RNA-protein interactions reveals the pivotal role of lncRNA1840 in tomato fruit maturation.

Long non-coding RNAs (lncRNAs) play crucial roles in various biological processes in plants. However, the functional mechanism of lncRNAs in fruit ripening, particularly the transition from unripe to ripe stages, remains elusive. One such lncRNA1840, reported by our group, was found to have important role in tomato fruit ripening. In the present study, we gain insight into its functional role in fruit ripening. CRISPR-Cas9 mediated lncRNA1840 mutants caused the delayed tomato fruit ripening. Notably, loss function of lncRNA1840 did not directly impact ethylene signaling but rather delay ethylene synthesis. Transcriptomic analysis revealed differences in the expression of ripening related genes in lncRNA1840 mutants, suggesting that it is involved in gene regulation of fruit ripening. We used Chromatin Isolation by RNA Purification (ChIRP)-Seq to identify lncRNA1840 binding sites on chromatin. ChIRP-seq suggested that lncRNA1840 had occupancy on 40 genes, but none of them is differentially expressed genes in transcriptomic analysis, which indicated lncRNA1840 might indirectly modulate the gene expression. ChIRP-mass spectrometry analysis identified potential protein interactors of lncRNA1840, Pre-mRNA processing splicing factor 8, highlighting its involvement in post-transcriptional regulatory pathways. In summary, lncRNA1840 is key player in tomato plant growth and fruit ripening, with multifaceted roles in gene expression and regulatory networks.

RNA editing factor SlORRM2 regulates the formation of fruit pointed tips in tomato.

Domestication of tomato (Solanum lycopersicum) has led to large variation in fruit size and morphology. The development of the distal end of the fruit is a critical factor in determining its overall shape. However, the intricate mechanisms underlying distal fruit development require further exploration. This study aimed to investigate the regulatory role of an organelle RNA recognition motif (RRM)-containing protein SlORRM2 in tomato fruit morphology development. Mutant plants lacking SlORRM2 exhibited fruits with pointed tips at the distal end. However, this phenotype could be successfully restored through the implementation of a "functional complementation" strategy. Our findings suggest that the formation of pointed tips in the fruits of the CR-slorrm2 mutants is linked to alterations in the development of the ovary and style. We observed a substantial decrease in the levels of indole-3-acetic acid (IAA) and altered expression of IAA-related response genes in the ovary and style tissues of CR-slorrm2. Moreover, our data demonstrated that SlORRM2 plays a role in regulating mitochondrial RNA editing sites, particularly within genes encoding various respiratory chain subunits. Additionally, the CR-slorrm2 mutants exhibited modified organellar morphology and increased levels of reactive oxygen species. These findings provide valuable insights into the mechanisms underlying the formation of fruit pointed tips in tomato and offer genetic resources for tomato breeding.

SlRBP1 promotes translational efficiency via SleIF4A2 to maintain chloroplast function in tomato.

Many glycine-rich RNA-binding proteins (GR-RBPs) have critical functions in RNA processing and metabolism. Here, we describe a role for the tomato (Solanum lycopersicum) GR-RBP SlRBP1 in regulating mRNA translation. We found that SlRBP1 knockdown mutants (slrbp1) displayed reduced accumulation of total chlorophyll and impaired chloroplast ultrastructure. These phenotypes were accompanied by deregulation of the levels of numerous key transcripts associated with chloroplast functions in slrbp1. Furthermore, native RNA immunoprecipitation-sequencing (nRIP-seq) recovered 61 SlRBP1-associated RNAs, most of which are involved in photosynthesis. SlRBP1 binding to selected target RNAs was validated by nRIP-qPCR. Intriguingly, the accumulation of proteins encoded by SlRBP1-bound transcripts, but not the mRNAs themselves, was reduced in slrbp1 mutants. Polysome profiling followed by RT-qPCR assays indicated that the polysome occupancy of target RNAs was lower in slrbp1 plants than in wild-type. Furthermore, SlRBP1 interacted with the eukaryotic translation initiation factor SleIF4A2. Silencing of SlRBP1 significantly reduced SleIF4A2 binding to SlRBP1-target RNAs. Taking these observations together, we propose that SlRBP1 binds to and channels RNAs onto the SleIF4A2 translation initiation complex and promotes the translation of its target RNAs to regulate chloroplast functions.

Dicer-like2b suppresses the wiry leaf phenotype in tomato induced by tobacco mosaic virus.

Dicer-like (DCL) proteins are principal components of RNA silencing, a major defense mechanism against plant virus infections. However, their functions in suppressing virus-induced disease phenotypes remain largely unknown. Here, we identified a role for tomato (Solanum lycopersicum) DCL2b in regulating the wiry leaf phenotype during defense against tobacco mosaic virus (TMV). Knocking out SlyDCL2b promoted TMV accumulation in the leaf primordium, resulting in a wiry phenotype in distal leaves. Biochemical and bioinformatics analyses showed that 22-nt virus-derived small interfering RNAs (vsiRNAs) accumulated less abundantly in slydcl2b mutants than in wild-type plants, suggesting that SlyDCL2b-dependent 22-nt vsiRNAs are required to exclude virus from leaf primordia. Moreover, the wiry leaf phenotype was accompanied by upregulation of Auxin Response Factors (ARFs), resulting from a reduction in trans-acting siRNAs targeting ARFs (tasiARFs) in TMV-infected slydcl2b mutants. Loss of tasiARF production in the slydcl2b mutant was in turn caused by inhibition of miRNA390b function. Importantly, silencing SlyARF3 and SlyARF4 largely restored the wiry phenotype in TMV-infected slydcl2b mutants. Our work exemplifies the complex relationship between RNA viruses and the endogenous RNA silencing machinery, whereby SlyDCL2b protects the normal development of newly emerging organs by excluding virus from these regions and thus maintaining developmental silencing.

Split G-Quadruplex Programmed Recyclable AIE-Biosensor for Label-Free Detection of miRNA in Acute Kidney Injury.

We herein rationally designed a target-recyclable AIE-biosensor based on a split G-quadruplex for label-free detection of miRNA in acute kidney injury. Initially, the PG was in an "OFF" state, and the two split segments (G4-a and G4-b) of G4 were tethered at the two terminals of P1 and far away from each other due to the rigid duplex structure formed by the partially complementary intermediate sequences of P2 and P1, bringing MG with quenched fluorescence. In the presence of target, the 5'-PO4 P2 was displaced from PG probe and competitively hybridized with target, which led to G4-a and G4-b tending to form an intact intermolecular G-quadruplex, providing sites for MG intercalation, thus generating an activated "ON" fluorescence signal due to the restriction of intermolecular motion. Successively, relying on the λ-exonuclease (λ-Exo) cleavage reaction-assisted target recycling, more amounts of targets will be liberated, accompanied by forming more G-quadruplex and binding more MG, resulting in a strong fluorescence signal, further realizing the sensitive detection of the targets. As a proof of concept, miRNA-21 was chosen as the model target. Endowing with the precise target recognition and efficient cleavage activity of λ-Exo, the AIE-biosensor exhibited excellent detection sensitivity and specificity, which could quantitatively detect miRNA-21 down to 10.36 fM with a single mismatch specificity. The results revealed that the distinctive attributes of noninvasive, simple, and efficient in this G-quadruplex-based AIE-biosensor offered promising prospects for extensive applications in AKI screening and early clinical diagnosis.

Construction a novel osteoporosis model in immune-deficient mice with natural ageing.

Osteoporosis (OP) predominantly affects elderly individuals. Stem cells show potential for treating OP. However, animal models with normal immune function can eliminate implanted human cells. This study utilized naturally aging NOD/SCID mice, which exhibit immunodeficiency, to create a human osteoporosis model. This approach helps to minimize the premature immune clearance of transplanted allogeneic or xenogeneic cells in preclinical studies, allowing for a more accurate replication of the clinical pharmacological and pharmacokinetic processes involved in stem cell interventions for osteoporosis. NOD/SCID mice were fed until 12, 32, and 43 weeks of age, respectively, and then euthanized. We harvested lumbar vertebra for Micro-Computed Tomography (Micro-CT) scanning and pathological examination. Additionally, we performed biomechanical testing of lumbar vertebra to assess the severity of osteoporosis. We utilized real-time RT-PCR to assess gene expression changes associated with bone metabolism, aging, inflammation, oxidative stress, and the Tgf-ß1/Smad3 signaling pathway. In addition, the protein expression levels of P16, Tgf-ß1 and Smad3 were detected using Western Blotting (WB). In comparison to 12-week-old mice, the 32-week-old and 43-week-old mice displayed significantly sparser and fractured trabeculae in their lumbar vertebra, lower bone mineral density (BMD), and changes in bone microstructural parameters (∗∗P < 0.01, ∗∗∗P < 0.001). Additionally, compared to 12-week-old mice, the 32-week-old and 43-week-old mice exhibited decreased expression of osteogenic genes (Alp, Opg, Sp7, Col1a1), increased expression of osteoclastic gene (Rankl), the number of TRAP-positive osteoclasts significantly increased in 32-week-old and 43-week-old mice compared to 12-week-old mice. The expression of genes related to aging and inflammatory (P16, Il-1ß, Tnf-α) increases with advancing age (∗P < 0.05, ∗∗P < 0.01, ∗∗∗P < 0.001). The expression of oxidative stress-related genes (Sod1, Sod2, Foxo3, Nrf2), as well as Tgf-ß1 and Smad3 decreased with age (∗P < 0.05, ∗∗P < 0.01, ∗∗∗P < 0.001). As age increases, the levels of P16 protein increase, Tgf-ß1 and Smad3 proteins decrease. Our study successfully replicated osteoporosis models in NOD/SCID mice at both 32 and 43 weeks, with the latter exhibiting more severe osteoporosis. This condition seems to be driven by factors such as aging, inflammation, oxidative stress, and the Tgf-ß1/Smad3 signaling pathway.

M-type refractive index profile erbium-doped fiber for high-efficiency multicore EDFA.

Cladding-pumped multicore erbium-doped fiber is an important element for future spatial division multiplexing (SDM) amplification. We propose an M-type erbium-doped multicore fiber to achieve high-efficiency SDM amplification. The performance of cladding-pumped erbium-doped fiber with a central refractive index depression has been investigated, and the M-type fiber has better amplification performance than conventional fibers by reducing the signal mode overlap with the doped region. The experiment results show that the M-type 4-core erbium-doped fiber has a gain improvement of 2.8 dB compared with conventional 4-core fiber. The pump conversion efficiency (PCE) has been enhanced from 4.47% to 8.01%. For a 7.0 W pump power at 976 nm, the M-type fiber exhibits an average gain of 20.0 dB and an average noise fiber of 6.8 dB at the L-band. The core-to-core gain variation is less than 1.6 dB.

High-power polarization-maintaining LP11-mode fiber laser based on long-period fiber grating for precise welding.

An LP11-mode output all-fiber laser was presented, utilizing long-period fiber gratings (LPFGs) and polarization-maintaining optical fiber (PMF). The LPFG was designed and fabricated, achieving a 90.56% efficiency in LP01 to LP11 mode conversion. Furthermore, the transmission stability of LP11-mode in the PMF was also explored, with the spatial mode overlap ratio exceeding 0.95. Ultimately, the high-power polarization-maintaining (PM) fiber laser, capable of the LP11 mode output, was constructed, with the output power of 600 W and the beam quality M2 of 2.84. During the process of welding a thick Al-plate, the LP11 fiber laser exhibits a notable 1.88 times greater depth of fusion compared to the commercial single-mode fiber laser, when operating at the laser welding head speed of 100 mm/s. For applications demanding non-circular symmetric high-order modes, this research holds substantial potential for widespread adoption within the field of industrial processing.

High-efficiency cladding-pumped Er/Yb co-doped alumino-phosphosilicate fiber for an extended L-band amplification.

Extending the gain bandwidth of L-band optical fiber amplifier has provoked a widespread interest. To date, achieving a high-efficiency extended L-band amplification remains a challenge. Here, we report a cladding-pumped Er/Yb co-doped alumino-phosphosilicate fiber, prepared by the modified chemical vapor deposition process. We demonstrate the efficiency of alumino-phosphosilicate glass for cladding-pumped Er/Yb co-doped fiber, with a gain per unit fiber length of 0.45 dB/m at 1625 nm and a gain ripple of ∼9.4 dB. For 0.8 W pump power, the fiber exhibits a 20 dB gain bandwidth covering 1575-1625 nm and 6.9 dB noise figure at 1625 nm. Additionally, the utilization of multi-mode laser diode enables further significant power savings and cost reduction. To the best of our knowledge, Er/Yb co-doped fiber in alumino-phosphosilicate glass is first proposed, with a cladding-pumped scheme for enhancing an extended L-band performance.

High bismuth-doped germanosilicate fiber for efficient E + S-band amplification.

Bismuth-doped germanosilicate fiber (BGSF), the active media of fiber amplifiers, has attracted widespread attention. Here, we report a BGSF with a high bismuth concentration of 0.075 wt. % and achieve high-efficiency E + S-band amplification, which was prepared by the modified chemical vapor deposition (MCVD) process. The small signal absorption (SSA) and unsaturated loss (UL) of BGSF at 1310 nm are 1.32 and 0.11 dB/m, respectively. The results show a record with only 45 m BGSF was created, to the best of our knowledge, which provides a maximum gain of 39.24 dB with an NF of 6.2 dB at 1430 nm under -20 dBm input signal power.

Pluronic F127-Lipoic Acid Adhesive Nanohydrogel Combining with Ce3+/Tannic Acid/Ulinastatin Nanoparticles for Promoting Wound Healing.

Developing strong anti-inflammatory wound dressings is of great significance for protecting inflammatory cutaneous wounds and promoting wound healing. The present study develops a nanocomposite Pluronic F127 (F127)-based hydrogel dressing with injectable, tissue adhesive, and anti-inflammatory performance. Briefly, Ce3+/tannic acid/ulinastatin nanoparticles (Ce3+/TA/UTI NPs) are fabricated. Meanwhile, α-lipoic acid is bonded to the ends of F127 to prepare F127-lipoic acid (F127LA) and its nanomicelles. Due to the gradual viscosity change instead of mutation during phase transition, the mixed Ce3+/TA/UTI NPs and F127LA nanomicelles show well-performed injectability at 37 °C and can form a semisolid composite nanohydrogel that can tightly attach to the skin at 37 °C. Furthermore, ultraviolet (UV) irradiation without a photoinitiator transforms the semisolid hydrogel into a solid hydrogel with well-performed elasticity and toughness. The UV-cured composite nanohydrogel acts as a bioadhesive that can firmly adhere to tissues. Due to the limited swelling property, the hydrogel can firmly adhere to tissues in a wet environment, which can seal wounds and provide a reliable physical barrier for the wounds. Ce3+/TA/UTI NPs in the hydrogel exhibit lipopolysaccharide (LPS)-scavenging ability and reactive oxygen species (ROS)-scavenging ability and significantly reduce the expression of inflammatory factors in wounds at the early stage, accelerating LPS-induced wound healing.

Melatonin improves cholestatic liver disease via the gut-liver axis.

Cholestatic liver disease is characterized by disturbances in the intestinal microbiota and excessive accumulation of toxic bile acids (BA) in the liver. Melatonin (MT) can improve liver diseases. However, the underlying mechanism remains unclear. This study aimed to explore the mechanism of MT on hepatic BA synthesis, liver injury, and fibrosis in 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC)-fed and Mdr2-/- mice. MT significantly improved hepatic injury and fibrosis with a significant decrease in hepatic BA accumulation in DDC-fed and Mdr2-/- mice. MT reprogramed gut microbiota and augmented fecal bile salt hydrolase activity, which was related to increasing intestinal BA deconjugation and fecal BA excretion in both DDC-fed and Mdr2-/- mice. MT significantly activated the intestinal farnesoid X receptor (FXR)/fibroblast growth factor 15 (FGF-15) axis and subsequently inhibited hepatic BA synthesis in DDC-fed and Mdr2-/- mice. MT failed to improve DDC-induced liver fibrosis and BA synthesis in antibiotic-treated mice. Furthermore, MT provided protection against DDC-induced liver injury and fibrosis in fecal microbiota transplantation mice. MT did not decrease liver injury and fibrosis in DDC-fed intestinal epithelial cell-specific FXR knockout mice, suggesting that the intestinal FXR mediated the anti-fibrosis effect of MT. In conclusion, MT ameliorates cholestatic liver diseases by remodeling gut microbiota and activating intestinal FXR/FGF-15 axis-mediated inhibition of hepatic BA synthesis and promotion of BA excretion in mice.

Development of an ic-ELISA and immunochromatographic assay strip for the rapid detection of chloridazon in oranges and celery.

Chloridazon (CLZ) is a selective herbicide used in the control of annual broadleaf weeds. The misuse or abuse of CLZ may result in the accumulation of CLZ in crops and water, which can pose a risk to human health. In this study, a hapten of CLZ with three carbon spacer arms was designed and a highly sensitive and specific antibody against CLZ was prepared with a half-maximal inhibitory concentration of 0.630 ng mL-1 and a linear range of 0.181-2.195 ng mL-1.Based on this antibody, we developed an immunochromatographic assay (ICA) strip for the detection of CLZ in oranges and celery. Under optimized conditions, the visual limit of detection was 2 ng mL-1 and 10 ng mL-1 in oranges and celery, respectively, and the cut-off value was 50 ng mL-1. In CLZ-spiked samples and the recovery test, the results of the ICA strip were consistent with those of indirect competitive enzyme-linked immunosorbent assay (ic-ELISA). Therefore, the ICA strip developed in our study represents an efficient and reliable method for the rapid screening of CLZ in oranges and celery.

A hairpin-contained i-motif guided DNA nanoantenna for sensitive and specific sensing of tumor extracellular pH gradients.

Antenna, as a converter, could receive and convert signals from the outside world flexibly. Inspired by the behavior of antennas receiving external signals, we developed a pH-stimulated and aptamer-anchored Y-shaped DNA nanoantenna (termed pH-Apt-YNA) for sensitive and specific sensing of tumor extracellular pH gradients. The nanoantenna consisted of three functional nucleic acid sequences, an I-strand, Apt-Y-R and Y-L-G, where the I-strand endowed the DNA nanoantenna with the ability to receive and convert signals, the Apt-Y-R containing an aptamer fragment gave the DNA nanoantenna the ability to specifically anchor target tumor cells, and the complementarity of Y-L-G with the other two sequences ensured the stability of the DNA nanoantenna. Initially, the DNA nanoantenna was in a "silent" state, and rhodamine green was close to BHQ2, leading to suppressed signal emission. When the DNA nanoantenna anchored on the surface of target cancer cells through the aptamer recognition domain, the I-strand tended to fold into a hairpin-contained i-motif tetramer structure owing to the extracellular low pH stimuli, resulting in the DNA nanoantenna changing into an "active" state. In the meantime, rhodamine green moved far away from BHQ2, resulting in a strong signal output. The results demonstrate that the pH-Apt-YNA presents a sensitive pH sensing capacity within a narrow pH range of 6.2-7.4 and exhibits excellent specificity for the imaging of target cancer cell extracellular pH. Based on these advantages, we therefore anticipate that our facile design of the DNA nanoantenna with sensitive responsiveness provides a new way and great promise in the application of sensing pH-related physiological and pathological processes.

Density-based detection of cell transition states to construct disparate and bifurcating trajectories.

Tree- and linear-shaped cell differentiation trajectories have been widely observed in developmental biologies and can be also inferred through computational methods from single-cell RNA-sequencing datasets. However, trajectories with complicated topologies such as loops, disparate lineages and bifurcating hierarchy remain difficult to infer accurately. Here, we introduce a density-based trajectory inference method capable of constructing diverse shapes of topological patterns including the most intriguing bifurcations. The novelty of our method is a step to exploit overlapping probability distributions to identify transition states of cells for determining connectability between cell clusters, and another step to infer a stable trajectory through a base-topology guided iterative fitting. Our method precisely re-constructed various benchmark reference trajectories. As a case study to demonstrate practical usefulness, our method was tested on single-cell RNA sequencing profiles of blood cells of SARS-CoV-2-infected patients. We not only re-discovered the linear trajectory bridging the transition from IgM plasmablast cells to developing neutrophils, and also found a previously-undiscovered lineage which can be rigorously supported by differentially expressed gene analysis.

Integrated histological, physiological, and transcriptome analysis reveals the post-exposure recovery mechanism of nitrite in Litopenaeus vannamei.

Nitrite is one of the most common toxic pollutants in intensive aquaculture and is harmful to aquatic animals. Recovery mechanisms post exposure to nitrite in shrimp have rarely been investigated. This study focuses on the effect of nitrite exposure and post-exposure recovery on the histological and physiological aspects of Litopenaeus vannamei and utilizes transcriptome sequencing to analyze the molecular mechanisms of adaptation to nitrite exposure. The results showed that histopathological damage to the hepatopancreas and gills caused by short-term nitrite exposure resolved with recovery. The total antioxidant capacity (T-AOC), superoxide dismutase (SOD), and catalase (CAT) of shrimp were significantly reduced during nitrite exposure and returned to the control level after recovery, malondialdehyde (MDA) levels were opposite to them. Restoration of the antioxidant system after exposure mitigated oxidative damage. Nitrite exposure results in reduced activity of the immuno-enzymes acid phosphatase (ACP) and alkaline phosphatase (AKP), which can be recovered to the control level. L. vannamei can adapt to nitrite exposure by regulating Na+/K+-ATPase (NKA) activity. Transcriptome analysis revealed that activation of glutathione metabolism and peroxisomal pathways facilitated the mitigation of oxidative damage in L. vannamei during the recovery period. Excessive oxidative damage activates the apoptosis and p53 pathways. Additionally, Sestrin2 and STEAP4 may have a positive effect on recovery in shrimp. These results provide evidence for the damage caused by nitrite exposure and the recovery ability of L. vannamei. This study can complement the knowledge of the mechanisms of adaptation and recovery of shrimp under nitrite exposure.

All-in-One Polymer Gel Electrolyte towards High-Efficiency and Stable Fiber Zinc-Air Battery.

Fiber zinc-air batteries are explored as promising power systems for wearable and portable electronic devices due to their intrinsic safety and the use of ambient oxygen as cathode material. However, challenges such as limited zinc anode reversibility and sluggish cathode reaction kinetics result in poor cycling stability and low energy efficiency. To address these challenges, we design a polydopamine-based all-in-one gel electrolyte (PAGE) that simultaneously regulates the reversibility of zinc anodes and the kinetics of air cathodes through polydopamine interfacial and redox chemistry, respectively. The intrinsic catechol and carboxylate groups in PAGE regulate the transport and solvation structure of Zn2+, facilitating dendrite-free zinc deposition with a lamellar stacking morphology. Additionally, the oxidation of redox-active catechol groups in PAGE replaces the sluggish oxygen evolution reaction on the air cathode and reduces the energy barrier for charging, enabling fiber zinc-air batteries to achieve a significantly improved energy efficiency of 95% and a longer lifespan of 40 hours. Further integration into self-powered electronic textiles underscores its potential for next-generation wearable systems.

Multigene editing: current approaches and beyond.

CRISPR/Cas9 multigene editing is an active and widely studied topic in the fields of biomedicine and biology. It involves a simultaneous participation of multiple single-guide RNAs (sgRNAs) to edit multiple target genes in a way that each gene is edited by one of these sgRNAs. There are possibly numerous sgRNA candidates capable of on-target editing on each of these genes with various efficiencies. Meanwhile, each of these sgRNA candidates may cause unwanted off-target editing at many other genes. Therefore, selection optimization of these multiple sgRNAs is demanded so as to minimize the number of sgRNAs and thus reduce the collective negative effects caused by the off-target editing. This survey reviews wet-laboratory approaches to the implementation of multigene editing and their needs of computational tools for better design. We found that though off-target editing is unavoidable during the gene editing, those disfavored cuttings by some target genes' sgRNAs can potentially become on-target editing sites for some other genes of interests. This off-to-on role conversion is beneficial to optimize the sgRNA selection in multigene editing. We present a preference cutting score to assess those beneficial off-target cutting sites, which have a few mismatches with their host genes' on-target editing sites. These potential sgRNAs can be prioritized for recommendation via ranking their on-target average cutting efficiency, the total off-target site number and their average preference cutting score. We also present case studies on cancer-associated genes to demonstrate tremendous usefulness of the new method.

Single-cell multi-omics sequencing: application trends, COVID-19, data analysis issues and prospects.

Single-cell sequencing is a biotechnology to sequence one layer of genomic information for individual cells in a tissue sample. For example, single-cell DNA sequencing is to sequence the DNA from every single cell. Increasing in complexity, single-cell multi-omics sequencing, or single-cell multimodal omics sequencing, is to profile in parallel multiple layers of omics information from a single cell. In practice, single-cell multi-omics sequencing actually detects multiple traits such as DNA, RNA, methylation information and/or protein profiles from the same cell for many individuals in a tissue sample. Multi-omics sequencing has been widely applied to systematically unravel interplay mechanisms of key components and pathways in cell. This survey overviews recent developments in single-cell multi-omics sequencing, and their applications to understand complex diseases in particular the COVID-19 pandemic. We also summarize machine learning and bioinformatics techniques used in the analysis of the intercorrelated multilayer heterogeneous data. We observed that variational inference and graph-based learning are popular approaches, and Seurat V3 is a commonly used tool to transfer the missing variables and labels. We also discussed two intensively studied issues relating to data consistency and diversity and commented on currently cared issues surrounding the error correction of data pairs and data imputation methods. The survey is concluded with some open questions and opportunities for this extraordinary field.

Sequencing dropout-and-batch effect normalization for single-cell mRNA profiles: a survey and comparative analysis.

Single-cell mRNA sequencing has been adopted as a powerful technique for understanding gene expression profiles at the single-cell level. However, challenges remain due to factors such as the inefficiency of mRNA molecular capture, technical noises and separate sequencing of cells in different batches. Normalization methods have been developed to ensure a relatively accurate analysis. This work presents a survey on 10 tools specifically designed for single-cell mRNA sequencing data preprocessing steps, among which 6 tools are used for dropout normalization and 4 tools are for batch effect correction. In this survey, we outline the main methodology for each of these tools, and we also compare these tools to evaluate their normalization performance on datasets which are simulated under the constraints of dropout inefficiency, batch effect or their combined effects. We found that Saver and Baynorm performed better than other methods in dropout normalization, in most cases. Beer and Batchelor performed better in the batch effect normalization, and the Saver-Beer tool combination and the Baynorm-Beer combination performed better in the mixed dropout-and-batch effect normalization. Over-normalization is a common issue occurred to these dropout normalization tools that is worth of future investigation. For the batch normalization tools, the capability of retaining heterogeneity between different groups of cells after normalization can be another direction for future improvement.