Biology subjects

Song, X.

Publications and source records attributed to Song, X..

At least 199 records · Page 11Linked to original sources

bioRxiv2020

A potent neutralizing human antibody reveals the N-terminal domain of the Spike protein of SARS-CoV-2 as a site of vulnerability

The pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents a global public health threat. Most research on therapeutics against SARS-CoV-2 focused on the receptor binding domain (RBD) of the Spike (S) protein, whereas the vulnerable epitopes and functional mechanism of non-RBD regions are poorly understood. Here we isolated and characterized monoclonal antibodies (mAbs) derived from convalescent COVID-19 patients. An mAb targeting the N-terminal domain (NTD) of the SARS-CoV-2 S protein, named 4A8, exhibits high neutralization potency against both authentic and pseudotyped SARS-CoV-2, although it does not block the interaction between angiotensin-converting enzyme 2 (ACE2) receptor and S protein. The cryo-EM structure of the SARS-CoV-2 S protein in complex with 4A8 has been determined to an overall resolution of 3.1 Angstrom and local resolution of 3.4 Angstrom for the 4A8-NTD interface, revealing detailed interactions between the NTD and 4A8. Our functional and structural characterizations discover a new vulnerable epitope of the S protein and identify promising neutralizing mAbs as potential clinical therapy for COVID-19.

biochemistry↗

bioRxiv2020

De novo mutation in ancestral generations evolves haplotypes contributing to disease

PurposeThe variome of the Turkish (TK) population, a population with a considerable history of admixture and consanguinity, has not been deeply investigated deeply for its potential impact on the genomic architecture of disease traits. MethodsWe generated and analyzed a database of variants derived from exome sequencing (ES) data of 773 TK unrelated, clinically affected individuals with various suspected Mendelian disease traits, and 643 unaffected relatives. ResultsUsing uniform manifold approximation and projection (UMAP), we showed that the TK genomes are more similar to those of Europeans and consist of two main subpopulations: clusters 1 and 2 (N=235 and 1,181) that differ in admixture proportion and variome (https://turkishvariomedb.shinyapps.io/tvdb/). Furthermore, the higher inbreeding coefficient (F) values observed in the TK affected compared to unaffected individuals correlated with a larger median span of long-sized (>2.64 Mb) runs of homozygosity (ROH) regions (p-value=2.09e-18). We show that long-sized ROHs are more likely to be formed on recently configured haplotypes enriched for rare homozygous deleterious variants in the TK-affected compared to TK-unaffected individuals (p-value= 3.35e-11). Analysis of genotype-phenotype correlations reveals that genes with rare homozygous deleterious variants in long-sized ROHs provide the most comprehensive set of molecular diagnoses for the observed disease traits with a systematic quantitative analysis of HPO (Human Phenotype Ontology) terms. ConclusionOur findings support the notion that novel rare variants on newly configured haplotypes arising within the recent past generations of a family or clan contribute significantly to recessive disease traits in the TK population.

genomics↗

bioRxiv2020

Rottlerin ameliorates DSS-induced colitis by improving intestinal barrier function via activation of the Epac-2/Rap-1 signaling pathway.

OBJECTIVESRottlerin, a pan PDE inhibitor, has a variety of pharmacological activities, including enhancing barrier function and mediating anti-inflammatory activity by changing the distribution of occludin and ZO-1. Nevertheless, the function of rottlerin on Crohn disease (CD) keep unknown. Our aim of the study is to investigate the role of rottlerin on CD-like colitis and its mechanism. METHODSWild-type mice which were 8-10 weeks old were randomly divided into three treatment groups: (i) the normal feeding, no administration (control) group, (ii) the group administered 3% dextran sodium sulfate (DSS) alone, and (iii) the group administered rottlerin (100 mg/kg) and 3% DSS. In this study, the effect of rottlerin on the function and structure of the intestinal barrier was investigated, and the possible mechanism was discussed. We performed signaling pathway analysis and flow cytometry to identify the detailed mechanisms by which rottlerin (10 g/mL) treatment inhibits cell growth arrest and the attenuation of TJ proteins in LPS-treated FHs 74 int cells. RESULTSRottlerin treatment significantly ameliorated colitis induced by DSS in WT mice, which was manifested by a decrease in inflammation score, the attenuation of inflammatory factors and the inhibition of destruction on intestinal barrier structure. Rottlerin enhanced the levels of occludin and ZO-1, and improved the function of intestinal barrier, which may have been why rottlerin ameliorated colitis in WT mice. The anti-inflammatory effect of rottlerin may be partly due to the activation of Epac-2/Rap-1 signaling. CONCLUSIONSRottlerin may treat CD in humans via enhancing TJ proteins expression and improving the function of intestinal barrier.

cell biology↗

bioRxiv2020

A dataset of speed-resolved blood perfusion and oxygen saturation in human skin response to thermal stimulation

The functional status of vessels can be determined by assessing blood perfusion. By integrating diffuse reflectance spectroscopy (DRS) and laser Doppler Flowmetry (LDF), the speed-resolved blood perfusion and blood oxygen saturation can be measured simultaneously by Enhanced Perfusion and Oxygen Saturation (EPOS). The dataset presented in this descriptor contains EPOS data recorded from a forearm point exposed to different levels of thermal stimulation, the classical LDF at control points, the R-R time series and data regarding characteristics of subjects. All data were recorded from 60 recruited healthy subjects. Half of the subjects received different levels of thermal stimulation, and half of them were blank controls. We believe that this dataset will lead to the development of local blood perfusion methods that can be used to index vessel function assessments. This publicly available dataset will be beneficial to the microcirculation evaluation.

bioengineering↗

bioRxiv2020

Role of RgsA in oxidative stress resistance in Pseudomonas aeruginosa

Pseudomonas aeruginosa is an extremely common opportunistic pathogen in clinical practice. Patients with metabolic disorders, hematologic diseases, malignancies, who have undergone surgery or who have received certain treatments are susceptible to this bacterium. In addition, P. aeruginosa is a multidrug-resistant that tends to form biofilms and is refractory to treatment. Small regulatory RNAs are RNA molecules that are 40-500 nucleotides long, possess regulatory function, are ubiquitous in bacteria, and are also known as small RNA (sRNA). sRNAs play important regulatory roles in various vital life processes in diverse bacteria and their quantity and diversity of regulatory functions exceeds that of proteins. In this study, we showed that deletion of the sRNA RgsA decreases the growth rate and ability to resist different concentrations and durations of peroxide in P. aeruginosa. These decreases occur not only in the planktonic state, but also in the biofilm state. Finally, protein mass spectrometry was employed to understand changes in the entire protein spectrum. The results presented herein provide a description of the role of RgsA in the life activities of P. aeruginosa at the molecular, phenotypic, and protein levels.

microbiology↗

bioRxiv2020

ProTrack: An Interactive Multi-Omics Data Browser for Proteogenomic Studies

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) initiative has generated extensive multi-omics data resources of deep proteogenomic profiles for multiple cancer types. To enable the broader community of biological and medical researchers to intuitively query, explore, and download data and analysis results from various CPTAC projects, we built a prototype user-friendly web application called "ProTrack" with the CPTAC clear cell renal cell carcinoma (ccRCC) data set (http://ccrcc.cptac-data-view.org). Here we describe the salient features of this application which provides a dynamic, comprehensive, and granular visualization of the rich proteogenomic data. Statement of SignificanceThe CPTAC initiative (https://proteomics.cancer.gov/) has generated multi-omics data for multiple cancer types to understand the proteogenomic aberrations of these malignancies. Collectively this effort has so far produced a large data resource for the research community, including high-throughput profiles for proteome, phosphoproteome, whole exome, whole genome, transcriptome, and DNA methylome. To make this valuable data-resource useful to the larger research community, there is a pressing need for development of user-friendly, readily accessible, and easily shared analytic and visualization tools for aligning multi-omics data and exploring alterations in key cancer genes, to drive and support new biological hypotheses. To bridge this gap, we have developed CPTAC ProTrack, an interactive web application which uses a multilayered, client-server architecture in order to deliver an interactive web experience to any user of a modern web-browser. This tool is intentionally designed accessible for researchers, biologists, and clinicians who are interested in multi-omic data without any need to code.

bioinformatics↗

bioRxiv2020

Clonal Evolution of Acute Myeloid Leukemia Revealed by High-Throughput Single-Cell Genomics

One of the pervasive features of cancer is the diversity of mutations found in malignant cells within the same tumor; a phenomenon called clonal diversity or intratumor heterogeneity. Clonal diversity allows tumors to adapt to the selective pressure of treatment and likely contributes to the development of treatment resistance and cancer recurrence. Thus, the ability to precisely delineate the clonal substructure of a tumor, including the evolutionary history of its development and the co-occurrence of its mutations, is necessary to understand and overcome treatment resistance. However, DNA sequencing of bulk tumor samples cannot accurately resolve complex clonal architectures. Here, we performed high-throughput single-cell DNA sequencing to quantitatively assess the clonal architecture of acute myeloid leukemia (AML). We sequenced a total of 556,951 cells from 77 patients with AML for 19 genes known to be recurrently mutated in AML. The data revealed clonal relationship among AML driver mutations and identified mutations that often co-occurred (e.g., NPM1/FLT3-ITD, DNMT3A/NPM1, SRSF2/IDH2, and WT1/FLT3-ITD) and those that were mutually exclusive (e.g., NRAS/KRAS, FLT3-D835/ITD, and IDH1/IDH2) at single-cell resolution. Reconstruction of the tumor phylogeny uncovered history of tumor development that is characterized by linear and branching clonal evolution patterns with latter involving functional convergence of separately evolved clones. Analysis of longitudinal samples revealed remodeling of clonal architecture in response to therapeutic pressure that is driven by clonal selection. Furthermore, in this AML cohort, higher clonal diversity ([≥]4 subclones) was associated with significantly worse overall survival. These data portray clonal relationship, architecture, and evolution of AML driver genes with unprecedented resolution, and illuminate the role of clonal diversity in therapeutic resistance, relapse and clinical outcome in AML.

cancer biology↗

bioRxiv2020

IRESbase: a Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites

Internal Ribosome Entry Sites (IRESs) are functional RNA elements that can directly recruit ribosomes to an internal position of the mRNA in a cap-independent manner to initiate translation. Recently, IRES elements have attracted much attention for their critical roles in various processes including translation initiation of a new type of RNA, circular RNA, with no 5' cap to support classical cap-dependent translation. Thus, an integrative data resource of IRES elements with experimental evidences will be useful for further studies. In this study, we present a comprehensive database of IRESs (IRESbase) by curating the experimentally validated functional minimal IRES elements from literature and annotating their host linear and circular RNA information. The current version of IRESbase contains 1328 IRESs, including 774 eukaryotic IRESs and 554 viral IRESs from 11 eukaryotic organisms and 198 viruses. As our database collected only IRES of minimal length with functional evidences, the median length of IRESs in IRESbase is 174 nucleotides. By mapping IRESs to human circRNAs and lncRNAs, 2191 circRNAs and 168 lncRNAs were found to contain at least one entire or partial IRES sequences. The IRESbase is available at http://reprod.njmu.edu.cn/cgi-bin/iresbase/index.php.

bioinformatics↗

bioRxiv2019

Seq2DFunc: 2-dimensional convolutional neural network on graph representation of synthetic sequences from massive-throughput assay

In recent years, a pipeline of massively parallel reporter assay (MPRA), and next-generation sequencing (NGS) provided large-scale datasets to investigate biological mechanisms in detail. However, bigger data often leads to larger complexity. As a result, theories derived from low-throughput experiments lose explanatory power, requiring new methods to create predictive models. Here we focus on modeling functions of nucleic acid sequences, as a study case of massive-throughput assays. We report a deep learning approach, training a two-dimensional convolutional neural network (CNN) on an ordered graph representation of nucleic acid sequences to predict their functions (Seq2DFunc). To compare the performance of Seq2DFunc with conventional methods, we obtained customized database on a CRISPR RNA processing assay. For this specific assay, analyses of sequence and RNA structure determinants failed to explain the results regardless of dataset size. 1-dimensional CNN of raw sequences generate generally failed to converge at < 10,000 or fewer sequences. By contrast, Seq2DFunc trained on [~] 7,000 sequences still provided 86% accuracy. Given a sufficient dataset ([~] 120,000 sequences) for training, Seq2DFunc (96% accuracy, 0.93 f1-score) still outperformed the best 1D CNN (92% accuracy, 0.83 f1-score). We anticipate Seq2DFunc can be a versatile downstream tool for deciphering massive-throughput assays for many fundamental studies. In addition, the use of smaller dataset is especially beneficial to reduce the experiment budget or required sequencing depth.

synthetic biology↗

bioRxiv2019

Extensive Mammalian Germline Genome Engineering

Xenotransplantation, specifically the use of porcine organs for human transplantation, has long been sought after as an alternative for patients suffering from organ failure. However, clinical application of this approach has been impeded by two main hurdles: 1) risk of transmission of porcine endogenous retroviruses (PERVs) and 2) molecular incompatibilities between donor pigs and humans which culminate in rejection of the graft. We previously demonstrated that all 25 copies of the PERV elements in the pig genome could be inactivated and live pigs successfully generated. In this study, we improved the scale of porcine germline editing from targeting a single repetitive locus with CRISPR to engineering 13 different genes using multiple genome engineering methods. we engineered the pig genome at 42 alleles using CRISPR-Cas9 and transposon and produced PERVKO{middle dot}3KO{middle dot}9TG pigs which carry PERV inactivation, xeno-antigen KO and 9 effective human transgenes. The engineered pigs exhibit normal physiology, fertility, and germline transmission of the edited alleles. In vitro assays demonstrated that these pigs gain significant resistance to human humoral and cell mediated damage, and coagulation dysregulations, similar to that of allotransplantation. Successful creation of PERVKO{middle dot}3KO{middle dot}9TG pigs represents a significant step forward towards safe and effective porcine xenotransplantation, which also represents a synthetic biology accomplishment of engineering novel functions in a living organism. One Sentence SummaryExtensive genome engineering is applied to modify pigs for safe and immune compatible organs for human transplantation

synthetic biology↗

bioRxiv2019

Effects of a novel three-dimensional grid intrauterine device on the uterus, steroid receptor and PAX2 of rhesus macaques

Intrauterine devices (IUDs) is the most effective methods of the reversible and long-acting contraception. 1) To develop a novel three-dimensional grid intrauterine device (3-DGIUD) with nickel-titanium (Ni-Ti) and silicone rubber. 2) To observe the effect of the 3-DGIUD on contraceptive efficacy and the change of uterus, endometrial sex steroid receptor, PAX2 in rhesus macaques (Macaca mulatta). The materials of the 3-DGIUD were the nitinol wire and the silicone rubber. The frame of the 3-DGIUD was three-dimensional and grid-like. Twenty adult female rhesus macaques were divided into the 3-DGIUD group (placing the 3-DGIUD, n=9), the sham operation group (no placing the 3-DGIUD, n=9) and the control group (n=2). On the 10th-day after surgery, the 3-DGIUD group and the sham operation group macaques were caged together with male macaques (female: male = 1:1). The uterus, 3-DGIUD and pregnancy of 18 female rhesus monkeys were examined by abdominal ultrasound every month. The endometrium pathological examination was carried out and the expression of PAX2 and hormone receptor (ER, PR) was detected by immunohistochemical staining. After 3-DGIUD was placed in case group for 3 and 12 months, only 1 of female macaque was pregnant in 9. The contraceptive effective rate was 88.9% (8/9). The 3-DGIUD in the uterus of macaques was observed by ultrasound. In the sham operation group, 9 macaques were pregnant (9/9). There was significant difference in uterine size of the 3-DGIUD group between pre-placement and after surgery for 3 and 12 months (P<0.05). The endometrial epithelium was intact, just a small number of glands vacuoles and a few neutrophils infiltration around the 3-DGIUD. The expression of endometrial ER, PR and PAX2 in 3-DGIUD group on 12 months after surgery was similar to those in control macaque. The 3-DGIUD has a good contraceptive effect on female macaques, and has no significant affection on the expression of endometrial steroid receptor and PAX2 in rhesus monkeys.

zoology↗

bioRxiv2019

Integrated Sequencing & Array Comparative Genomic Hybridization in Familial Parkinson’s Disease

BackgroundParkinsons disease (PD) is a genetically heterogeneous condition; both single nucleotide variants (SNVs) and copy number variants (CNVs) are important genetic risk factors. We examined the utility of combining exome sequencing and genome-wide array-based comparative genomic hybridization (aCGH) for identification of PD genetic risk factors. MethodsWe performed exome sequencing on 110 subjects with PD and a positive family history; 99 subjects were also evaluated using genome-wide aCGH. We interrogated exome sequencing and array comparative genomic hybridization data for pathogenic SNVs and CNVs at Mendelian PD gene loci. SNVs were confirmed via Sanger sequencing. CNVs were confirmed with custom-designed high-density aCGH, droplet digital PCR, and breakpoint sequencing. ResultsUsing exome sequencing, we discovered individuals with known pathogenic single nucleotide variants in GBA (p.E365K, p.T408M, p.N409S, p.L483P) and LRRK2 (p.R1441G and p.G2019S). Two subjects were each double heterozygotes for variants in GBA and LRRK2. Based on aCGH, we additionally discovered cases with an SNCA duplication and heterozygous intragenic GBA deletion. Five additional subjects harbored both SNVs (p.N52fs, p.T240M, p.P437L, p.W453*) and likely disrupting CNVs at the PARK2 locus, consistent with compound heterozygosity. In nearly all cases, breakpoint sequencing revealed microhomology, a mutational signature consistent with CNV formation due to DNA replication errors. ConclusionsIntegrated exome sequencing and aCGH yielded a genetic diagnosis in 19.3% of our familial PD cohort. Our analyses highlight potential mechanisms for SNCA and PARK2 CNV formation, uncover multilocus pathogenic variation, and identify novel SNVs and CNVs for further investigation as potential PD risk alleles.

genetics↗

bioRxiv2019

Diversity and complexity of the large surface protein family in the compacted genomes of various Pneumocystis species

Pneumocystis, a major opportunistic pathogen in patients with a broad range of immunodeficiencies, contains abundant surface proteins encoded by a multi-copy gene family, termed the major surface glycoprotein (Msg) gene superfamily. This superfamily has been identified in all Pneumocystis species characterized to date, highlighting its important role in Pneumocystis biology. In this report, through a comprehensive and in-depth characterization of 459 msg genes from 7 Pneumocystis species, we demonstrate, for the first time, the phylogeny and evolution of conserved domains in Msg proteins, and provide detailed description of the classification, unique characteristics and phylogenetic relatedness of five Msg families. We further describe the relative expression levels of individual msg families in two rodent Pneumocystis species, the substantial variability of the msg repertoires in P. carinii from laboratory and wild rats, and the distinct features of the expression site for the classic msg genes in Pneumocystis from 8 mammalian host species. Our analysis suggests a wide variety of functions for this superfamily, not only conferring antigenic variation to allow immune evasion but also mediating life-stage development, optimizing cell mobility and adhesion, and adapting to specific host niches or environmental conditions. This study provides a rich source of information that lays the foundation for the continued experimental exploration of the functions of the Msg superfamily in Pneumocystis biology.

molecular biology↗

bioRxiv2019

Field decomposition of Bt-506 corn leaf and its effect on Collembola in the black soil region of China

The litters of Bt corn would go into the soil through straw returning and field ploughing after cultivation. To clarify whether the leaf litter decomposition rate and the non-target soil Collembola were influenced by the Bt protein or other litter properties in leaf litters of Bt corn in Northeast China, leaf litterbags of Bt-506, its near isoline Zheng 58 and a local type Zhengdan 958 were used in the field in Northeast China. The leaf decomposition rate, the leaf properties and the collembolan community in litterbags were investigated later. After seven months, only 43.5 ng/g Bt protein in Bt-506 leaf litter was left. All the investigated indices were not significantly different between Bt-506 and its near isoline Zheng 58. But when compared with local type Zhengdan 958, Bt-506 and its near isoline Zheng 58 contained lower non-structural carbohydrate content but higher total nitrogen content, and had lower litter decomposition rate and less abundance of Collembola. Collembolan abundance and litter decomposition rate were both significantly correlated with the non-structural carbohydrate and total nitrogen contents of the leaf litters. Field study results revealed Bt protein did not affect the leaf litter decomposition rate and the collembolan community in leaf litterbags in short term. The significant differences of these investigated indices among corn types were caused by the different non-structural carbohydrate and total nitrogen contents in leaf litter.

ecology↗

bioRxiv2019

Inosine is an alternative carbon supply that supports effector T cell proliferation and anti-tumor function under glucose restriction

T cells undergo a characteristic metabolic rewiring that fulfills the dramatically increased bioenergetic, biosynthetic, and redox demands following antigen stimulation. A robust adaptive immune system requires effector T cells to respond and adapt to fluctuations in environmental nutrient levels imposed by infectious and inflammatory sites in different tissues. Inevitably, such responsiveness and adaptation reflect metabolic plasticity, allowing T cells to elicit immune functions by using a wide range of nutrient substrates. Here, we show that effector T cells utilize inosine, as an alternative substrate, to support cell growth and function in the absence of glucose. T cells metabolize inosine into hypoxanthine and phosphorylated ribose by purine nucleoside phosphorylase (PNP). Using Stable Isotope-Resolved Metabolomics (SIRM), we demonstrated that ribose moiety of inosine can enter into central metabolic pathways to provide ATP and biosynthetic precursors. Accordingly, the dependence of T cells on extracellular glucose for growth and effector functions can be relieved by inosine. On the other hand, cancer cells display diverse capacity to utilize inosine as a carbon resource. Moreover, the supplement of inosine enhances the anti-tumor efficacy of immune-checkpoint blockade or adoptive T cell transfer, reflecting the capability of inosine in relieving tumor-imposed metabolic restrictions on T cells in vivo.

immunology↗

bioRxiv2019

Germline RNA helicases couple RNA binding to P granule assembly at nuclear periphery

P granules are phase-separated liquid droplets that play important roles in the maintenance of the germ cell fate in C. elegans. The localization and formation of P granules are highly dynamic, but mechanisms that regulate such processes remain poorly understood. Here we show that germline RNA helicases (GLHs) control the formation and disassembly of germ granules through their binding and release of RNAs, respectively. In addition, the FGG repeats in the GLHs promote the formation of germ granules at the perinucleus. Proteomic analyses of a mutation that traps RNA-bound GLH-1 complex revealed transient interactions of GLH-1 with several Argonautes and RNA binding proteins. Finally, we found that defects in perinuclear P granule formation correlate with the fertility defects observed in various GLH mutants. Together, our results highlight the versatile roles of RNA helicases in controlling the formation of liquid droplets in space and time.

cell biology↗

bioRxiv2019

Pumilio Proteins Exert Distinct Biological Functions and Multiple Modes of Post-Transcriptional Regulation in Embryonic Stem Cell Pluripotency and Early Embryogenesis

Gene regulation in embryonic stem cells (ESCs) has been extensively studied at the epigenetic-transcriptional levels, but not at the post-transcriptional levels. Pumilio (Pum) proteins are among the few known translational regulators required for stem cell maintenance in invertebrates and plants. Here we report the essential function of two murine Pum proteins, Pum1 and Pum2, in ESCs and early embryogenesis. Pum1/2 double mutants are developmentally delayed at the morula stage and lethal by embryonic day 8.5 (e8.5). Correspondingly, Pum1/2 double mutant ESCs display severely reduced self-renewal and differentiation, revealing the combined function of Pum1 and Pum2 in ESC pluripotency. Remarkably, Pum1-deficient ESCs show increased expression of pluripotency genes but not differentiation genes, indicating that Pum1 mainly promote differentiation; whereas Pum2-deficient ESCs show decreased expression of pluripotency genes and accelerated differentiation, indicating that Pum2 promotes self-renewal. Thus, Pum1 and Pum2 each uniquely contributes to one of the two complementary aspects of pluripotency. Furthermore, we show that Pum1 and Pum2 achieve ESC functions by forming a negative auto- and inter-regulatory feedback loop that directly regulates at least 1,486 mRNAs. Pum1 and Pum2 regulate target mRNAs not only by repressing translation as expected but also by promoting translation and enhancing or reducing mRNA stability of different target mRNAs. Together, these findings reveal the distinct roles of individual mammalian Pum proteins in ESCs and their collectively essential functions in ESC pluripotency and embryogenesis. Moreover, they demonstrate three novel modes of regulation of Pum proteins towards target mRNAs.\n\nSIGNIFICANCE STATEMENTThis report demonstrates the essential functions of mammalian Pumilio (Pum) proteins for embryonic stem cells (ESCs) pluripotency and embryogenesis. Moreover, it reveals the contrasting but complementary function of individual Pum proteins in regulating distinct aspects of ESC pluripotency, despite their largely overlapping expression and extremely high homology. Furthermore, it unravels a complex regulatory network in which Pum1 and Pum2 form a negative auto- and inter-regulatory feedback loop that regulates 1,486 mRNAs not only by translational repression as expected but also by promoting translation and enhancing or reducing stability of different target mRNAs, which reveals novel modes of post-transcriptional regulation mediated by Pum.

developmental biology↗

bioRxiv2019

Multidimensional Data Organization and Random Access in Large-Scale DNA Storage Systems

With impressive density and coding capacity, DNA offers a promising solution for building long-lasting data archival storage systems. In recent implementations, data retrieval such as random access typically relies on a large library of non-interacting PCR primers. While several algorithms automate the primer design process, the capacity and scalability of DNA-based storage systems are still fundamentally limited by the availability of experimentally validated orthogonal primers. In this work, we combine the nested and semi-nested PCR techniques to virtually enforce multidimensional data organization in large DNA storage systems. The strategy effectively pushes the limit of DNA storage capacity and reduces the number of primers needed for efficient random access from very large address space. Specifically, our design requires k * n unique primers to index nk data entries, where k specifies the number of dimensions and n indicates the number of data entries stored in each dimension. We strategically leverage forward/reverse primer pairs from the same or different address layers to virtually specify and maintain data retrievals in the form of rows, columns, tables, and blocks with respect to the original storage pool. This architecture enables various random-access patterns that could be tailored to preserve the underlying data structures and relations (e.g., files and folders) within the storage content. With just one or two rounds of PCR, specific data subsets or individual datum from the large multidimensional storage can be selectively enriched for simple extraction by gel electrophoresis or readout via sequencing.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC=\"FIGDIR/small/743369v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (39K):\norg.highwire.dtl.DTLVardef@bcbfcorg.highwire.dtl.DTLVardef@7d1498org.highwire.dtl.DTLVardef@1d31becorg.highwire.dtl.DTLVardef@ce396e_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗