Is systemic lupus erythematosus linked to Immunoglobulin G4 Autoantibodies?

Systemic lupus erythematosus (SLE) is a systemic autoimmune disorder characterized by a hyperactive immune system with multiple abnormalities in B-cell proliferation, antibody production, T-cell regulation, and immune complex (IC) formation. In humans, Immunoglobulin (Ig) G is found in four subclasses. IgG1-IgG4, which are distinguished by both structural and biological differences. Fab-arm Exchange (FAE), specific biases in the IgG4 response repertoire, and a decreased capacity to induce effector functions mediated by interactions in the fragment crystallizable (Fc) region are just a few of the distinctive characteristics of IgG4. The recent finding of the presence of double-stranded DNA (dsDNA) and antinuclear antibody (ANA)-IgG4 has raised attention to this IgG subclass and its possible role in SLE. IgG4 was previously believed to just have anti-inflammatory effects by inhibiting immune responses, but recent studies have shown that these antibodies can also play a role in the onset and development of some clinical disorders. To consider the clinical effects of IgG4 presence, it is necessary to discuss its characteristics, which could underlie the potential role it can play in SLE. Therefore, this study aimed to comprehensively review the role of IgG4 in SLE to elucidate the collective incidence of high IgG4 levels reported in some SLE patients.

Chromosome-level genome assembly of an oligophagous leaf beetle Ophraella communa (Coleoptera: Chrysomelidae).

The leaf beetle Ophraella communa LeSage (Coleoptera: Chrysomelidae) is an effective biological control agent of the common ragweed. Here, we assembled a chromosome-level genome of the O. communa by combining Illumina, Nanopore, and Hi-C sequencing technologies. The genome size of the final genome assembly is 733.1 Mb, encompassing 17 chromosomes, with an improved contig N50 of 7.05 Mb compared to the original version. Genome annotation reveals 25,873 protein-coding genes, with functional annotations available for 22,084 genes (85.35%). Non-coding sequence annotation identified 204 rRNAs, 626 tRNAs, and 1791 small RNAs. Repetitive elements occupy 414.41 Mb, constituting 57.76% of the genome. This high-quality genome is fundamental for advancing biological control strategies employing O. communa.

Chromosome-level genome assembly of the two-spotted spider mite Tetranychus urticae.

The two-spotted spider mite, Tetranychus urticae Koch (Acari: Tetranychidae), is a notorious pest in agriculture that has developed resistance to almost all chemical types used for its control. Here, we assembled a chromosome-level genome for the TSSM using Illumina, Nanopore, and Hi-C sequencing technologies. The assembled contigs had a total length of 103.94 Mb with an N50 of 3.46 Mb, with 87.7 Mb of 34 contigs anchored to three chromosomes. The chromosome-level genome assembly had a BUSCO completeness of 94.8%. We identified 15,604 protein-coding genes, with 11,435 genes that could be functionally annotated. The high-quality genome provides invaluable resources for the genetic and evolutionary study of TSSM.

Chromosome-level genome assembly of the western flower thrips Frankliniella occidentalis.

The western flower thrips Frankliniella occidentalis (Thysanoptera: Thripidae) is a global invasive species that causes increasing damage by direct feeding on crops and transmission of plant viruses. Here, we assemble a previously published scaffold-level genome into a chromosomal level using Hi-C sequencing technology. The assembled genome has a size of 302.58 Mb, with a contig N50 of 1533 bp, scaffold N50 of 19.071 Mb, and BUSCO completeness of 97.8%. All contigs are anchored on 15 chromosomes. A total of 16,312 protein-coding genes are annotated in the genome with a BUSCO completeness of 95.2%. The genome contains 492 non-coding RNA, and 0.41% of interspersed repeats. In conclusion, this high-quality genome provides a convenient and high-quality resource for understanding the ecology, genetics, and evolution of thrips.

Nuclear and mitochondrial genomes of the plum fruit moth Grapholita funebrana.

The plum fruit moth Grapholita funebrana (Tortricidae, Lepidoptera) is an important pest of many wild and cultivated stone fruits and other plants in the family Rosaceae. Here, we assembled its nuclear and mitochondrial genomes using Illumina, Nanopore, and Hi-C sequencing technologies. The nuclear genome size is 570.9 Mb, with a repeat rate of 51.28%, and a BUCSO completeness of 97.7%. The karyotype for males is 2n = 56. We identified 17,979 protein-coding genes, 5,643 tRNAs, and 94 rRNAs. We also determined the mitochondrial genome of this species and annotated 13 protein-coding genes, 22 tRNAs, and 2 rRNA. These genomes provide resources to understand the genetics, ecology, and genome evolution of the tortricid moths.

Optimizing Acute Coronary Syndrome Patient Treatment: Leveraging Gated Transformer Models for Precise Risk Prediction and Management.

BACKGROUND: Acute coronary syndrome (ACS) is a severe cardiovascular disease with globally rising incidence and mortality rates. Traditional risk assessment tools are widely used but are limited due to the complexity of the data. METHODS: This study introduces a gated Transformer model utilizing machine learning to analyze electronic health records (EHRs) for an enhanced prediction of major adverse cardiovascular events (MACEs) in ACS patients. The model's efficacy was evaluated using metrics such as area under the curve (AUC), precision-recall (PR), and F1-scores. Additionally, a patient management platform was developed to facilitate personalized treatment strategies. RESULTS: Incorporating a gating mechanism substantially improved the Transformer model's performance, especially in identifying true-positive cases. The TabTransformer+Gate model demonstrated an AUC of 0.836, a 14% increase in average precision (AP), and a 6.2% enhancement in accuracy, significantly outperforming other deep learning approaches. The patient management platform enabled healthcare professionals to effectively assess patient risks and tailor treatments, improving patient outcomes and quality of life. CONCLUSION: The integration of a gating mechanism within the Transformer model markedly increases the accuracy of MACE risk predictions in ACS patients, optimizes personalized treatment, and presents a novel approach for advancing clinical practice and research.

Mitochondrial genome rearrangements and phylogenomics of the Hymenoptera (Insecta) using an expanded taxon sample.

The order Hymenoptera is one of the most species-rich insect orders, with more than 150,000 described extant species. Many hymenopteran insects have very different mitochondrial genome (mitogenome) organizations compared to the putative ancestral organization of insects. In this study, we sequenced 18 mitogenomes of representatives in the order Hymenoptera to increase taxonomic sampling. A total of 475 species were used in phylogenetic analyses, including 18 new mitogenomes and 457 existing mitogenomes. Using a site-heterogeneous model, Bayesian's inference from amino acid data yielded more resolved relationships among Hymenoptera than maximum-likelihood analysis and coalescent-based species analyses. The monophyly of Symphyta was not supported. The Xyeloidea was the earliest branching clade in the Hymenoptera. The Orussoidea was closely related to Apocrita. Within Apocrita, the Parasitoida was non-monophyletic. The monophyly of most Parasitoida superfamilies received strong support. The Proctotrupomorpha clade was supported in Bayesian's analysis. The Apoidea was monophyletic when excluding Ampulex compressa from consideration. The superfamilies Vespoidea and Chrysidoidea were found to be non-monophyletic. Comparisons of mitochondrial gene order revealed a higher frequency of gene rearrangement among lineages with a parasitoid lifestyle, particularly prominent in Chalcidoidea. The degree of gene rearrangement ranked second in specific taxa of Cynipoidea and Ichneumonoidea.

Nuclear and mitochondrial genomes of Polylopha cassiicola: the first assembly in Chlidanotinae (Tortricidae).

Tortricidae is one of the largest families in Lepidoptera, including subfamilies of Tortricinae, Olethreutinae, and Chlidanotinae. Here, we assembled the gap-free genome for the subfamily Chlidanotinae using Illumina, Nanopore, and Hi-C sequencing from Polylopha cassiicola, a pest of camphor trees in southern China. The nuclear genome is 302.03 Mb in size, with 36.82% of repeats and 98.4% of BUCSO completeness. The karyotype is 2n = 44 for males. We identified 15412 protein-coding genes, 1052 tRNAs, and 67 rRNAs. We also determined the mitochondrial genome of this species and annotated 13 protein-coding genes, 22 tRNAs, and one rRNA. These high-quality genomes provide valuable information for studying phylogeny, karyotypic evolution, and adaptive evolution of tortricid moths.

Chromosome-level genome assembly of the predatory stink bug Arma custos.

The stink bug Arma custos (Hemiptera: Pentatomidae) is a predatory enemy successfully used for biocontrol of lepidopteran and coleopteran pests in notorious invasive species. In this study, a high-quality chromosome-scale genome assembly of A. custos was achieved through a combination of Illumina sequencing, PacBio HiFi sequencing, and Hi-C scaffolding techniques. The final assembled genome was 969.02 Mb in size, with 935.94 Mb anchored to seven chromosomes, and a scaffold N50 length of 135.75 Mb. This genome comprised 52.78% repetitive elements. The detected complete BUSCO score was 99.34%, indicating its completeness. A total of 13,708 protein-coding genes were predicted in the genome, and 13219 of them were annotated. This genome provides an invaluable resource for further research on various aspects of predatory bugs, such as biology, genetics, and functional genomics.

A chromosome-level genome for the flower thrips Frankliniella intonsa.

The flower thrips Frankliniella intonsa (Thysanoptera: Thripidae) is a common insect found in flowers of many plants. Sometimes, F. intonsa causes damage to crops through direct feeding and transmission of plant viruses. Here, we assembled a chromosomal level genome of F. intonsa using the Illumina, Oxford Nanopore (ONT), and Hi-C technologies. The assembled genome had a size of 209.09 Mb, with a contig N50 of 997 bp, scaffold N50 of 13.415 Mb, and BUSCO completeness of 92.5%. The assembled contigs were anchored on 15 chromosomes. A set of 14,109 protein-coding genes were annotated in the genome with a BUSCO completeness of 95.0%. The genome contained 491 non-coding RNA and 0.57% of interspersed repeats. This high-quality genome provides a valuable resource for understanding the ecology, genetics, and evolution of F. intonsa, as well as for controlling thrips pests.

Rapid and Repeated Climate Adaptation Involving Chromosome Inversions following Invasion of an Insect.

Following invasion, insects can become adapted to conditions experienced in their invasive range, but there are few studies on the speed of adaptation and its genomic basis. Here, we examine a small insect pest, Thrips palmi, following its contemporary range expansion across a sharp climate gradient from the subtropics to temperate areas. We first found a geographically associated population genetic structure and inferred a stepping-stone dispersal pattern in this pest from the open fields of southern China to greenhouse environments of northern regions, with limited gene flow after colonization. In common garden experiments, both the field and greenhouse groups exhibited clinal patterns in thermal tolerance as measured by critical thermal maximum (CTmax) closely linked with latitude and temperature variables. A selection experiment reinforced the evolutionary potential of CTmax with an estimated h2 of 6.8% for the trait. We identified 3 inversions in the genome that were closely associated with CTmax, accounting for 49.9%, 19.6%, and 8.6% of the variance in CTmax among populations. Other genomic variations in CTmax outside the inversion region were specific to certain populations but functionally conserved. These findings highlight rapid adaptation to CTmax in both open field and greenhouse populations and reiterate the importance of inversions behaving as large-effect alleles in climate adaptation.

The complete mitochondrial genome of Aphidius colemani (Hymenoptera: Braconidae: Aphidiinae).

The genome-level features are crucial genetic resources for species identification and phylogenetic analysis. Here, the complete mitochondrial genome of Aphidius colemani Viereck 1912 (Hymenoptera: Braconidae: Aphidiinae) was sequenced, determined and analyzed. The circular genome is 16,372 bp in length with an overall base composition of 38.9% for A, 46.2% for T, 6.7% for C, and 8.2% for G. The mitochondrial genome of A. colemani contained 13 protein-coding genes that initiated by the ATN codon, 22 transfer RNA genes, two ribosomal RNA genes (rRNAs), and a control region (CR). It shared the same gene arrangement patterns that occurred in two tRNA clusters of trnI-trnQ-trnM and trnW-trnC-trnY with Aphidius gifuensis. Phylogenetic analyses using Bayesian inference and Maximum-likelihood methods supported that the two species of Aphidiinae formed a clade and sister to other subfamilies of Braconidae.

Plasticity of cold and heat stress tolerance induced by hardening and acclimation in the melon thrips.

Extreme temperatures threaten species under climate change and can limit range expansions. Many species cope with changing environments through plastic changes. This study tested phenotypic changes in heat and cold tolerance under hardening and acclimation in the melon thrips, Thrips palmi Karny (Thysanoptera: Thripidae), an agricultural pest of many vegetables. We first measured the critical thermal maximum (CTmax) of the species by the knockdown time under static temperatures and found support for an injury accumulation model of heat stress. The inferred knockdown time at 39 °C was 82.22 min. Rapid heat hardening for 1 h at 35 °C slightly increased CTmax by 1.04 min but decreased it following exposure to 31 °C by 3.46 min and 39 °C by 6.78 min. Heat acclimation for 2 and 4 days significantly increased CTmax at 35 °C by 1.83, and 6.83 min, respectively. Rapid cold hardening at 0 °C and 4 °C for 2 h, and cold acclimation at 10 °C for 3 days also significantly increased cold tolerance by 6.09, 5.82, and 2.00 min, respectively, while cold hardening at 8 °C for 2 h and acclimation at 4 °C and 10 °C for 5 days did not change cold stress tolerance. Mortality at 4 °C for 3 and 5 days reached 24.07 % and 43.22 % respectively. Our study showed plasticity for heat and cold stress tolerance in T. palmi, but the thermal and temporal space for heat stress induction is narrower than for cold stress induction.

Chromosome-level genome assembly of the Japanese sawyer beetle Monochamus alternatus.

The Japanese sawyer beetle Monochamus alternatus (Coleoptera: Cerambycidae) is a pest in pine forests and acts as a vector for the pine wood nematode Bursaphelenchus xylophilus, which causes the pine wilt disease. We assembled a high-quality genome of M. alternatus at the chromosomal level using Illumina, Nanopore, and Hi-C sequencing technologies. The assembled genome is 767.12 Mb, with a scaffold N50 of 82.0 Mb. All contigs were assembled into ten pseudo-chromosomes. The genome contains 63.95% repeat sequences. We identify 16, 284 protein-coding genes in the genome, of which 11,244 were functionally annotated. The high-quality genome of M. alternatus provides an invaluable resource for the biological, ecological, and genetic study of this beetle and opens new avenues for understanding the transmission of pine wood nematode by insect vectors.

Stable composition of gut microbiome in the Asian ladybeetle Coccinella septempunctata reared on natural and artificial diets.

The Asian ladybeetle, Coccinella septempunctata, is an important insect of predatory natural enemy, which has a strong control effect and application prospects for aphids, whiteflies, mealybugs, and other small-sized pests of agriculture and forestry crops. Gut microbiota composition posed impacts on development of insects. In order to clarify the effect of artificial feed feeding on the intestinal microbial species and structure of C. septempunctata, we compared the intestinal microbial flora of C. septempunctata reared on bean aphids and artificial food for 15 days. Results show that Proteobacteria was the dominant component in all groups at phylum level, Rhodobacter, Methylovigula, Burkholderia, and Bradyrhizobium were the dominant bacteria among all groups at genus level. As to the differences in bacterial community structure and diversity, there is no significant difference between Shannon index and Simpson index, the principal components analysis of the bacterial communities, and the samples were roughly distributed in different regions. After 15 days of feeding, artificial diet did not significantly reduce the microbial diversity of the gut of C. septempunctata compared to the aphid group, and there was no significant effect on the abundance of dominant flora in the gut of C. septempunctata, C. septempunctata gut has a similar core microbiota. This study clarifies the effects in intestinal microbial diversity and composition structure of the C. septempunctata with artificial diet, and provides a theoretical basis for understanding the intestinal microorganisms and optimizating the artificial diet of C. septempunctata.

Chromosome-level genome assembly of the giant ladybug Megalocaria dilatata.

The giant ladybug Megalocaria dilatata (Fabricius) is a potential biocontrol agent and a valuable model for coccinellid genomics and evolutionary biology. However, the lack of a reference genome for M. dilatata has impeded further explorations into its evolution and constrained its use in pest management. Here, we assembled and annotated a high-quality, chromosome-level genome of M. dilatata. The resulting assembly spans 772.3 Mb, with a scaffold N50 of 72.48 Mb and a GC content of 34.23%. The Hi-C data aided in anchoring the assembly onto 10 chromosomes ranging from 43.35 to 108.16 Mb. We identified 493.33 Mb of repeat sequences, accounting for 63.88% of the assembled genome. Our gene prediction identified 25,346 genes, with 81.89% annotated in public protein databases. The genome data will provide a valuable resource for studying the biology and evolution of Coccinellidae, aiding in pest control strategies and advancing research in the field.

Molecularly imprinted polymers by reflux precipitation polymerization for selective solid-phase extraction of quinolone antibiotics from urine.

Molecularly imprinted polymers (MIPs) possess high specific cavities towards the template molecules, thus solid-phase extraction (SPE) based on MIPs using the target as the template has been widely used for selective extraction. However, the performance of SPE depends strongly on the shape and the distribution of the MIP sorbents, and rapid synthesis of MIPs with uniform particles remains a challenge. Our previous studies have shown that reflux precipitation polymerization (RPP) was a simple and rapid method for the synthesis of uniform MIPs. However, synthesis of MIPs by RPP for a group of targets using only one of the targets as the template has rarely been reported. In this work, MIPs with specific recognition capability for a group of quinolone antibiotics were synthesized for the first time via RPP with only ofloxacin as the template. The synthesized MIPs displayed good adsorption performance and selectivity (IF > 3.5) towards five quinolones, and subsequently were used as SPE adsorbents. Based on this MIPs-SPE, after systematic optimization of the SPE operation parameters during loading, washing and elution, an efficient and sensitive enough SPE method for separation and enrichment of the five quinolones in urine was developed and evaluated in combination with LC-MS/MS. The results showed that MIPs-SPE-LC-MS/MS has a good correlation (R2 ≥ 0.9961) in the linear range of 1-500 µg L-1. The limit of detection (LOD) and limit of quantification (LOQ) for the five quinolones were 0.10-0.14 µg L-1 and 0.32-0.48 µg L-1, respectively. In addition, the proposed method demonstrated good reproducibility (≤ 13 %) and high accuracy (92 %-113 %). We are confident that this method holds significant promise for the analysis of quinolones within the contexts of forensic medicine, epidemiology, and environmental chemistry.

Genome- and Transcriptome-wide Association Studies to Discover Candidate Genes for Diverse Root Phenotypes in Cultivated Rice.

Root system architecture plays a crucial role in nutrient and water absorption during rice production. Genetic improvement of the rice root system requires elucidating its genetic control. Genome-wide association studies (GWASs) have identified genomic regions responsible for rice root phenotypes. However, candidate gene prioritization around the peak region often suffers from low statistical power and resolution. Transcriptomics enables other statistical mappings, such as transcriptome-wide association study (TWAS) and expression GWAS (eGWAS), which improve candidate gene identification by leveraging the natural variation of the expression profiles. To explore the genes responsible for root phenotypes, we conducted GWAS, TWAS, and eGWAS for 12 root phenotypes in 57 rice accessions using 427,751 single nucleotide polymorphisms (SNPs) and the expression profiles of 16,901 genes expressed in the roots. The GWAS identified three significant peaks, of which the most significant peak responsible for seven root phenotypes (crown root length, crown root surface area, number of crown root tips, lateral root length, lateral root surface area, lateral root volume, and number of lateral root tips) was detected at 6,199,732 bp on chromosome 8. In the most significant GWAS peak region, OsENT1 was prioritized as the most plausible candidate gene because its expression profile was strongly negatively correlated with the seven root phenotypes. In addition to OsENT1, OsEXPA31, OsSPL14, OsDEP1, and OsDEC1 were identified as candidate genes responsible for root phenotypes using TWAS. Furthermore, a cis-eGWAS peak SNP was detected for OsDjA6, which showed the eighth strongest association with lateral root volume in the TWAS. The cis-eGWAS peak SNP for OsDjA6 was in strong linkage disequilibrium (LD) with a GWAS peak SNP on the same chromosome for lateral root volume and in perfect LD with another SNP variant in a putative cis-element at the 518 bp upstream of the gene. These candidate genes provide new insights into the molecular breeding of root system architecture.

Chromosome-level genome assembly of an agricultural pest Zeugodacus tau (Diptera: Tephritidae).

The fruit fly Zeugodacus tau (Diptera: Tephritidae) is a major pest of melons and other cucurbits in Southeast Asia. In this study, we used Illumina, Nanopore, and Hi-C sequencing technologies to assemble a reference genome of Z. tau at the chromosomal level. The assembled genome was 421.79 Mb and consisted of six chromosomes (one X-chromosome + five autosomes). The contig N50 was 4.23 Mb. We identified 20,922 protein-coding genes, of which 17,251 (82.45%) were functionally annotated. Additionally, we found 247 rRNAs, 435 tRNAs, 67 small nuclear RNAs, and 829 small RNAs in the genome. Repetitive elements accounted for 55.30 Mb (13.15%) of the genome. This high-quality genome assembly is valuable for evolutionary and genetic studies of Z. tau and its relative species.

Relaxed purifying selection pressure drives accelerated and dynamic gene rearrangements in thrips (Insecta: Thysanoptera) mitochondrial genomes.

Insect mitochondrial genomes (mitogenome) generally present a typical gene order, which is considered as the ancestral arrangement. All sequenced mitogenomes in the Thysanoptera display high levels of gene rearrangement. Due to limited number of thrips mitogenomes sequenced, how gene rearrangement may be shaped by evolution remain unclear. Here, we analyzed 33 thrips mitogenomes, including 14 newly sequenced. These mitogenomes were diverse in organization, nucleotides substitution and gene arrangements. We found 28 highly rearranged gene orders with the breakpoints of gene rearrangements from 25 to 33. Reconstruction of the ancestors mitochondrial gene arrangements states indicated that Tubulifera have more complex pathways than Terebrantia in the gene order evolution. Molecular calibration estimated that divergence of two suborders occurred in the middle Triassic while the radiation of thrips was associated with the arose and flourish of angiosperm. Our evolutionary hypothesis testing suggests that relaxation of selection pressure enabled the early phase of Thysanoptera evolution, followed by a stronger selective pressure fixed diversification. Our analyses found gene inversion increases the nonsynonymous substitution rates and provide an evolutionary hypothesis driving the diverse gene orders.