Dynamic insights into research trends and trajectories in early reading: an analytical exploration via dynamic topic modeling.

Introduction: Early reading has gained significant attention in the academic community. With the increasing volume of literature on this subject, it has become crucial to assess the current research landscape and identify emerging trends. Methods: This study utilized the dynamic topic model to analyze a corpus of 1,638 articles obtained from the Web of Science Core Collection to furnish a lucid understanding of the prevailing research and forecast possible future directions. Results: Our in-depth assessment discerned 11 cardinal topics, among which notable ones were interventions' impacts on early reading competencies; foundational elements of early reading: phonological awareness, letters, and, spelling; and early literacy proficiencies in children with autism spectrum disorder. Although most topics have received consistent research attention, there has been a marked increase in some topics' popularity, such as foundational elements of early reading and early literary proficiencies in children with autism spectrum disorder. Conversely, other topics exhibited a downturn. Discussion: This analytical endeavor has yielded indispensable insights for scholars, decision-makers, and field practitioners, steering them toward pivotal research interrogatives, focal interest zones, and prospective research avenues. As per our extensive survey, this paper is a pioneering holistic purview of the seminal areas of early reading that highlights expected scholarly directions.

[Eukaryotic expression of GP5 and M protein of porcine reproductive and respiratory syndrome virus and immunogenicity evaluation].

In order to understand the prevalence and evolution of porcine reproductive and respiratory syndrome virus (PRRSV) in China and to develop subunit vaccine against the epidemic lineage, the genetic evolution analysis of PRRSV strains isolated in China from 2001 to 2021 was performed. The representative strains of the dominant epidemic lineage were selected to optimize the membrane protein GP5 and M nucleotide sequences, which were used, with the interferon and the Fc region of immunoglobulin, to construct the eukaryotic expression plasmids pCDNA3.4-IFNα-GP5-Fc and pCDNA3.4-IFNα-M-Fc. Subsequently, the recombinant proteins IFNα-GP5-Fc and IFNα-M-Fc were expressed by HEK293T eukaryotic expression system. The two recombinant proteins were mixed with ISA206VG adjuvant to immunize weaned piglets. The humoral immunity level was evaluated by ELISA and neutralization test, and the cellular immunity level was detected by ELISPOT test. The results showed that the NADC30-like lineage was the main epidemic lineage in China in recent years, and the combination of IFNα-GP5-Fc and IFNα-M-Fc could induce high levels of antibody and cellular immunity in piglets. This study may facilitate the preparation of a safer and more effective new PRRSV subunit vaccine.

Complete mitogenome assembly of Selenicereus monacanthus revealed its molecular features, genome evolution, and phylogenetic implications.

BACKGROUND: Mitochondria are the powerhouse of the cell and are critical for plant growth and development. Pitaya (Selenicereus or Hylocereus) is the most important economic crop in the family Cactaceae and is grown worldwide, however its mitogenome is unreported. RESULTS: This study assembled the complete mitogenome of the red skin and flesh of pitaya (Selenicereus monacanthus). It is a full-length, 2,290,019 bp circular molecule encoding 59 unique genes that only occupy 2.17% of the entire length. In addition, 4,459 pairs of dispersed repeats (≥ 50 bp) were identified, accounting for 84.78% of the total length, and three repeats (394,588, 124,827, and 13,437 bp) mediating genomic recombination were identified by long read mapping and Sanger sequencing. RNA editing events were identified in all 32 protein-coding genes (PCGs), among which four sites (nad1-2, nad4L-2, atp9-copy3-223, and ccmFC-1309) were associated with the initiation or termination of PCGs. Seventy-eight homologous fragments of the chloroplast genome were identified in the mitogenome, the longest having 4,523 bp. In addition, evolutionary analyses suggest that S. monacanthus may have undergone multiple genomic reorganization events during evolution, with the loss of at least nine PCGs (rpl2, rpl10, rps2, rps3, rps10, rps11, rps14, rps19, and sdh3). CONCLUSIONS: This study revealed the genetic basis of the S. monacanthus mitogenome, and provided a scientific basis for further research on phenotypic traits and germplasm resource development.

Identification and evolution analysis of YUCCA genes of Medicago sativa and Medicago truncatula and their expression profiles under abiotic stress.

The YUCCAs (YUC) are functionally identified flavin-containing monooxidases (FMOs) in plants that act as an important rate-limiting enzyme functioning in the auxin synthesis IPA (indole-3-pyruvic acid) pathway. In this study, 12 MsYUCs and 15 MtYUCs containing characteristic conserved motifs were identified in M. sativa (Medicago sativa L.) and M. truncatula (Medicago truncatula Gaertn.), respectively. Phylogenetic analysis revealed that YUC proteins underwent an evolutionary divergence. Both tandem and segmental duplication events were presented in MsYUC and MtYUC genes. Comparative syntenic maps of M. sativa with M. truncatula, Arabidopsis (Arabidopsis thaliana), or rice (Oryza sativa L.) were constructed to illustrate the evolution relationship of the YUC gene family. A large number of cis-acting elements related to stress response and hormone regulation were revealed in the promoter sequences of MsYUCs. Expression analysis showed that MsYUCs had a tissue-specific, genotype-differential expression and a differential abiotic stress response pattern based on transcriptome data analysis of M. sativa online. In addition, RT-qPCR confirmed that salt stress significantly induced the expression of MsYUC1/MsYUC10 but significantly inhibited MsYUC2/MsYUC3 expression and the expression of MsYUC10/MsYUC11/MsYUC12 was significantly induced by cold treatment. These results could provide valuable information for functional analysis of YUC genes via gene engineering of the auxin synthetic IPA pathway in Medicago.

Co-evolution at protein-protein interfaces guides inference of stoichiometry of oligomeric protein complexes by de novo structure prediction.

The quaternary structure with specific stoichiometry is pivotal to the specific function of protein complexes. However, determining the structure of many protein complexes experimentally remains a major bottleneck. Structural bioinformatics approaches, such as the deep learning algorithm Alphafold2-multimer (AF2-multimer), leverage the co-evolution of amino acids and sequence-structure relationships for accurate de novo structure and contact prediction. Pseudo-likelihood maximization direct coupling analysis (plmDCA) has been used to detect co-evolving residue pairs by statistical modeling. Here, we provide evidence that combining both methods can be used for de novo prediction of the quaternary structure and stoichiometry of a protein complex. We achieve this by augmenting the existing AF2-multimer confidence metrics with an interpretable score to identify the complex with an optimal fraction of native contacts of co-evolving residue pairs at intermolecular interfaces. We use this strategy to predict the quaternary structure and non-trivial stoichiometries of Bacillus subtilis spore germination protein complexes with unknown structures. Co-evolution at intermolecular interfaces may therefore synergize with AI-based de novo quaternary structure prediction of structurally uncharacterized bacterial protein complexes.

Identification and functional characterization of eight novel tpp family genes from Bacillus thuringiensis.

BACKGROUND: Bacillus thuringiensis (Bt) and its transgenic crops are widely used as biological control agents for agricultural pests. The tpp family is a branch of Bt insecticidal genes and consists of a few members. Research on the Tpp family proteins has focused on the binary toxins Gpp34Ab/Tpp35Ab and Tpp1/Tpp2, which need to function together to achieve insecticidal activity. However, only a few tpp family genes have been reported to exert insecticidal activity independently. This study aimed to identify and characterize tpp family genes that independently perform insecticidal functions. RESULTS: A total of 162 nucleotide sequences homologous to the single component Bt insecticidal gene tpp78Aa were obtained from the genome data of 1368 wild-type Bt strains, and 25 new full-length tpp family genes were identified. Eight new tpp family genes were successfully cloned and expressed, and bioassays of the expressed products were performed against five different pests. Bioassay results showed that these proteins exerted high insecticidal activity only against Laodelphax striatellus, a globally important rice pest, and were named Tpp78Ab1, Tpp78Bb1, Tpp78Ca1, Tpp78Da1, Tpp80Aa3, Tpp80Ac1, Tpp80Ad1, and Tpp80Ae1. The LC50 values of Tpp78Ab1, Tpp78Bb1, Tpp78Ca1, and Tpp80Ae1 against L. striatum were 8.1, 8.6, 10.1, and 9.6 µg mL-1 , respectively. The phylogenetic tree and conserved motifs indicated that the Tpp family had a common evolutionary ancestor. During evolution, the C-terminal pore-forming domain of the Tpp family adopted a similar arrangement; however, the N-terminal conserved motif showed high variability. CONCLUSION: Twenty-five full-length tpp family genes were identified. Eight new tpp family genes were cloned successfully, which could independently achieve insecticidal activity against L. striatellus. This provides abundant genetic resources for the biological control of important rice pests. In this study, we found that the relative conservation of the Tpp family proteins in the lengthy evolutionary process and the diversity generated for adapting to the environment can lay a theoretical foundation for an in-depth analysis of the function and evolution of the Tpp family. © 2023 Society of Chemical Industry.

Exploring Oxidoreductases from Extremophiles for Biosynthesis in a Non-Aqueous System.

Organic solvent tolerant oxidoreductases are significant for both scientific research and biomanufacturing. However, it is really challenging to obtain oxidoreductases due to the shortages of natural resources and the difficulty to obtained it via protein modification. This review summarizes the recent advances in gene mining and structure-functional study of oxidoreductases from extremophiles for non-aqueous reaction systems. First, new strategies combining genome mining with bioinformatics provide new insights to the discovery and identification of novel extreme oxidoreductases. Second, analysis from the perspectives of amino acid interaction networks explain the organic solvent tolerant mechanism, which regulate the discrete structure-functional properties of extreme oxidoreductases. Third, further study by conservation and co-evolution analysis of extreme oxidoreductases provides new perspectives and strategies for designing robust enzymes for an organic media reaction system. Furthermore, the challenges and opportunities in designing biocatalysis non-aqueous systems are highlighted.

Identification and validation of new MADS-box homologous genes in 3010 rice pan-genome.

KEY MESSAGE: Identification and validation of ten new MADS-box homologous genes in 3010 rice pan-genome for rice breeding. The functional genome is significant for rice breeding. MADS-box genes encode transcription factors that are indispensable for rice growth and development. The reported 15,362 novel genes in the rice pan-genome (RPAN) of Asian cultivated rice accessions provided a useful gene reservoir for the identification of more MADS-box candidates to overcome the limitation for the usage of only 75 MADS-box genes identified in Nipponbare for rice breeding. Here, we report the identification and validation of ten MADS-box homologous genes in RPAN. Origin and identity analysis indicated that they are originated from different wild rice accessions and structure of motif analysis revealed high variations in their amino acid sequences. Phylogenetic results with 277 MADS-box genes in 41 species showed that all these ten MADS-box homologous genes belong to type I (SRF-like, M-type). Gene expression analysis confirmed the existence of these ten MADS-box genes in IRIS_313-10,394, all of them were expressed in flower tissues, and six of them were highly expressed during seed development. Altogether, we identified and validated experimentally, for the first time, ten novel MADS-box genes in RPAN, which provides new genetic sources for rice improvement.

Characterization and functional analysis of AhGPAT9 gene involved in lipid synthesis in peanut (Arachis hypogaea L.).

GPAT enzymes (glycerol-3-phosphate 1-O-acyltransferase, EC 2.3.1.15) catalyze the initial and rate-limiting step of plant glycerolipid biosynthesis for membrane homeostasis and lipid accumulation, yet little research has been done on peanuts. By reverse genetics and bioinformatics analyses, we have characterized an AhGPAT9 isozyme, of which the homologous product is isolated from cultivated peanut. QRT-PCR assay revealed a spatio-temporal expression pattern that the transcripts of AhGPAT9 accumulating in various peanut tissues are highly expressed during seed development, followed by leaves. Green fluorescent protein tagging of AhGPAT9 confirmed its subcellular accumulation in the endoplasmic reticulum. Compared with the wild type control, overexpressed AhGPAT9 delayed the bolting stage of transgenic Arabidopsis, reduced the number of siliques, and increased the seed weight as well as seed area, suggesting the possibility of participating in plant growth and development. Meanwhile, the mean seed oil content from five overexpression lines increased by about 18.73%. The two lines with the largest increases in seed oil content showed a decrease in palmitic acid (C16:0) and eicosenic acid (C20:1) by 17.35% and 8.33%, respectively, and an increase in linolenic acid (C18:3) and eicosatrienoic acid (C20:3) by 14.91% and 15.94%, respectively. In addition, overexpressed AhGPAT9 had no significant effect on leaf lipid content of transgenic plants. Taken together, these results suggest that AhGPAT9 is critical for the biosynthesis of storage lipids, which contributes to the goal of modifying peanut seeds for improved oil content and fatty acid composition.

HGTphyloDetect: facilitating the identification and phylogenetic analysis of horizontal gene transfer.

BACKGROUND: Horizontal gene transfer (HGT) is an important driver in genome evolution, gain-of-function, and metabolic adaptation to environmental niches. Genome-wide identification of putative HGT events has become increasingly practical, given the rapid growth of genomic data. However, existing HGT analysis toolboxes are not widely used, limited by their inability to perform phylogenetic reconstruction to explore potential donors, and the detection of HGT from both evolutionarily distant and closely related species. RESULTS: In this study, we have developed HGTphyloDetect, which is a versatile computational toolbox that combines high-throughput analysis with phylogenetic inference, to facilitate comprehensive investigation of HGT events. Two case studies with Saccharomyces cerevisiae and Candida versatilis demonstrate the ability of HGTphyloDetect to identify horizontally acquired genes with high accuracy. In addition, HGTphyloDetect enables phylogenetic analysis to illustrate a likely path of gene transmission among the evolutionarily distant or closely related species. CONCLUSIONS: The HGTphyloDetect computational toolbox is designed for ease of use and can accurately find HGT events with a very low false discovery rate in a high-throughput manner. The HGTphyloDetect toolbox and its related user tutorial are freely available at https://github.com/SysBioChalmers/HGTphyloDetect.

Complete mitochondrial genome of Rectorisluxiensis (Teleostei, Cyprinidae): characterisation and phylogenetic implications.

Mitochondrial genomes (mitogenomes) are widely used in scientific studies on phylogenetic relationships, molecular evolution and population genetics. Here, we sequenced and analysed the mitogenome of Rectorisluxiensis, a Yangtze River drainage endemic, but threatened cyprinid fish of Labeoninae. The complete mitogenome of R.luxiensis was 16,592 bp in length, encoding 13 protein coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a control region. The mitogenome showed a high A+T content (58.2%) and a positive AT-skew (0.10) and negative GC-skew (-0.25) base composition pattern. All the 13 PCGs were found to start with ATG codons, except for the COXI, in which GTG was the start codon. The ratio of non-synonymous and synonymous substitutions (Ka/Ks) of all the 13 PCGs were less than 1, indicating negative or purifying selection evolved in these genes. Comparatively speaking, the evolutionary rate of ATP8 was the fastest and ND4L was the slowest. All tRNAs could fold into a typical cloverleaf secondary structure, except tRNASer1 that lacked a dihydrouridine arm. Phylogenetic relationships, based on the PCGs dataset of 91 mitogenomes of Labeoninae, showed that R.luxiensis grouped with Rectorisposehensis and they formed a monophyletic Rectoris. However, many non-monophyletic genera were revealed in labeoninae fishes, such as Cirrhinus, Decorus, Garra, Labeo and Pseudocrossocheilus, which indicated that the validities of some traditional genera required a further check. This study reported the complete mitogenome of R.luxiensis for the first time, which provided valuable data for future molecular evolution and conservation related studies of Rectoris and other species in Labeoninae.

Spatiotemporal Evolution of Carbon Emissions According to Major Function-Oriented Zones: A Case Study of Guangdong Province, China.

Studying the spatiotemporal evolution of carbon emissions from the perspective of major function-oriented zones (MFOZs) is crucial for making a carbon reduction policy. However, most previous research has ignored the spatial characteristics and MFOZ influence. Using statistical and spatial analysis tools, we explored the spatiotemporal characteristics of carbon emissions in Guangdong Province from 2001 to 2021. The following results were obtained: (1) Carbon emissions fluctuated from 2020 to 2021 because of COVID-19. (2) Over the last 20 years, the proportion of carbon emissions from urbanization development zones (UDZs) has gradually decreased, whereas those of the main agricultural production zones (MAPZs) and key ecological function zones (KEFZs) have increased. (3) Carbon emissions efficiency differed significantly among the three MFOZs. (4) Carbon emissions from coastal UDZs were increasingly apparent; however, the directional characteristics of MAPZ and KEFZ emissions were not remarkable. (5) Carbon transfer existed among the three kinds of MFOZs, resulting in the economy and carbon emissions being considerably misaligned across Guangdong Province. These results indicated that the MFOZ is noteworthy in revealing how carbon emissions evolved. Furthermore, spatiotemporal characteristics, especially spatial characteristics, can help formulate carbon reduction policies for realizing carbon peak and neutrality goals in Guangdong Province.

Survey on sentiment analysis: evolution of research methods and topics.

Sentiment analysis, one of the research hotspots in the natural language processing field, has attracted the attention of researchers, and research papers on the field are increasingly published. Many literature reviews on sentiment analysis involving techniques, methods, and applications have been produced using different survey methodologies and tools, but there has not been a survey dedicated to the evolution of research methods and topics of sentiment analysis. There have also been few survey works leveraging keyword co-occurrence on sentiment analysis. Therefore, this study presents a survey of sentiment analysis focusing on the evolution of research methods and topics. It incorporates keyword co-occurrence analysis with a community detection algorithm. This survey not only compares and analyzes the connections between research methods and topics over the past two decades but also uncovers the hotspots and trends over time, thus providing guidance for researchers. Furthermore, this paper presents broad practical insights into the methods and topics of sentiment analysis, while also identifying technical directions, limitations, and future work.

Molecular characteristics of novel chaphamaparvovirus identified in chickens.

Chicken chaphamaparvovirus (CkChpV) is a novel parvovirus species that belongs to the Chaphamaparvovirus genus and is frequently detected in different vertebrates exhibiting diarrhea symptoms. In this study, screening tests were performed on samples from 478 chickens, including 357 with diarrhea and 121 healthy, collected from 25 farms in China to investigate CkChpV infection in China. CkChpV, avian nephritis virus, rotavirus, chicken parvovirus, Newcastle disease virus, infectious bronchitis virus, chicken proventricular necrosis virus, and chicken circovirus were all detected in the samples at a positivity rate of 32%, 9%, 6%, 2%, 2%, 1%, 0%, and 0%, respectively. Statistical analyses suggested a correlation between the infection by the virus and diarrhea (P < 0.05). The genome of 9 strains from the CkChpV-positive samples, whose length was 4,432 nucleotides, have been completely sequenced. The strains shared 97.2 to 98.7% genomic similarity, 98.1 to 99.1%, and 98.2 to 99.2% amino acid similarity, respectively, for NS1 and VP1 compared with CkChpV strain RS/BR/15/2S in GenBank. The genetic relationship between these strains and CkChpV was established through phylogenetic analysis. These findings indicated the infection existence of CkChpV in China, which enriches our understanding of the diversity of the chaphamaparvoviruses and its host spectrum.

Characterization and molecular evolution analysis of Periploca forrestii inferred from its complete chloroplast genome sequence.

Periploca forrestii, a medicinal plant of the family Apocynaceae, is known as an effective and widely used clinical prescription for the treatment of rheumatoid diseases. In this study, we de novo sequenced and assembled the completement chloroplast (cp) genome of P. forrestii based on combined Oxford Nanopore PromethION and Illumina data. The cp genome was 153 724 bp in length and had four subregions. Moreover, an 84 433 bp large single-copy and a 17 731 bp small single-copy were separated by 25 780 bp inverted repeats (IRs). The cp genome included 132 genes with 18 duplicates in the IRs. A total of 45 repeat structures and 183 simple sequence repeats were detected. Codon usage showed a bias toward A/T-ending codons. A comparative study of Apocynaceae revealed that an IR expansion occurred on P. forrestii. The Ka/Ks values of eight species of Apocynaceae suggested that positive selection was exerted on the psaI and ycf2 genes, which might reflect specific adaptions to the P. forrestii particular growth environment. Phylogenetic analysis indicated that Periplocoideae was a sister to Asclepiadoideae, forming a monophyletic group in the family Apocynaceae. This study provided an important P. forrestii genomic resource for future evolutionary studies and the phylogenetic reconstruction of the family Apocynaceae.

Complete mitochondrial genome of Syzygium samarangense reveals genomic recombination, gene transfer, and RNA editing events.

Wax apple (Syzygium samarangense) is a commercial fruit that belongs to one of the most species-rich tree genera in the world. We report here the first complete S. samarangense mitogenome obtained using a hybrid assembly strategy. The mitogenome was a 530,242 bp circular molecule encoding 61 unique genes accounting for 7.99% of the full-length genome. Additionally, 167 simple sequence repeats, 19 tandem repeats, and 529 pairs of interspersed repeats were identified. Long read mapping and Sanger sequencing revealed the involvement of two forward repeats (35,843 bp and 22,925 bp) in mediating recombination. Thirteen homologous fragments in the chloroplast genome were identified, accounting for 1.53% of the mitogenome, and the longest fragment was 2,432 bp. An evolutionary analysis showed that S. samarangense underwent multiple genomic reorganization events and lost at least four protein-coding genes (PCGs) (rps2, rps7, rps11, and rps19). A total of 591 RNA editing sites were predicted in 37 PCGs, of which nad1-2, nad4L-2, and rps10-2 led to the gain of new start codons, while atp6-1156, ccmFC-1315 and rps10-331 created new stop codons. This study reveals the genetic features of the S. samarangense mitogenome and provides a scientific basis for further studies of traits with an epistatic basis and for germplasm identification.

In vitro characterization and molecular epidemiology of Cryptococcus spp. isolates from non-HIV patients in Guangdong, China.

Background: The burden of cryptococcosis in mainland China is enormous. However, the in vitro characterization and molecular epidemiology in Guangdong, a key region with a high incidence of fungal infection in China, are not clear. Methods: From January 1, 2010, to March 31, 2019, clinical strains of Cryptococcus were collected from six medical centres in Guangdong. The clinical information and characteristics of the strains were analysed. Furthermore, molecular types were determined. Results: A total of 84 strains were collected, mostly from male and young or middle-aged adult patients. Pulmonary and cerebral infections (82.1%) were most common. All strains were Cryptococcus neoformans, grew well at 37°C and had capsules around their cells. One melanin- and urea- and one melanin+ and urea- variants were found. Although most strains exhibited a low minimum inhibitory concentration (MIC) value for voriconazole (mean: 0.04 µg/mL) and posaconazole (mean: 0.12 µg/mL), the results for these isolates showed a high degree of variation in the MIC values of fluconazole and 5-fluorocytosine, and resistance was observed for 4 out of 6 drugs. A significant proportion of these strains had MIC values near the ECV values, particularly in the case of amphotericin B. The proportion of strains near the clinical breakpoints was as follows: fluconazole: 3.66%; voriconazole: 3.66%; itraconazole: 6.10%; posaconazole: 13.41%; amphotericin B: 84.15%; 5-fluorocytosine: 2.44%. These strains were highly homogeneous and were dominated by the Grubii variant (95.2%), VNI (94.0%), α mating (100%), and ST5 (89.3%) genotypes. Other rare types, including ST4, 31, 278, 7, 57 and 106, were also found. Conclusion: Phenotypically variant and non-wild-type strains were found in Guangdong, and a significant proportion of these strains had MIC values near the ECV values towards the 6 antifungal drugs, and resistance was observed for 4 out of 6 drugs. The molecular type was highly homogeneous but compositionally diverse, with rare types found. Enhanced surveillance of the aetiology and evolution and continuous monitoring of antifungal susceptibility are needed to provide references for decision-making in the health sector and optimization of disease prevention and control.

Eukaryotic expression of GP5 and M protein of porcine reproductive and respiratory syndrome virus and immunogenicity evaluation / 生物工程学报

In order to understand the prevalence and evolution of porcine reproductive and respiratory syndrome virus (PRRSV) in China and to develop subunit vaccine against the epidemic lineage, the genetic evolution analysis of PRRSV strains isolated in China from 2001 to 2021 was performed. The representative strains of the dominant epidemic lineage were selected to optimize the membrane protein GP5 and M nucleotide sequences, which were used, with the interferon and the Fc region of immunoglobulin, to construct the eukaryotic expression plasmids pCDNA3.4-IFNα-GP5-Fc and pCDNA3.4-IFNα-M-Fc. Subsequently, the recombinant proteins IFNα-GP5-Fc and IFNα-M-Fc were expressed by HEK293T eukaryotic expression system. The two recombinant proteins were mixed with ISA206VG adjuvant to immunize weaned piglets. The humoral immunity level was evaluated by ELISA and neutralization test, and the cellular immunity level was detected by ELISPOT test. The results showed that the NADC30-like lineage was the main epidemic lineage in China in recent years, and the combination of IFNα-GP5-Fc and IFNα-M-Fc could induce high levels of antibody and cellular immunity in piglets. This study may facilitate the preparation of a safer and more effective new PRRSV subunit vaccine.

A genetically novel avian Hepatitis E virus in China.

Hepatitis E virus (HEV) infection has a global distribution with diverse hosts, including mammals and avians. In this study, an avian Hepatitis E virus (aHEV) strain with a high mortality rate of about 30%, designated as SDXT20, was obtained from the liver of 30-week-old Hubbard chickens with severe hepatosplenomegaly in 2020 in Eastern China and HEV was proved to be the only pathogen by next-generation sequencing. Its complete genome, which encodes three open reading frames (ORFs), is 6649 nt in length. ORF1-3 encodes three proteins with lengths of 1532 aa, 606 aa, and 82 aa, respectively, and ORF2 and ORF3 overlap with each other. BLAST-based similarity analysis of the complete viral genome demonstrated that SDXT20 had merely 80.5-92.2% similarity with avian Avihepevirus magniiecur strains and 50.4%-54.8% lower similarity with Paslahepevirus balayani, Rocahepevirus ratti, and Chirohepevirus eptesici species. Further genetic evolution analysis of the complete genome and ORF2 revealed that the isolate was genetically distinct from known aHEVs, and it belonged to a novel genetically distinct aHEV. This study provides data for further analysis of the multi-host and cross-host genetic evolution of HEVs.

Enzyme activity engineering based on sequence co-evolution analysis.

The utility of engineering enzyme activity is expanding with the development of biotechnology. Conventional methods have limited applicability as they require high-throughput screening or three-dimensional structures to direct target residues of activity control. An alternative method uses sequence evolution of natural selection. A repertoire of mutations was selected for fine-tuning enzyme activities to adapt to varying environments during the evolution. Here, we devised a strategy called sequence co-evolutionary analysis to control the efficiency of enzyme reactions (SCANEER), which scans the evolution of protein sequences and direct mutation strategy to improve enzyme activity. We hypothesized that amino acid pairs for various enzyme activity were encoded in the evolutionary history of protein sequences, whereas loss-of-function mutations were avoided since those are depleted during the evolution. SCANEER successfully predicted the enzyme activities of beta-lactamase and aminoglycoside 3'-phosphotransferase. SCANEER was further experimentally validated to control the activities of three different enzymes of great interest in chemical production: cis-aconitate decarboxylase, α-ketoglutaric semialdehyde dehydrogenase, and inositol oxygenase. Activity-enhancing mutations that improve substrate-binding affinity or turnover rate were found at sites distal from known active sites or ligand-binding pockets. We provide SCANEER to control desired enzyme activity through a user-friendly webserver.