in antibiotic-treated C57BL/6 mice. All isolates encoded a complete Tcd pathogenicity locus and achieved similar colonization densities in mice. Disease severity varied, however, with 5 isolates causing lethal infections, 16 isolates causing a range of moderate infections and 2 isolates resulting in no detectable disease. The avirulent ST1 isolates did not cause disease in highly susceptible Myd88-/- or germ-free mice. Genomic analysis of the avirulent isolates revealed a 69 base-pair deletion in the N-terminus of the cdtR gene, which encodes a response regulator for binary toxin (CDT) expression. Genetic deletion of the 69 base-pair cdtR sequence in the highly virulent ST1 R20291 C. difficile strain rendered it avirulent and reduced toxin gene transcription in cecal contents. Our study demonstrates that a natural deletion within cdtR attenuates virulence in the epidemic ST1 C. difficile strain without reducing colonization and persistence in the gut. Distinguishing strains on the basis of cdtR may enhance the specificity of diagnostic tests for C. difficile colitis.

microbiology↗

bioRxiv2022

Fingerprint SRS Imaging Unveils Ergosteryl Ester as a Metabolic Signature of Azole-Resistant Candida albicans

Candida albicans (C. albicans), a major fungal pathogen, causes life-threatening infections in immunocompromised individuals. Fluconazole (FLC) is recommended as first-line therapy for treatment of invasive fungal infections. Yet, the widespread use of FLC has resulted in increased antifungal resistance among different strains of Candida, especially C. albicans, which is a leading source of hospital-acquired infections. Here, by hyperspectral stimulated Raman scattering (hSRS) imaging of single fungal cells in the fingerprint window and pixel-wise spectral unmixing, we report aberrant ergosteryl ester accumulation in azole-resistant C. albicans compared to azole-susceptible species. This accumulation was a consequence of de novo lipogenesis. Lipid profiling by mass spectroscopy identified ergosterol oleate to be the major species stored in azole-resistant C. albicans. Blocking ergosterol esterification by oleate and suppressing sterol synthesis by FLC synergistically suppressed the viability of C. albicans in vitro and limited the growth of biofilm on mouse skin in vivo. Our findings highlight a metabolic marker and a new therapeutic strategy for targeting azole-resistant C. albicans by interrupting the esterified ergosterol biosynthetic pathway. Significance StatementInvasive fungal infections and increasing antifungal resistance are emerging threats to public health with high morbidity and mortality. Despite the advances in azole resistance mechanisms, it remains unclear why some fungal species are intrinsically resistant to or easily acquire resistance to multiple antifungal drugs. Here, using fingerprint SRS microscopy, we uncovered a molecular signature, aberrant ergosteryl ester accumulation, linked to the azole resistance of Candida species. An antifungal treatment strategy combining oleate (inhibitor of ersgosteryl esterification) and azole significantly attenuates the azole resistance and the viability of C. albicans in vitro and in vivo. Our work opens a new way to detect and treat azole-resistant fungal infections by targeting ergosterol metabolism.

microbiology↗

bioRxiv2022

Ancient origin and evolution of microbial mercury methylation

The origin of microbial mercury methylation has long been a mystery. Here we employed genome-resolved phylogenetic analyses to decipher the evolution of the mercury methylating gene, hgcAB, constrain the ancestral origin of the hgc operon, and explain the distribution of hgc in Bacteria and Archaea. We infer the extent to which vertical inheritance and horizontal gene transfer have influenced the evolution of mercury methylators and hypothesize that evolution of this trait bestowed the ability to produce an antimicrobial compound (MeHg+) on a potentially resource-limited early Earth. We speculate that, in response, the evolution of MeHg+-detoxifying alkylmercury lyase (encoded by merB) reduced a selective advantage for mercury methylators and resulted in widespread loss of hgc in Bacteria and Archaea. SignificanceNeurotoxic methylmercury (MeHg+(aq)) is synthesized from HgII(aq) in the environment by microorganisms possessing the gene pair hgcAB. Our phylogenetic analyses elucidate the origin and evolution of the hgc operon, and support a hypothesis that mercury methylation evolved as an antimicrobial production mechanism, possibly from competition for limited resources on the early Earth. We infer from our analyses that hgc has been primarily vertically inherited in Bacteria and Archaea, with extensive parallel loss, and note that few taxa possessing hgc also possess the gene encoding for MeHg+ demethylation, merB. Our findings support the interpretation that merB evolved as a defense mechanism against the evolution of microbial HgII(aq) methylation.

evolutionary biology↗

bioRxiv2022

Identification of RNA-based cell-type markers for the stem cell manufacture system with a statistical scoring function

Cell-type biomarkers are useful in stem cell manufacture to monitor cell purification, cell quantity, and quality. However, the study on cell-type markers, specifically for stem cell manufacture, is limited. The emerging questions are which RNA transcripts can serve as biomarkers during stem cell culture, and what method can efficiently and accurately discover these biomarkers. We developed a scoring function system to identify RNA biomarkers with RNA-seq data. We applied the method to two data sets, one for extracellular RNAs (ex-RNAs) and the other for intracellular microRNAs (miRNAs). The data set have RNA-seq data of ex-RNAs from cell culture media for six different types of cells, including human embryonic stem cells. To get the RNA-seq data from intracellular miRNAs, we cultured three types of cells: human embryonic stem cells (H9), neural stem cells (NSC), hESC-derived endothelial cells (EC) and conducted small RNA-seq to their intracellular miRNAs. Using these data, we identified a set of ex-RNAs/smRNAs as candidates of biomarkers for different types of cells for cell manufacture. We also used deep-learning based prediction methods and simulated data to validate these discovered biomarkers.

bioinformatics↗

bioRxiv2022

SCTC: inference of developmental potential from single-cell transcriptional complexity

Inference of single-cell developmental potential from scRNA-Seq data enables us to reconstruct the pseudo-temporal path of cell development, which is an important and challenging task for single-cell analysis. Single-cell transcriptional diversity (SCTD), measured by the number of expressed genes per cell, has been found to be negatively correlated with the development time, and thus can be considered as a hallmark of developmental potential. However, in some cases, the gene expression level of the cells in the early stages of development may be lower than that of the later stages, which may lead to incorrect estimation of differentiation states by gene diversity-based inference. Here we refer to the economic complexity theory and propose single-cell transcriptional complexity (SCTC) metrics as a measure of single-cell developmental potential, given the intrinsic similarities between biological and economic complex systems. We take into account not only the number of genes expressed by cells, but also the more sophisticated structure information of gene expression by treating the scRNA-seq count matrix as a bipartite network. We show that complexity metrics characterize the developmental potential more accurately than the diversity metrics. Especially, in the early stages of development, cells typically have lower gene expression level than that in the later stages, while their complexity in the early stages is significantly higher than that in the later stages. Based on the measurement of SCTC, we provide an unsupervised method for accurate, robust, and transferable inference of single-cell pseudotime. Our findings suggest that the complexity emerging from the interaction between cells and genes determines the developmental potential, which may bring new insights into the understanding of biological development from the perspective of the complexity theory.

bioinformatics↗

bioRxiv2022

Neural signatures of second language proficiency in narrative processing.

Making sense of speech in a second language relies on multiple abilities. Differences in brain activity related to proficiency in language tasks have often been attributed to processing demands. However, during naturalistic narrative comprehension, listeners at different proficiency levels may form different representations of the same speech. We hypothesized that the synchronization of these representations across people could thus be used to measure second-language proficiency. Using a searchlight shared response model, we found that highly proficient participants showed synchronization in regions similar to those of native speakers, including in the default mode network and in the lateral prefrontal cortex. In contrast, participants with low proficiency showed more synchronization in auditory cortex and word-level semantic processing areas in the temporal lobe. Moderate proficiency showed the greatest neural diversity, suggesting lower consistency in the source of this partial proficiency. Based on these synchronization differences, we were able to reliably classify the proficiency level or predict behavioral performance on an independent English test in held-out participants, suggesting the identified neural systems represented proficiency-sensitive information that was generalizable to other individuals. These findings suggest higher second-language proficiency leads to a more native-like neural processing of naturalistic language, including in systems beyond the cognitive control network or the core language network. HighlightsO_LINeural synchronization in second-language speech processing reflects proficiency. C_LIO_LIHigh-proficiency individuals neurally resemble native speakers. C_LIO_LILow-proficiency individuals are synchronized in perceptual and word semantics areas. C_LIO_LIProficiency level can be predicted using neural synchronization signatures. C_LI

neuroscience↗