A comprehensive workflow for optimizing RNA-seq data analysis.

BACKGROUND: Current RNA-seq analysis software for RNA-seq data tends to use similar parameters across different species without considering species-specific differences. However, the suitability and accuracy of these tools may vary when analyzing data from different species, such as humans, animals, plants, fungi, and bacteria. For most laboratory researchers lacking a background in information science, determining how to construct an analysis workflow that meets their specific needs from the array of complex analytical tools available poses a significant challenge. RESULTS: By utilizing RNA-seq data from plants, animals, and fungi, it was observed that different analytical tools demonstrate some variations in performance when applied to different species. A comprehensive experiment was conducted specifically for analyzing plant pathogenic fungal data, focusing on differential gene analysis as the ultimate goal. In this study, 288 pipelines using different tools were applied to analyze five fungal RNA-seq datasets, and the performance of their results was evaluated based on simulation. This led to the establishment of a relatively universal and superior fungal RNA-seq analysis pipeline that can serve as a reference, and certain standards for selecting analysis tools were derived for reference. Additionally, we compared various tools for alternative splicing analysis. The results based on simulated data indicated that rMATS remained the optimal choice, although consideration could be given to supplementing with tools such as SpliceWiz. CONCLUSION: The experimental results demonstrate that, in comparison to the default software parameter configurations, the analysis combination results after tuning can provide more accurate biological insights. It is beneficial to carefully select suitable analysis software based on the data, rather than indiscriminately choosing tools, in order to achieve high-quality analysis results more efficiently.

Trimerized S expressed by modified vaccinia virus Ankara (MVA) confers superior protection against lethal SARS-CoV-2 challenge in mice.

The reoccurrence of successive waves of SARS-CoV-2 variants suggests the exploration of more vaccine alternatives is imperative. Modified vaccinia virus Ankara (MVA) is a virus vector exhibiting excellent safety as well as efficacy for vaccine development. Here, a series of recombinant MVAs (rMVAs) expressing monomerized or trimerized S proteins from different SARS-CoV-2 variants are engineered. Trimerized S expressed from rMVAs is found predominantly as trimers on the surface of infected cells. Remarkably, immunization of mice with rMVAs demonstrates that S expressed in trimer elicits higher levels of binding IgG and IgA, as well as neutralizing antibodies for matched and mismatched S proteins than S in the monomer. In addition, trimerized S expressed by rMVA induces enhanced cytotoxic T-cell responses than S in the monomer. Importantly, the rMVA vaccines expressing trimerized S exhibit superior protection against a lethal SARS-CoV-2 challenge as the immunized animals all survive without displaying any pathological conditions. This study suggests that opting for trimerized S may represent a more effective approach and highlights that the MVA platform serves as an ideal foundation to continuously advance SARS-CoV-2 vaccine development. IMPORTANCE: MVA is a promising vaccine vector and has been approved as a vaccine for smallpox and mpox. Our analyses suggested that recombinant MVA expressing S in trimer (rMVA-ST) elicited robust cellular and humoral immunity and was more effective than MVA-S-monomer. Importantly, the rMVA-ST vaccine was able to stimulate decent cross-reactive neutralization against pseudoviruses packaged using S from different sublineages, including Wuhan, Delta, and Omicron. Remarkably, mice immunized with rMVA-ST were completely protected from a lethal challenge of SARS-CoV-2 without displaying any pathological conditions. Our results demonstrated that an MVA vectored vaccine expressing trimerized S is a promising vaccine candidate for SARS-CoV-2 and the strategy might be adapted for future vaccine development for coronaviruses.

Genomic analysis of lumpy skin disease virus asian variants and evaluation of its cellular tropism.

Lumpy skin disease virus (LSDV) is a poxvirus that mainly affects cattle and can lead to symptoms such as severe reduction in milk production as well as infertility and mortality, which has resulted in dramatic economic loss in affected countries in Africa, Europe, and Asia. In this study, we successfully isolated two strains of LSDV from different geographical regions in China. Comparative genomic analyses were performed by incorporating additional LSDV whole genome sequences reported in other areas of Asia. Our analyses revealed that LSDV exhibited an 'open' pan-genome. Phylogenetic analysis unveiled distinct branches of LSDV evolution, signifying the prevalence of multiple lineages of LSDV across various regions in Asia. In addition, a reporter LSDV expressing eGFP directed by a synthetic poxvirus promoter was generated and used to evaluate the cell tropism of LSDV in various mammalian and avian cell lines. Our results demonstrated that LSDV replicated efficiently in several mammalian cell lines, including human A549 cells. In conclusion, our results underscore the necessity for strengthening LSD outbreak control measures and continuous epidemiological surveillance.

Mussel-inspired near-infrared light-responsive gelatin-based hydrogels for enhancing MRSA-infected wound healing.

Infected wound management is a great challenge to healthcare, especially in emergencies such as accidents or battlefields. Hydrogels as wound dressings can replace or supplement traditional wound treatment strategies, such as bandages or sutures. It is significant to develop novel hydrogel-based wound dressings with simple operation, inexpensive, easy debridement, effective antibacterial, biocompatibility, etc. Here, we designed a novel gelatin-based hydrogel wound dressing Gel-TA-Fe3+. The hydrogels used tannic-modified gelatin as the main body and Fe3+ as the crosslinking agent to achieve a controllable rapid sol-gel transition. The hydrogels exhibited tough mechanical properties, excellent antibacterial ability, biocompatibility and an acceptable temperature response to near-infrared light (NIR). Moreover, the hydrogels could promote the healing process of MRSA-infected skin wound in rats. This multifunctional hydrogel was thought to have potential for emergency treatment of bacterial infected wound.

The role of ferroptosis in virus infections.

Regulated cell death (RCD) is a strategy employed by host cells to defend invasions of pathogens, such as viruses and bacteria. Ferroptosis is a type of RCD characterized by excessive accumulation of iron and lipid peroxidation. While ferroptosis is primarily considered as a mechanism associated with tumorigenesis, emerging evidence begin to suggest that it may play essential role during virus infections. Recent studies illustrated that activation of ferroptosis could either induce or prohibit various types of RCDs to facilitate virus replication or evade host surveillance. More experimental evidence has demonstrated how viruses regulate ferroptosis to influence replication, transmission, and pathogenesis. This review summarizes ferroptosis-related metabolism, including iron metabolism, lipid peroxidation, and antioxidant metabolism. Furthermore, we discuss the interplay between viral infections and host ferroptosis process, with a focus on the mechanism of how viruses exploit ferroptosis for its own replication. Understanding how ferroptosis impacts virus infection can offer valuable insights into the development of effective therapeutic strategies to combat virus infections.

Identification of WUSCHEL-related homeobox gene and truncated small peptides in transformation efficiency improvement in Eucalyptus.

BACKGROUND: The WUSCHEL-related Homeobox (WOX) genes, which encode plant-specific homeobox (HB) transcription factors, play crucial roles in regulating plant growth and development. However, the functions of WOX genes are little known in Eucalyptus, one of the fastest-growing tree resources with considerable widespread cultivation worldwide. RESULTS: A total of nine WOX genes named EgWOX1-EgWOX9 were retrieved and designated from Eucalyptus grandis. From the three divided clades marked as Modern/WUS, Intermediate and Ancient, the largest group Modern/WUS (6 EgWOXs) contains a specific domain with 8 amino acids: TLQLFPLR. The collinearity, cis-regulatory elements, protein-protein interaction network and gene expression analysis reveal that the WUS proteins in E. grandis involve in regulating meristems development and regeneration. Furthermore, by externally adding of truncated peptides isolated from WUS specific domain, the transformation efficiency in E. urophylla × E. grandis DH32-29 was significant enhanced. The transcriptomics data further reveals that the use of small peptides activates metabolism pathways such as starch and sucrose metabolism, phenylpropanoid biosynthesis and flavonoid biosynthesis. CONCLUSIONS: Peptides isolated from WUS protein can be utilized to enhance the transformation efficiency in Eucalyptus, thereby contributing to the high-efficiency breeding of Eucalyptus.

Human FAM111A inhibits vaccinia virus replication by degrading viral protein I3 and is antagonized by poxvirus host range factor SPI-1.

Zoonotic poxviruses such as mpox virus (MPXV) continue to threaten public health safety since the eradication of smallpox. Vaccinia virus (VACV), the prototypic poxvirus used as the vaccine strain for smallpox eradication, is the best-characterized member of the poxvirus family. VACV encodes a serine protease inhibitor 1 (SPI-1) conserved in all orthopoxviruses, which has been recognized as a host range factor for modified VACV Ankara (MVA), an approved smallpox vaccine and a promising vaccine vector. FAM111A (family with sequence similarity 111 member A), a nuclear protein that regulates host DNA replication, was shown to restrict the replication of a VACV SPI-1 deletion mutant (VACV-ΔSPI-1) in human cells. Nevertheless, the detailed antiviral mechanisms of FAM111A were unresolved. Here, we show that FAM111A is a potent restriction factor for VACV-ΔSPI-1 and MVA. Deletion of FAM111A rescued the replication of MVA and VACV-ΔSPI-1 and overexpression of FAM111A significantly reduced viral DNA replication and virus titers but did not affect viral early gene expression. The antiviral effect of FAM111A necessitated its trypsin-like protease domain and DNA-binding domain but not the PCNA-interacting motif. We further identified that FAM111A translocated into the cytoplasm upon VACV infection by degrading the nuclear pore complex via its protease activity, interacted with VACV DNA-binding protein I3, and promoted I3 degradation through autophagy. Moreover, SPI-1 from VACV, MPXV, or lumpy skin disease virus was able to antagonize FAM111A by prohibiting its nuclear export. Our findings reveal the detailed mechanism by which FAM111A inhibits VACV and provide explanations for the immune evasive function of VACV SPI-1.

A neutralizing-protective supersite of human monoclonal antibodies for yellow fever virus.

The yellow fever virus (YFV) is a life-threatening human pathogen. Owing to the lack of available therapeutics, non-vaccinated individuals are at risk. Here, we isolated eight human monoclonal antibodies that neutralize YFV infection. Five recognized overlapping epitopes and exhibited potent neutralizing activity. Two (YD6 and YD73) were ultra-potent and conferred complete protection against the lethal challenge of YFV as both prophylactics and therapeutics in a mouse model. Crystal structures revealed that YD6 engaged the YFV envelope protein in both pre- and post-fusion states, suggesting viral inhibition by a "double-lock" mechanism. The recognition determinants for YD6 and YD73 are clustered at the premembrane (prM)-binding site. Notably, antibodies targeting this site were present in minute traces in YFV-infected individuals but contributed significantly to neutralization, suggesting a vulnerable supersite of YFV. We provide two promising candidates for immunotherapy against YFV, and the supersite represents an ideal target for epitope-based vaccine design.

SRSF5-Mediated Alternative Splicing of M Gene is Essential for Influenza A Virus Replication: A Host-Directed Target Against Influenza Virus.

Splicing of influenza A virus (IAV) RNA is an essential process in the viral life cycle that involves the co-opting of host factors. Here, it is demonstrated that induction of host serine and arginine-rich splicing factor 5 (SRSF5) by IAV facilitated viral replication by enhancing viral M mRNA splicing. Mechanistically, SRSF5 with its RRM2 domain directly bounds M mRNA at conserved sites (M mRNA position 163, 709, and 712), and interacts with U1 small nuclear ribonucleoprotein (snRNP) to promote M mRNA splicing and M2 production. Mutations introduced to the three binding sites, without changing amino acid code, significantly attenuates virus replication and pathogenesis in vivo. Likewise, SRSF5 conditional knockout in the lung protects mice against lethal IAV challenge. Furthermore, anidulafungin, an approved antifungal drug, is identified as an inhibitor of SRSF5 that effectively blocks IAV replication in vitro and in vivo. In conclusion, SRSF5 as an activator of M mRNA splicing promotes IAV replication and is a host-derived antiviral target.

Recent progress in the mechanisms, preparations and applications of polymeric antifogging coatings.

Fog on a solid surface is prejudicial to its optical properties and will even cause hygienic and safety concerns in some exceptional cases. Thus, antifogging coatings have attracted great interest in fundamental research and industry applications. Superhydrophilic and superhydrophobic coatings have been mainly explored and described in the antifogging field. In recent years, hygroscopic antifogging coatings of hydrophilic and hydrophobic parties have been introduced due to their unique properties. In this review, three antifogging mechanisms are reviewed to provide design strategies for antifogging surfaces. The current techniques for fabricating polymeric antifogging coatings are discussed in depth. The recent progress in materials and structures for antifogging surfaces is briefly summarize. Finally, the practical applications and outlooks related to multifunctional antifogging coatings are mentioned.

Transdermal Insulin Delivery and Microneedles-based Minimally Invasive Delivery Systems.

Diabetes has become a serious threat to human health, causing death and pain to numerous patients. Transdermal insulin delivery is a substitute for traditional insulin injection to avoid pain from the injection. Transdermal methods include non-invasive and invasive methods. As the non-invasive methods could hardly get through the stratum corneum, minimally invasive devices, especially microneedles, could enhance the transappendageal route in transcutaneous insulin delivery, and could act as connectors between the tissue and outer environment or devices. Microneedle patches have been in quick development in recent years and with different types, materials and functions. In those patches, the smart microneedle patch could perform as a sensor and reactor responding to glucose to regulate the blood level. In the smart microneedles field, the phenylboronic acid system and the glucose oxidase system have been successfully applied on the microneedle platform. Insulin transdermal delivery strategy, microneedles technology and smart microneedles' development would be discussed in this review.

Ferrocene-modified Uio-66-NH2 hybrids with g-C3N4 as enhanced photocatalysts for degradation of bisphenol A under visible light.

Designing graphitic carbon nitride (CN) based heterostructured photocatalysts with high catalytic activity is highly desired for peroxymonosulfate (PMS) activation to degrade organic pollutants from water. Herein, a novel heterostructured composite (U-F@CN) consisting of ferrocene-modified Uio-66-NH2 (U-F) and CN was synthesized. The U-F@CN exhibited superior photocatalytic performance to degrade bisphenol A (BPA) in the presence of PMS under visible light. The experimental results indicated that BPA could be removed entirely by U-F@CN within 60 min under visible light irradiation. In addition, the outstanding photocatalytic activity could be maintained at high level in a wide pH range, appropriate temperature region and natural water condition. Benefiting from the good chemical stability, outstanding optical property and in-situ generation of interfacial heterojunction of U-F@CN, the interfacial transport of photogenerated charges could follow the Z-scheme mechanism, which can accelerate the charge separation and transport to yield abundant reactive active species (ROS) to efficiently active PMS and under visible light. This work provides a novel approach to design CN-based heterostructured photocatalysts with high stability and superior photocatalytic activity for environmental remediation.

State of the Art and Prospects in Metal-Organic Framework-Derived Microwave Absorption Materials.

Microwave has been widely used in many fields, including communication, medical treatment and military industry; however, the corresponding generated radiations have been novel hazardous sources of pollution threating human's daily life. Therefore, designing high-performance microwave absorption materials (MAMs) has become an indispensable requirement. Recently, metal-organic frameworks (MOFs) have been considered as one of the most ideal precursor candidates of MAMs because of their tunable structure, high porosity and large specific surface area. Usually, MOF-derived MAMs exhibit excellent electrical conductivity, good magnetism and sufficient defects and interfaces, providing obvious merits in both impedance matching and microwave loss. In this review, the recent research progresses on MOF-derived MAMs were profoundly reviewed, including the categories of MOFs and MOF composites precursors, design principles, preparation methods and the relationship between mechanisms of microwave absorption and microstructures of MAMs. Finally, the current challenges and prospects for future opportunities of MOF-derived MAMs are also discussed.

First-Principles Study on the Half-Metallicity of New MXene Materials Nd2NT2 (T = OH, O, S, F, Cl, and Br).

This work systematically studied the structure, magnetic and electronic properties of the MXene materials Nd2N and Nd2NT2 (T = OH, O, S, F, Cl, and Br) via first-principles calculations based on density functional theory. Results showed that Nd2NT2 (T = OH, O, S, F, Cl, and Br) have half-metallic characteristics whose half-metallic band gap width is higher than 1.70 eV. Its working function ranges from 1.83 to 6.50 eV. The effects of strain on its magnetic and electronic structures were evaluated. Results showed that the structure of Nd2NT2 (T = OH, O, S, and Br) transitions from a ferromagnetic half-metallic semiconductor to a ferromagnetic metallic and ferromagnetic semiconductor under different strains. By contrast, the structures of Nd2NF2 and Nd2NS2 were observed to transition from a half-metallic semiconductor to a ferromagnetic metallic semiconductor under different strains. Calculations of the electronic properties of different proportions of the surface functional groups of Nd2NT x (T = OH, O, and F; x = 0.5, 1(I, II), and 1.5) revealed that Nd2NO1.5 has the characteristics of semiconductors, whereas Nd2NO(II) possesses the characteristics of half-metallic semiconductors. The other structures were observed to exhibit the characteristics of metallic semiconductors. Prediction of Nd2NT2 (T = OH, O, S, F, Cl, and Br) increases the types of lanthanide MXene materials. They are appropriate candidate materials for preparing spintronic devices.