Biology subjects

Lin, Y.

Publications and source records attributed to Lin, Y..

At least 235 records · Page 13Linked to original sources

bioRxiv2023

Dose-response relationship for the resistance of human insulin to degradation by insulin-degrading enzyme

Deeper understanding of the mechanism of the action of insulin and insulin-degrading enzyme (IDE) is a central theme in research into physiology and the pathophysiology of type 2 diabetes mellitus. Despite significant progress regarding the substrate recruitment, unfolding, digestion, and release by IDE, the structure and function of the insulin hexamer during the degradation cycle of IDE remain to be fully characterized. In the present study, we have characterized the behavior of human insulin hexamer in the absence of zinc. Using cryo-electron microscopy, we also observed that these hexamers represented a structure similar to that of T6 insulin. More interestingly, we also observed complexes in which some of their monomeric insulin components are partially distorted at their hexametric symmetry. This ensures that insulin determines the kinetics of its degradation by IDE without the requirement for zinc. These findings provide new information regarding the molecular events in insulin assembly and disassembly that permit its selective digestion by IDE.

biochemistry↗

bioRxiv2023

Structural RNA components supervise the sequential DNA cleavage in R2 retrotransposon

Retroelements are the widespread jumping elements considered as major drivers for genome evolution, which can also be repurposed as gene-editing tools. Here, we determined the cryo-EM structures of eukaryotic R2 retrotransposon with ribosomal DNA target and regulatory RNAs. Combined with biochemical and sequencing analysis, we revealed two essential DNA regions, Drr and Dcr, required for R2 recognition and cleavage. The association of 3 regulatory RNA with R2 protein accelerates the first-strand cleavage, blocks the second-strand cleavage, and initiates the reverse transcription starting from the polyA tail. Removing 3 regulatory RNA by reverse transcription allows the association of 5 regulatory RNA and initiates the second-strand cleavage. Our work explained the DNA recognition and supervised sequential retrotransposition mechanisms by R2 machinery, providing novel insights into the retrotransposon and application reprogramming.

molecular biology↗

bioRxiv2023

Transcriptional Activation of Regenerative Hematopoiesis via Vascular Niche Sensing

Transition between activation and quiescence programs in hematopoietic stem and progenitor cells (HSC/HSPCs) is perceived to be governed intrinsically and by microenvironmental co-adaptation. However, HSC programs dictating both transition and adaptability, remain poorly defined. Single cell multiome analysis divulging differential transcriptional activity between distinct HSPC states, indicated for the exclusive absence of Fli-1 motif from quiescent HSCs. We reveal that Fli-1 activity is essential for HSCs during regenerative hematopoiesis. Fli-1 directs activation programs while manipulating cellular sensory and output machineries, enabling HSPCs co-adoptability with a stimulated vascular niche. During regenerative conditions, Fli-1 presets and enables propagation of niche-derived Notch1 signaling. Constitutively induced Notch1 signaling is sufficient to recuperate functional HSC impairments in the absence of Fli-1. Applying FLI-1 modified-mRNA transduction into lethargic adult human mobilized HSPCs, enables their vigorous niche-mediated expansion along with superior engraftment capacities. Thus, decryption of stem cell activation programs offers valuable insights for immune regenerative medicine.

cell biology↗

bioRxiv2023

In vitro screening of non-antibiotic alternative growth promoter combinations in broilers

Available research on non-antibiotic alternative growth promoter (NAGPs) mainly focuses on the effect of a single preparation on the substitution effect of antibiotics. However, different NAGP might work together in harmony. Studies related to NAGP combinations are lacking. This study aimed to screen six non-antibiotic alternative growth promoter combinations (NAGPCs) in vitro so as to find a better alternative method to ensure feed efficiency and the broiler health. Pepsin and 42-d broiler ileal fluid were used for the in vitro digestion test, and the optimal addition levels of NAGPs and NAGPCs were selected based on dry matter (DM) and organic matter (OM) digestibility, microbiota of digestive fluid, and antioxidant capacity of digestive fluid. Results showed the optimum addition amount of Mannose oligosaccharide (MOS), fruit oligosaccharide (FOS), mannanase (MAN), Bacillus subtilis (BS), sodium butyrate (SB), guanidinoacetic acid (CA), xylanase (XYL), glucose oxidase (GO), and phytase (PT) were 0.2%, 0.9%, 0.03%, 0.05%, 0.08%, 0.002%, 0.008%, and 0.004%. The six best combinations were 0.2%MOS + 0.03%MAN + 0.15%SB, 0.2%MOS + 0.03%MAN + 0.05%BS, 0.2%MOS + 0.9%FOS + 0.15%SB, 0.2%MOS + 0.9%FOS + 0.05%BS, 0.2%MOS + 0.9%FOS + 0.03%MAN, and 0.2%MOS + 0.05%BS + 0.004%PT. In conclusion, NAGPCs improved the apparent digestibility of ileal DM and OM, intestinal flora and antioxidant capacity. Comparatively, under this condition, using NAGPC has more beneficial effects than using non-antibiotic alternative growth promoter.

zoology↗

bioRxiv2023

Production of extracellular polymeric substances in granular sludge under selection for Accumulibacter and Competibacter

Granular sludge intensifies the removal of nutrients from wastewater. Granules structured by extracellular polymeric substances (EPS) can be recovered as biomaterial. Links between microbial selection and EPS formation during granulation need to get uncovered. We inoculated anaerobic-aerobic sequencing batch reactors with either flocs or granules to study the relationships between microbial selection, bioaggregation, exopolymer formation, and EPS composition. Selection for slow-growing organisms like the model polyphosphate- accumulating organism "Candidatus Accumulibacter" (max. 83% vs. amplicon sequencing read counts) and glycogen-accumulating organism "Ca. Competibacter" (max. 45%) sustained granulation. Gel-forming exopolymers were produced as high as above 40% of the volatile solids of the biomass by stepwise increase of the organic loading rate (0.3 to 2.0 g CODAc d-1 LR-1). Confocal laser scanning microscopy, FT-IR spectroscopy, and HPAE-PAD chromatography revealed the complex and dynamic chemical compositions of the structural EPS in relation to microbial population shifts along reactor regimes. The analysis of 20 representative genomes of "Ca. Accumulibacter" and "Ca. Competibacter" recovered from public databases revealed their functional potential to produce EPS among other representative wastewater microorganisms. The more than 40 functional gene categories annotated highlight the complexity of EPS metabolic networks from monomers processing to assembly, export, and epimerizations. The combination of ecological engineering principles and systems microbiology will help unravel and direct the production of EPS from wastewater, valorizing residual granular sludge into beneficial biomaterials for the circular economy. HighlightsO_LISelection for slow-growing organisms like PAOs and GAOs fostered a robust granulation. C_LIO_LIStructural EPS were produced above 40% of biomass volatile content under high loading. C_LIO_LIChemical composition of EPS evolved together with the microbial community composition. C_LIO_LIGenomic insights highlighted the genetic potential of PAOs and GAOs for EPS formation. C_LIO_LIMicrobial communities are complex; further are their EPS compositions and metabolisms. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC="FIGDIR/small/534144v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@a163e2org.highwire.dtl.DTLVardef@1a4ab94org.highwire.dtl.DTLVardef@1fc93d4org.highwire.dtl.DTLVardef@14d4b7f_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2023

Extensive variation in germline de novo mutations in Poecilia reticulata

The rate of germline mutation is fundamental to evolutionary processes, as it generates the variation upon which selection acts. The guppy, Poecilia reticulata, is a model of rapid adaptation, however the relative contribution of standing genetic variation versus de novo mutation to evolution in this species remains unclear. Here, we use pedigree-based approaches to quantify and characterize de novo mutations (DNMs) in three large guppy families. Our results suggest germline mutation rate in the guppy varies substantially across individuals and families. Most DNMs are shared across multiple siblings, suggesting they arose during early zygotic development. DNMs are randomly distributed throughout the genome, and male-biased mutation rate is low, as would be expected from the short guppy generation time. Overall, our study demonstrates remarkable variation in germline mutation rate and provides insights into rapid evolution of guppies.

evolutionary biology↗

bioRxiv2023

Scalable Solar-Driven Chemical Production by Semiconductor Biohybrids Synthesized from Wastewater Pollutants

Semiconductors biohybrids integrate the best of biological catalysts and semiconductor nanomaterials for solar-to-chemical conversion. To realize the potential of hybrid systems at the commercial level, it remains an urgent need for cost-competitive and environmentally friendly approaches to scaling up. Here, we successfully tackle this challenge through developing biohybrid route that co-utilize multi-pollutants in wastewater to produce semiconductor biohybrids in-situ for solar-to-chemical production. To achieve cost-effective biohybrid production, we introduced an aerobic sulfate reduction pathway into Vibrio natriegens to enable the direct utilization of the heavy metal ions (i.e., Cd2+), sulfate, and organics in the wastewater to biosynthesize functional semiconductor nanoparticles in living V. natriegens. Furthermore, 2,3-butanediol biosynthetic pathway was introduced into the V. natriegens hybrid to couple the solar energy for enhanced bioproduction. We demonstrated the scalability of this system in a 5-L illuminated fermenter using wastewater as the feedstock, which resulted in production of 13 g/L of 2,3-butanediol. Life cycle analysis showed this specific biohybrid route had a significantly lower cost and reduced CO2 emission compared to both pure sugars fermentation and fossil-based routes. In addition to providing a promising step toward sustainable commercializing semiconductor biohybrids for biomanufacturing, our work may lead to hybrid living matter toward future waste to wealth conversion.

synthetic biology↗

bioRxiv2023

Molecular mechanisms of coronary artery disease risk at the PDGFD locus

Platelet derived growth factor (PDGF) signaling has been extensively studied in the context of vascular disease, but the genetics of this pathway remain to be established. Genome wide association studies (GWAS) for coronary artery disease (CAD) have identified a risk locus at 11q22.3, and we have verified with fine mapping approaches that the regulatory variant rs2019090 and PDGFD represent the functional variant and putative functional gene. Further, FOXC1/C2 transcription factor (TF) binding at rs2019090 was found to promote PDGFD transcription through the CAD promoting allele. Employing a constitutive Pdgfd knockout allele along with SMC lineage tracing in a male atherosclerosis mouse model we mapped single cell transcriptomic, cell state, and lesion anatomical changes associated with gene loss. These studies revealed that Pdgfd promotes expansion, migration, and transition of SMC lineage cells to the chondromyocyte phenotype and vascular calcification. This is in contrast to protective CAD genes TCF21, ZEB2, and SMAD3 which we have shown to promote the fibroblast-like cell transition or perturb the pattern or extent of transition to the chondromyocyte phenotype. Further, Pdgfd expressing fibroblasts and pericytes exhibited greater expression of chemokines and leukocyte adhesion molecules, consistent with observed increased macrophage recruitment to the plaque. Despite these changes there was no effect of Pdgfd deletion on SMC contribution to the fibrous cap or overall lesion burden. These findings suggest that PDGFD mediates CAD risk through promoting SMC expansion and migration, in conjunction with deleterious phenotypic changes, and through promoting an inflammatory response that is primarily focused in the adventitia where it contributes to leukocyte trafficking to the diseased vessel wall.

genetics↗

bioRxiv2023

Characterizing Mineral Ellipsoids in New Bone Formation at the Interface of Ti6Al4V Porous Implants

The hierarchy of newly formed bone contains elements of disorder within an ordered multiscale structure, spanning from the macroscale to below the nanoscale. With mineralized structures presenting in the shape of ellipsoids in mature and mineralizing tissue, this work characterizes the heterogeneity in mineral ellipsoid packing at the interface of porous titanium implants. The characterization of mineral at the bone-implant interface offers insight into the osseointegration of titanium implants and the mechanical properties of the interfacial bone tissue. Using scanning transmission electron microscopy and plasma focused ion beam - scanning electron microscopy, mineral ellipsoids are characterized at the implant interface in both 2D and 3D. Heterogeneous in their size and shape within the newly formed bone tissue, ellipsoids are observed with alternating orientations corresponding to unique lamellar packets within 2-3 m of the titanium implant interface - although this motif is not universal, and a mineral-dense zone can also appear at the implant interface. Short-order ellipsoid orientation shifts are also present in the 3D probe of the implant interface, where an approximate 90{degrees} misorientation angle between neighbouring packets of mineral ellipsoid resolves with increasing distance from the titanium, possibly providing a strengthening mechanism to prevent crack propagation in the peri-implant bone. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=74 SRC="FIGDIR/small/524810v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@3c34a1org.highwire.dtl.DTLVardef@a3437borg.highwire.dtl.DTLVardef@a374e1org.highwire.dtl.DTLVardef@14e9572_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2023

BnIR: a multi-omics collaborative resource and tool platform for Brassica napus biological study

In the post-GWAS era, multi-omics techniques have shown great power and potential for candidate gene mining and functional genomics research. However, due to the lack of effective data integration and multi-omics analysis platforms, such techniques have not still been applied widely in rapeseed, an important oil crop worldwide. Here, we constructed a rapeseed multi-omics database (BnIR; http://yanglab.hzau.edu.cn/BnIR), which provides datasets of six omics including genomics, transcriptomics, variomics, epigenetics, phenomics and metabolomics, as well as numerous "variation-gene expression-phenotype" associations by using multiple statistical methods. In addition, a series of multi-omics search and analysis tools are integrated to facilitate the browsing and application of these datasets. BnIR is the most comprehensive multi-omics database for rapeseed so far, and two case studies demonstrated its power to mine candidate genes associated with specific traits and analyze their potential regulatory mechanisms. Short SummaryIn this study, we developed BnIR (http://yanglab.hzau.edu.cn/BnIR), a multi-omics database for rapeseed that integrates six omics datasets and "variation-gene expression-phenotype" associations. The database is equipped with a range of multi-omics tools for streamlined browsing and analysis. Through multiple case studies, we demonstrated BnIRs potential to identify candidate genes associated with specific traits and investigate their regulatory mechanisms.

bioinformatics↗

bioRxiv2023

Osseointegration of functionally-graded Ti6Al4V porous implants: Histology of the pore network

The additive manufacturing of titanium into porous geometries offers a means to generate low-stiffness endosseous implants with a greater surface area to improve osseointegration. In order to optimize pore size in the scaffolds, it is important to first understand the timeline of osseointegration in pre-clinical models. In this work, selective laser melting was used to produce gyroid-based scaffolds with a uniform pore size of 300 m or functionally-graded pore size from 600 m to 300 m before implantation in New Zealand white rabbit tibiae for 4 and 12 weeks. Initial in vitro assessment with Saos-2 cells showed favourable cell proliferation at pore sizes of 300 and 600 m. At four weeks, histological observations indicated some residual inflammation alongside neovessel infiltration into the scaffold interior and some early apposition of mineralized bone tissue. At twelve weeks, both scaffolds were filled with a mixture of adipocyte-rich marrow, micro-capillaries, and mineralized bone tissue. X-ray microcomputed tomography showed a higher bone volume fraction (BV/TV) and percentage of bone-implant contact (BIC) in the implants with 300 m pores than in the functionally-graded specimens, indicating that these smaller pore sizes may be favourable for osseointegration in leporine bone. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/521963v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@2e319aorg.highwire.dtl.DTLVardef@baa9deorg.highwire.dtl.DTLVardef@e66075org.highwire.dtl.DTLVardef@c6c8c4_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2022

Effects of nonantibiotic alternative growth promoter combinations on nutrient utilization, digestive enzyme activity, intestinal morphology, and cecal microflora of broilers

Given the ban on antibiotic growth promoters, six nonantibiotic alternative growth promoter combinations (NAGPCs) for broilers were evaluated. All birds were fed pellets of two basal diets--starter (0-21 d) and grower (22-42 d)--with either enramycin (ENR) or NAGPC supplemented. 1) control + 100 mg/kg ENR; 2) control diet (CON, basal diet); 3) control + 2,000 mg/kg mannose oligosaccharide (MOS) + 300 mg/kg mannanase (MAN) + 1,500 mg/kg sodium butyrate (SB) (MMS); 4) control + 2,000 mg/kg MOS + 300 mg/kg MAN + 500 mg/kg Bacillus subtilis (BS) (MMB); 5) control + 2,000 mg/kg MOS + 9,000 mg/kg fruit oligosaccharide (FOS) + 1,500 mg/kg SB (MFS); 6) control + 9,000 mg/kg FOS + 500 mg/kg BS (MFS) (MBP). The experiment used a completely random block design with six replicates per group: 50 Ross 308 broilers in the starter phase and 16 in the grower phase. All the NAGPCs significantly improved (P < 0.01) utilization of dry matter (DM), organic matter (OM), crude protein (CP), and crude fat (CF) on d 21, significantly increased DM, OM (P < 0.01), and CP (P < 0.05) on d 42, and significantly increased (P < 0.01) villus height, crypt depth, and the villus height to crypt depth ratio in the jejunum and ileum compared with CON and ENR. On d 21 and 42, trypsin, lipase, and amylase activity of the duodenum significantly increased in the MMS, MMB, MFB, and MFM groups. Compared with ENR and CON, MMS, MMB, and MBP increased the abundance of Firmicutes at d 21 and of Bacteroides at d 42 whereas MMB, MFB, and MBP decreased the abundance of Proteobacteria at d 21 and 42. Overall, the NAGPCs were found to have some beneficial effects and may be used as effective antibiotic replacements in broilers.

biophysics↗

bioRxiv2022

Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2

The recent emergence of multi-sample multi-condition single-cell multi-cohort studies allow researchers to investigate different cell states. The effective integration of multiple large-cohort studies promises biological insights into cells under different conditions that individual studies cannot provide. Here, we present scMerge2, a scalable algorithm that allows data integration of atlas-scale multi-sample multi-condition single-cell studies. We have generalised scMerge2 to enable the merging of millions of cells from single-cell studies generated by various single-cell technologies. Using a large COVID-19 data collection with over five million cells from 1000+ individuals, we demonstrate that scMerge2 enables multi-sample multi-condition scRNA-seq data integration from multiple cohorts and reveals signatures derived from cell-type expression that are more accurate in discriminating disease progression. Further, we demonstrate that scMerge2 can remove dataset variability in CyTOF, imaging mass cytometry and CITE-seq experiments, demonstrating its applicability to a broad spectrum of single-cell profiling technologies.

bioinformatics↗

bioRxiv2022

Covidscope: An atlas-scale COVID-19 resource for single-cell meta analysis at sample and cell levels

With the recent advancement in single-cell technologies and the increased availability of integrative tools, challenges arise in easy and fast access to large collections of cell atlas. Existing cell atlas portals rarely are open sourced and adaptable, and do not support meta-analysis at cell level. Here, we present an open source, highly optimised and scalable architecture, named Scope+, to allow quick access, meta-analysis and cell-level selection of the atlas data. We applied this architecture to our well-curated 5 million Covid-19 blood and immune cells, as a portal, Covidscope (https://covidsc.d24h.hk/). We achieved efficient access to atlas-scale data via three strategies, such as server-side rendering, novel database optimization strategies and an innovative architectural design. Scope+ serves as an open source architecture for researchers to build on with their own atlas, and demonstrated its capability in the Covidscope portal for an effective meta-analysis to atlas data at cellular resolution for reproducible research.

bioinformatics↗

bioRxiv2022

Evaluation of the zoonotic potential of tick-borne viruses in public datasets

Tick-borne viruses remain a substantial zoonotic risk worldwide, so knowledge of the diversity of tick viruses has potential health consequences. Despite their importance, large amounts of sequences in public datasets from tick meta-genomic and -transcriptomic projects remain unannotated, sequence data that could contain undocumented viruses. Through data mining and bioinformatic analyses of more than 37,800 public meta-genomic and -transcriptomic datasets, we found 83 unannotated contigs exhibiting high identity with known tick viruses. These putative viral contigs were classified into three RNA viral families (Alphatetraviridae, Orthomyxoviridae, Chuviridae) and one DNA viral family (Asfaviridae). After manual checking of quality and dissimilarity toward other sequences in the dataset, these 83 contigs were reduced to five putative novel Alphatetra-like viral contigs, four putative novel Orthomyxo-like viral contigs, and one Chu-like viral contig which clustered with known tick-borne viruses, forming a separate clade within the viral families. We further attempted to assess which previously known tick viruses likely represent zoonotic risks and thus deserve further investigation. We ranked the human infection potential of 136 known tick-borne viruses using a genome composition-based machine learning model. We found five high-risk tick-borne viruses (Langat virus, Lonestar tick chuvirus 1, Grotenhout virus, Taggert virus, and Johnston Atoll virus) that have not been known to infect human and two viral families (Nairoviridae and Phenuiviridae) that contain a large proportion of potential zoonotic tick-borne viruses. This adds to the knowledge of tick virus diversity and highlights the importance of surveillance of newly emerging tick-borne diseases. ImportanceTicks are important hosts of pathogens. Despite this, numerous tick-borne viruses are still unknown or poorly characterised. To overcome this, we re-examined currently known tick-borne viruses and identified putative novel viruses associated with ticks in public datasets. Using genome-based machine learning approach, we predicted five high-risk tick-borne viruses that have not yet been reported to cause human infections. Additionally, we highlighted two viral families, Nairoviridae and Phenuiviridae, which are potential public health threats. Our analysis also revealed 10 putative novel RNA viral contigs clustered with known tick-borne viruses. Our study highlights the importance of monitoring ticks and the viruses they carry in endemic areas to prevent and control zoonotic infectious disease outbreaks. To achieve this, we advocate for a multidisciplinary approach within a One Health and EcoHealth framework that considers the relationship between zoonotic disease outbreaks and their hosts, humans, and the environment.

microbiology↗

bioRxiv2022

Tree segmentation in airborne laser scanning data is only accurate for canopy trees

Individual tree segmentation from airborne laser scanning data is a longstanding and important challenge in forest remote sensing. There are a number of segmentation algorithms but robust intercomparison studies are rare due to the difficulty of obtaining reliable reference data. Here we provide a benchmark data set for temperate and tropical broadleaf forests generated from labelled terrestrial laser scanning data. We compare the performance of four widely used tree segmentation algorithms against this benchmark data set. All algorithms achieved reasonable accuracy for the canopy trees, but very low accuracy for the understory trees. The point cloud based algorithm AMS3D (Adaptive Mean Shift 3D) had the highest overall accuracy, closely followed by the 2D raster based region growing algorithm Dalponte2016+. This result was consistent across both forest types. This study emphasises the need to assess tree segmentation algorithms directly using benchmark data. We provide the first openly available benchmark data set for tropical forests and we hope future studies will extend this work to other regions.

ecology↗

bioRxiv2022

Robust and High-Throughput Analytical Flow Proteomics Analysis of Cynomolgus Monkey and Human Matrices with Zeno SWATH Data Independent Acquisition

Modern mass spectrometers routinely allow deep proteome coverage in a single experiment. These methods are typically operated at nano and micro flow regimes, but they often lack throughput and chromatographic robustness, which is critical for large-scale studies. In this context, we have developed, optimized and benchmarked LC-MS methods combining the robustness and throughput of analytical flow chromatography with the added sensitivity provided by the Zeno trap across a wide range of cynomolgus monkey and human matrices of interest for toxicological studies and clinical biomarker discovery. SWATH data independent acquisition (DIA) experiments with Zeno trap activated (Zeno SWATH DIA) provided a clear advantage over conventional SWATH DIA in all sample types tested with improved sensitivity, quantitative robustness and signal linearity as well as increased protein coverage by up to 9-fold. Using a 10-min gradient chromatography, up to 3,300 proteins were identified in tissues at 2 {micro}g peptide load. Importantly, the performance gains with Zeno SWATH translated into better biological pathway representation and improved the ability to identify dysregulated proteins and pathways associated with two metabolic diseases in human plasma. Finally, we demonstrate that this method is highly stable over time with the acquisition of reliable data over the injection of 1,000+ samples (14.2 days of uninterrupted acquisition) without the need for human intervention or normalization. Altogether, Zeno SWATH DIA methodology allows fast, sensitive and robust proteomic workflows using analytical flow and is amenable to large-scale studies. This work provides detailed method performance assessment on a variety of relevant biological matrices and serves as a valuable resource for the proteomics community.

biochemistry↗

bioRxiv2022

Deep Learning for Predicting 16S rRNA Copy Number

BackgroundCulture-independent 16S rRNA gene metabarcoding is a commonly used method in microbiome profiling. However, this approach can only reflect the proportion of sequencing reads, rather than the actual cell fraction. To achieve more quantitative cell fraction estimates, we need to resolve the 16S gene copy numbers (GCN) for different community members. Currently, there are several bioinformatic tools available to estimate 16S GCN, either based on taxonomy assignment or phylogeny. MethodHere we develop a novel algorithm, Stacked Ensemble Model (SEM), that estimates 16S GCN directly from the 16S rRNA gene sequence strings, without resolving taxonomy or phylogeny. For accessibility, we developed a public, end-to-end, web-based tool based on the SEM model, named Artificial Neural Network Approximator for 16S rRNA Gene Copy Number (ANNA16). ResultsBased on 27,579 16S rRNA gene sequence data (rrnDB database), we show that ANNA16 outperforms the most commonly used 16S GCN prediction algorithms. The prediction error range in the 5-fold cross validation of SEM is completely lower than all other algorithms for the 16S full-length sequence and partially lower at 16S subregions. The final test and a mock community test indicate ANNA16 is more accurate than all currently available tools (i.e., rrnDB, CopyRighter, PICRUSt2, & PAPRICA). SHAP value analysis indicates ANNA16 mainly learns information from rare insertions. ConclusionANNA16 represents a deep learning based 16S GCN prediction tool. Compared to the traditional GCN prediction tools, ANNA16 has a simple structure, faster inference speed without precomputing, and higher accuracy. With increased 16S GCN data in the database, future studies could improve the prediction errors for rare, high-GCN taxa due to current under sampling.

bioinformatics↗