Multikingdom characterization of gut microbiota in patients with rheumatoid arthritis and rheumatoid arthritis-associated interstitial lung disease.

Rheumatoid arthritis-associated interstitial lung disease (RA-ILD) is a serious and common extra-articular disease manifestation. Patients with RA-ILD experience reduced bacterial diversity and gut bacteriome alterations. However, the gut mycobiome and virome in these patients have been largely neglected. In this study, we performed whole-metagenome shotgun sequencing on fecal samples from 30 patients with RA-ILD, and 30 with RA-non-ILD, and 40 matched healthy controls. The gut bacteriome and mycobiome were explored using a reference-based approach, while the gut virome was profiled based on a nonredundant viral operational taxonomic unit (vOTU) catalog. The results revealed significant alterations in the gut microbiomes of both RA-ILD and RA-non-ILD groups compared with healthy controls. These alterations encompassed changes in the relative abundances of 351 bacterial species, 65 fungal species, and 4,367 vOTUs. Bacteria such as Bifidobacterium longum, Dorea formicigenerans, and Collinsella aerofaciens were enriched in both patient groups. Ruminococcus gnavus (RA-ILD), Gemmiger formicilis, and Ruminococcus bromii (RA-non-ILD) were uniquely enriched. Conversely, Faecalibacterium prausnitzii, Bacteroides spp., and Roseburia inulinivorans showed depletion in both patient groups. Mycobiome analysis revealed depletion of certain fungi, including Saccharomyces cerevisiae and Candida albicans, in patients with RA compared with healthy subjects. Notably, gut virome alterations were characterized by an increase in Siphoviridae and a decrease in Myoviridae, Microviridae, and Autographiviridae in both patient groups. Hence, multikingdom gut microbial signatures showed promise as diagnostic indicators for both RA-ILD and RA-non-ILD. Overall, this study provides comprehensive insights into the fecal virome, bacteriome, and mycobiome landscapes of RA-ILD and RA-non-ILD gut microbiota, thereby offering potential biomarkers for further mechanistic and clinical research.

Widely Targeted Metabolomics Provides New Insights into Nutritional Profiling and Reveals the Flavonoid Pathway of Pea (Pisum sativum L.).

To learn more about the nutritional composition and health benefits for human consumers of peas, we used a widely targeted metabolomics-based approach to reveal the metabolite components from three main varieties, and a total of 1095 metabolites were identified. A comparison of 487 differentially accumulated metabolites shared among three varieties of fresh and dried peas found most of the amino acids and derivatives were downregulated and most of the lipids and flavonoids were upregulated in dried peas. Furthermore, comparing the main nutrient profiles exclusively showed that there were few differences in free fatty acids, sugars, vitamins, and alkaloids between dried and fresh peas. Peas are especially enriched with B-group vitamins. Through detailed identification and classification, the flavonoid pathway of peas was revealed; a variety of glycosylated derivatives from kaempferol, quercetin, and luteolin were confirmed to be abundant in peas. It was also found that isoflavones are richer in peas than in many other plants, and putatively the isoflavone synthesis pathway originates from liquiritigenin and naringenin. Our study not only offers guidance for understanding the nutritional components of peas, but also provides the basis for healthy diet analysis of the edible value and health benefits of peas.

Deep learning reconstruction for turbo spin echo to prospectively accelerate ankle MRI: A multi-reader study.

PURPOSE: To evaluate a deep learning reconstruction for turbo spin echo (DLR-TSE) sequence of ankle magnetic resonance imaging (MRI) in terms of acquisition time, image quality, and lesion detectability by comparing with conventional TSE. METHODS: Between March 2023 and May 2023, patients with an indication for ankle MRI were prospectively enrolled. Each patient underwent a conventional TSE protocol and a prospectively undersampled DLR-TSE protocol. Four experienced radiologists independently assessed image quality using a 5-point scale and reviewed structural abnormalities. Image quality assessment included overall image quality, differentiation of anatomic details, diagnostic confidence, artifacts, and noise. Interchangeability analysis was performed to evaluate the equivalence of DLR-TSE relative to conventional TSE for detection of structural pathologies. RESULTS: In total, 56 patients were included (mean age, 32.6 ± 10.6 years; 35 men). The DLR-TSE (233 s) protocol enabled a 57.4 % reduction in total acquisition time, compared with the conventional TSE protocol (547 s). DLR-TSE images had superior overall image quality, fewer artifacts, and less noise (all P < 0.05), compared with conventional TSE images, according to mean ratings by the four readers. Differentiation of anatomic details, diagnostic confidence, and assessments of structural abnormalities showed no differences between the two techniques (P > 0.05). Furthermore, DLR-TSE demonstrated diagnostic equivalence with conventional TSE, based on interchangeability analysis involving all analyzed structural abnormalities. CONCLUSION: DLR can prospectively accelerate conventional TSE to a level comparable with a 4-minute comprehensive examination of the ankle, while providing superior image quality and similar lesion detectability in clinical practice.

The development and initial validation of IgG4-related disease damage index: a consensus report from Chinese IgG4-RD Consortium.

OBJECTIVE: To develop and conduct an initial validation of the Damage Index for IgG4-related disease (IgG4-RD DI). METHODS: A draft of index items for assessing organ damages in patients with IgG4-RD was generated by experts from the Chinese IgG4-RD Consortium (CIC). The preliminary DI was refined using the Delphi method, and a final version was generated by consensus. 40 IgG4-RD cases representing four types of clinical scenarios were then selected, each with two time points of assessment for at least 3 years of follow-up. 48 rheumatologists from 35 hospitals nationwide were invited to evaluate organ damage using the CIC IgG4-RD DI. The intraclass correlation coefficient (ICC) and the Kendall-W coefficient of concordance (KW) were used to assess the inter-rater reliability. The criterion validity of IgG4-RD DI was tested by calculating the sensitivity and specificity of raters. RESULTS: IgG4-RD DI is a cumulative index consisting of 14 domains of organ systems, including a total of 39 items. The IgG4-RD DI was capable of distinguishing stable and increased damage across the active disease subgroup and stable disease subgroup. In terms of scores at baseline and later observations by all raters, overall consistency in scores at baseline and later observations by all raters was satisfactory. ICC at the two time points was 0.69 and 0.70, and the KW was 0.74 and 0.73, respectively. In subgroup analysis, ICC and KW in all subgroups were over 0.55 and 0.61, respectively. The analysis of criterion validity showed a good performance with a sensitivity of 0.86 (95% CI 0.82 to 0.88), a specificity of 0.79 (95% CI 0.76 to 0.82) and an area under the curve of 0.88 (95% CI 0.85 to 0.91). CONCLUSION: The IgG4-RD DI is a useful approach to analyse disease outcomes, and it has good operability and credibility. It is anticipated that the DI will become a useful tool for therapeutic trials and studies of prognosis in patients with IgG4-RD.

Isobaric Tags for Relative and Absolute Quantitation-Based Proteomics Analysis Revealed Proteins Involved in Drought Response during the Germination Stage in Faba Bean.

The faba bean, a significant cool-season edible legume crop, is susceptible to drought during the germination stage. Research regarding the genetic regulation of drought tolerance throughout this stage in the faba bean is limited. The differentially expressed proteins (DEPs) in faba beans between the drought-tolerant variety C105 and the drought-sensitive variant E1 during seed germination were identified in this work, accomplished through isobaric tags for relative and absolute quantitation (iTRAQ) analysis. A total of 3827 proteins were identified in the two varieties of germinating seeds. Compared to those of variety E1, an increase in 108 DEPs and a decrease in 61 DEPs were observed in variety C105 under drought. Conversely, in the control group, variety C105 showed 108 significantly upregulated DEPs and 55 significantly downregulated DEPs. GO and KEGG analyses showed that the DEPs associated with glutathione metabolism and protein processing demonstrated significant increases in response to drought stress. Protein-protein interaction (PPI) analysis unveiled three closely connected functional modules of protein translation, DNA replication, and post-translational modification, originating from 22 DEPs derived from the germination period of two varieties under drought stress. To verify the proteomic function, we selected three differentially expressed protein coding genes, which were overexpressed or silenced in tobacco, thereby enhancing the drought resistance of tobacco. This was accompanied via altered levels of superoxide dismutase or peroxidase in transgenic plants under drought stress. The possible mechanism for drought tolerance in germinating seeds of faba bean involves increasing protein translation, decreasing DNA replication, and modifying chromatin. These findings offer invaluable insights into the reaction mechanism in response to drought stress in faba beans. The identified DEPs could be utilized in faba bean breeding initiatives to manage drought.

Cutaneous leukocytoklastic vasculitis in a patient with ankylosing spondylitis: A case report.

Extra-articular manifestations (EAMs) in ankylosing spondylitis (AS) are common and most extra-articular manifestations such as acute iritis and inflammatory bowel disease are positively correlated with disease activity of AS. Vasculitis is an extra-articular manifestation of AS. However cutaneous leukocytoclastic vasculitis (CLV) is uncommon in AS patients. In this article, we report a case of a 66-year-old female patient who has had AS for long time. Although the patient's articular manifestations were stable, the aortic aneurysm and CLV continued to occur sequentially. This article reminds clinicians that even AS patients with stable articular manifestations should be followed up regularly. All extra-articular manifestations of AS patients should be taken seriously and treated as soon as possible under the guidance of rheumatoid immunologists.

Evaluation of Open Versus Arthroscopic Anterior Talofibular Ligament Reconstruction for Chronic Lateral Ankle Instability With Talar and Subtalar Cartilage MRI T2 Mapping: A 3-Year Prospective Study.

BACKGROUND: Previous studies have examined patients with chronic lateral ankle instability (CLAI) undergoing open and arthroscopic anterior talofibular ligament (ATFL) reconstruction, reporting equivalent clinical results between the 2 procedures. However, data on the magnetic resonance imaging (MRI) outcomes on cartilage health after the 2 procedures are limited. PURPOSE: To compare the cartilage MRI T2 values of the talar and subtalar joints between patients with CLAI undergoing open and arthroscopic ATFL reconstruction. STUDY DESIGN: Cohort study; Level of evidence, 3. METHODS: A prospective study was conducted on patients who underwent open or arthroscopic ATFL reconstruction between January 2018 and December 2019, with a mean follow-up duration of 3 years. MRI scans and American Orthopaedic Foot & Ankle Society (AOFAS) and Tegner score estimations were completed by patients ≤1 week before surgery, as a baseline measurement, and at a 3-year follow-up. A total of 21 healthy volunteers were included who underwent MRI at baseline. Cartilage health was evaluated using MRI T2 mapping. The talar and subtalar cartilage regions were segmented into 14 subregions. RESULTS: At baseline, patients with CLAI had substantially higher T2 values in the medial anterior, medial center, medial posterior, and lateral center regions on the talus compared with the healthy controls (P = .009, .003, .001, and .025, respectively). Remarkable increases in T2 values in the lateral posterior region on the talus were observed from baseline to follow-up in the open group (P = .007). Furthermore, T2 values were considerably higher in the medial center, medial posterior, lateral posterior, and lateral posterior calcaneal facets of the posterior subtalar joint at follow-up in the arthroscopic group compared with the baseline values (P = .025, .002, .006, and .044, respectively). No obvious differences in ΔT2 values were noted between the 2 groups at follow-up. The AOFAS and Tegner scores remarkably improved from baseline to follow-up for the 2 groups (open: 3.25 ± 0.58 vs 5.13 ± 0.81, P < .001; arthroscopic: 3.11 ± 0.90 vs 5.11 ± 1.08, P < .001), with no considerable difference between them. CONCLUSION: The elevated T2 values of cartilage could not be fully recovered after open or arthroscopic ATFL reconstruction. Both arthroscopic and open ATFL reconstruction displayed similar effects on cartilage health concerning ΔT2, but the arthroscopic group demonstrated more degenerative cartilage subregions than the open group.

Prospective Comparison of Standard and Deep Learning-reconstructed Turbo Spin-Echo MRI of the Shoulder.

Background Deep learning (DL)-based MRI reconstructions can reduce imaging times for turbo spin-echo (TSE) examinations. However, studies that prospectively use DL-based reconstructions of rapidly acquired, undersampled MRI in the shoulder are lacking. Purpose To compare the acquisition time, image quality, and diagnostic confidence of DL-reconstructed TSE (TSEDL) with standard TSE in patients indicated for shoulder MRI. Materials and Methods This prospective single-center study included consecutive adult patients with various shoulder abnormalities who were clinically referred for shoulder MRI between February and March 2023. Each participant underwent standard TSE MRI (proton density- and T1-weighted imaging; conventional TSE sequence was used as reference for comparison), followed by a prospectively undersampled accelerated TSEDL examination. Six musculoskeletal radiologists evaluated images using a four-point Likert scale (1, poor; 4, excellent) for overall image quality, perceived signal-to-noise ratio, sharpness, artifacts, and diagnostic confidence. The frequency of major pathologic features and acquisition times were also compared between the acquisition protocols. The intergroup comparisons were performed using the Wilcoxon signed rank test. Results Overall, 135 shoulders in 133 participants were evaluated (mean age, 47.9 years ± 17.1 [SD]; 73 female participants). The median acquisition time of the TSEDL protocol was lower than that of the standard TSE protocol (288 seconds [IQR, 288-288 seconds] vs 926 seconds [IQR, 926-950 seconds], respectively; P < .001), achieving a 69% lower acquisition time. TSEDL images were given higher scores for overall image quality, perceived signal-to-noise ratio, and artifacts (all P < .001). Similar frequency of pathologic features (P = .48 to > .99), sharpness (P = .06), or diagnostic confidence (P = .05) were noted between images from the two protocols. Conclusion In a clinical setting, TSEDL led to reduced examination time and higher image quality with similar diagnostic confidence compared with standard TSE MRI in the shoulder. © RSNA, 2024 Supplemental material is available for this article. See also the editorial by Chang and Chow in this issue.

Male vitellogenin regulates gametogenesis through a testis-enriched big protein in Chrysopa pallens.

In insects, vitellogenin (Vg) is generally viewed as a female-specific protein. Its primary function is to supply nutrition to developing embryos. Here, we reported Vg from the male adults of a natural predator, Chrysopa pallens. The male Vg was depleted by RNAi. Mating with Vg-deficient male downregulated female Vg expression, suppressed ovarian development and decreased reproductive output. Whole-organism transcriptome analysis after male Vg knockdown showed no differential expression of the known spermatogenesis-related regulators and seminal fluid protein genes, but a sharp downregulation of an unknown gene, which encodes a testis-enriched big protein (Vcsoo). Separate knockdown of male Vg and Vcsoo disturbed the assembly of spermatid cytoplasmic organelles in males and suppressed the expansion of ovary germarium in mated females. These results demonstrated that C. pallens male Vg signals through the downstream Vcsoo and regulates male and female reproduction.

Diagnosis of neuropsychiatry disorder in patients with anti-MDA5 antibody dermatomyositis: A case report.

Anti-melanoma differentiation-associated gene 5 (MDA5) dermatomyositis (DM) is a rare disease that can be easily misdiagnosed. Anti-MDA5 dermatomyositis is a subtype of DM. It is distinguished by the presence of significant mucocutaneous characteristics, palmar papules, panniculitis, interstitial lung disease (ILD), and clinically amyopathic dermatomyositis (CADM). When combined with rapidly progressing ILD (RP-ILD), anti-MDA5 DM can be fatal. The literature indicates that nervous system involvement is uncommon in patients with anti-MDA5 DM. We report a case of anti-MDA5 DM with neuropsychiatric abnormalities and ILD. The patient suffered from persistent worsening mental disorders, while his ILD was relatively stable. The patient's neuropsychiatric abnormalities gradually subsided after receiving treatment with glucocorticoids, immunoglobulins, and immunosuppressants, leaving only a slow response and memory loss.

Cost-effectiveness analysis of artificial intelligence-based diabetic retinopathy screening in rural China based on the Markov model.

This study assessed the cost-effectiveness of different diabetic retinopathy (DR) screening strategies in rural regions in China by using a Markov model to make health economic evaluations. In this study, we determined the structure of a Markov model according to the research objectives, which required parameters collected through field investigation and literature retrieval. After perfecting the model with parameters and assumptions, we developed a Markov decision analytic model according to the natural history of DR in TreeAge Pro 2011. For this model, we performed Markov cohort and cost-effectiveness analyses to simulate the probabilistic distributions of different developments in DR and the cumulative cost-effectiveness of artificial intelligence (AI)-based screening and ophthalmologist screening for DR in the rural population with diabetes mellitus (DM) in China. Additionally, a model-based health economic evaluation was performed by using quality-adjusted life years (QALYs) and incremental cost-effectiveness ratios. Last, one-way and probabilistic sensitivity analyses were performed to assess the stability of the results. From the perspective of the health system, compared with no screening, AI-based screening cost more (the incremental cost was 37,257.76 RMB (approximately 5,211.31 US dollars)), but the effect was better (the incremental utility was 0.33). Compared with AI-based screening, the cost of ophthalmologist screening was higher (the incremental cost was 14,886.76 RMB (approximately 2,070.19 US dollars)), and the effect was worse (the incremental utility was -0.31). Compared with no screening, the incremental cost-effectiveness ratio (ICER) of AI-based DR screening was 112,146.99 RMB (15,595.47 US dollars)/QALY, which was less than the threshold for the ICER (< 3 times the per capita gross domestic product (GDP), 217,341.00 RMB (30,224.03 US dollars)). Therefore, AI-based screening was cost-effective, which meant that the increased cost for each additional quality-adjusted life year was merited. Compared with no screening and ophthalmologist screening for DR, AI-based screening was the most cost-effective, which not only saved costs but also improved the quality of life of diabetes patients. Popularizing AI-based DR screening strategies in rural areas would be economically effective and feasible and can provide a scientific basis for the further formulation of early screening programs for diabetic retinopathy.

Genome-Wide Identification of bZIP Transcription Factors in Faba Bean Based on Transcriptome Analysis and Investigation of Their Function in Drought Response.

Faba bean is an important cool-season edible legume crop that is constantly threatened by abiotic stresses such as drought. The basic leucine zipper (bZIP) gene family is one of the most abundant and diverse families of transcription factors in plants. It regulates plant growth and development and plays an important role in the response to biotic and abiotic stresses. In this study, we identified 18 members of the faba bean bZIP transcription factor family at the genome-wide level based on previous faba bean drought stress transcriptome sequencing data. A phylogenetic tree was constructed to group the 18 VfbZIP proteins into eight clades. Analysis of cis-acting elements in the promoter region suggested that these 18 VfbZIPs may be involved in regulating abiotic stress responses such as drought. Transcriptome data showed high expression of seven genes (VfbZIP1, VfbZIP2, VfbZIP5, VfbZIP7, VfbZIP15, VfbZIP17, and VfbZIP18) in the drought-tolerant cultivar under drought stress, in which VfbZIP1, VfbZIP2, and VfbZIP5 were consistently expressed as detected by quantitative real-time polymerase chain reaction (qRT-PCR) compared to the transcriptome data. Ectopic overexpression of the three VfbZIPs in tobacco, based on the potato Virus X (PVX) vector, revealed that VfbZIP5 enhanced the drought tolerance. Overexpressed VfbZIP5 in plants showed lower levels of proline (PRO), malondialdehyde (MDA), and peroxidase (POD) compared to those overexpressing an empty vector under 10 days of drought stress. Protein-protein interaction (PPI) analysis showed that VfbZIP5 interacted with seven proteins in faba bean, including VfbZIP7 and VfbZIP10. The results depict the importance of VfbZIPs in response to drought stress, and they would be useful for the improvement of drought tolerance.

First Report of Botrytis cinerea Causing Stem Rot on Pea (Pisum sativum L.) in China.

Pea (Pisum sativum L.) is one of the most important cool season legumes consumed as vegetable in the world. In March 2022, a severe stem rot was observed on pea cultivars in vegetative stage in Wuhan, Hubei Province, China (30°39' N, 114°66' E). The infection started on the lower stems, and the lesions were water soaked, then girdled the stem, resulting in wilting of the leaves. Eventually, the entire plant died, and some necrotic stems were covered with gray conidia. To investigate the causal agent, small pieces cut from diseased stems were surface sterilized with 2% NaOCl for 1 min, then incubated on potato dextrose agar (PDA) at 25°C for 3 days. Pure cultures were obtained by hyphal tip transfer and five isolates were studied further. Colonies initially appeared white, turned gray from the center, then became taupe with cottony aerial mycelia, and finally black hard, round or irregular sclerotia (0.92 to 5.34 × 0.86 to 4.42 mm, n = 20) developed. The sealing film of several plates were removed after 5 days, and abundant conidia were produced 3 days later. The conidia are terminally arranged at the end of long, grayish branched conidiophores, conidia are unicellular, hyaline and round or elliptical, (9.2 to 11.4 × 6.7 to 9.2 µm, n = 50), and the conidiophores are (10.7 to 13.0 µm × 760 to 1080 µm, n=20) in size. The morphological characteristics were consistent with descriptions of Botrytis cinerea (Li et al., 2016). Genomic DNA of the five isolates was extracted, and the internal transcribed spacer region (ITS), glyceraldehyde-3-phosphate dehydrogenase (G3PDH) gene, heat-shock protein 60 (HSP60) gene, and DNA-dependent RNA polymerase subunit II (RPB2) gene were amplified using the primers described by Aktaruzzaman et al. (2018). The sequences were deposited in GenBank (accession nos. ON533694 and ON566787-ON566790 for ITS; ON600613 to ON600617 for HSP60; ON600608 to ON600612 for G3PDH; ON600603 to ON600607 for RPB2). The BLASTn analysis of these sequences showed that the isolates had high similarity (99 to 100%) with other B. cinerea isolates. A phylogenetic tree was constructed by MEGA11, and our isolates clustered in the B. cinerea clade. In pathogenicity test, 2-week-old seedlings of pea cultivar 'Zhongqin1' were inoculated. Mycelial plugs (5 mm diameter) taken from a 3-day-old colony of each isolate were placed on the axil of a stipule at the 4th node of potted pea plants (n=5 per isolate), and PDA plugs were placed on the same location of control (n=3). Inoculated and control plants were kept in a humid plastic box at 23°C for 2 days, and then placed in a glasshouse. Symptoms with water-soaked lesions were observed on the inoculated plants after 2 days, stems showed soft rot and broke off after 3 to 5 days, disease symptoms similar to those in the field, while the controls remained healthy. The pathogen was re-isolated from the affected stems, fulfilling Koch's postulates. B. cinerea had been reported to cause foliar, pod, seed and stem rot of pea after flowering in many pea production regions in the world (Kraft and Pfleger, 2001). Pea was recorded as a host of B. cinerea in Zhejiang, Sichuan and Yunnan Provinces (Tai, F. L. 1979; Zhuang, W.-Y. 2005; Zhang, Z. 2006.), but there has been no detailed disease description and identification of pathogen. To our knowledge, this is the first report of B. cinerea causing stem rot on pea in vegetative stage in China. Since B. cinerea can infect pea at any developmental stage, it could have a high economic impact as green pea production increases in China.

Clinical evaluation of AI-assisted screening for diabetic retinopathy in rural areas of midwest China.

BACKGROUND: Although numerous studies have described the application of artificial intelligence (AI) in diabetic retinopathy (DR) screening among diabetic populations, studies among populations in rural areas are rare. The purpose of this study was to evaluate the application value of an AI-based diagnostic system for DR screening in rural areas of midwest China. METHODS: In this diagnostic accuracy study, diabetes mellitus (DM) patients in the National Basic Public Health Information Systems of Licheng County and Lucheng County of Changzhi city from July to December 2020 were selected as the target population. A total of 7824 eyes of 3933 DM patients were enrolled in this screening; the patients included 1395 males and 2401 females, with an average age of 19-87 years (63±8.735 years). All fundus photographs were collected by a professional ophthalmologist under natural pupil conditions in a darkroom using the Zhiyuan Huitu fundus image AI analysis software EyeWisdom. The AI-based diagnostic system and ophthalmologists were tasked with diagnosing the photos independently, and the consistency rate, sensitivity and specificity of the two methods in diagnosing DR were calculated and compared. RESULTS: The prevalence rates of DR according to the ophthalmologist and AI diagnoses were 22.7% and 22.5%, respectively; the consistency rate was 81.6%. The sensitivity and specificity of the AI system relative to the ophthalmologists' grades were 81.2% (95% confidence interval [CI]: 80.3% 82.1%) and 94.3% (95% CI: 93.7% 94.8%), respectively. There was no significant difference in diagnostic outcomes between the methods (χ2 = 0.329, P = 0.566, P>0.05), and the AI-based diagnostic system had high consistency with the ophthalmologists' diagnostic results (κ = 0.752). CONCLUSION: Our research demonstrated that DR patients in rural area hospitals can be screened feasibly. Compared with that of the ophthalmologists, however, the accuracy of the AI system must be improved. The results of this study might lend support to the large-scale application of AI in DR screening among different populations.

Resequencing of 558 Chinese mungbean landraces identifies genetic loci associated with key agronomic traits.

Mungbean is a warm-season annual food legume and plays important role in supplying food and nutritional security in many tropical countries. However, the genetic basis of its agronomic traits remains poorly understood. Therefore, we resequenced 558 Chinese mungbean landraces and produced a comprehensive map of mungbean genomic variation. We phenotyped all landraces in six different environments. Genome-wide association studies (GWAS) produced 110 signals significantly associated with nine agronomic traits, for which several candidate genes were identified. Overall, this study provides new insight into the genetic architecture of mungbean agronomic traits. Moreover, the genome-wide variations identified here should be valuable resources for future breeding studies of this important food legume.

iTRAQ based protein profile analysis revealed key proteins involved in regulation of drought-tolerance during seed germination in Adzuki bean.

Adzuki bean is an important legume crop due to its high-quality protein, fiber, vitamins, minerals as well as rich bioactive substances. However, it is vulnerable to drought at the germination stage. However, little information is available about the genetic control of drought tolerance during seed germination in adzuki bean. In this study, some differential expression proteins (DEPs) were identified during seed germination between the drought-tolerant variety 17235 and drought-sensitive variety 17033 in adzuki bean using iTRAQ method. A total of 2834 proteins were identified in the germinating seeds of these two adzuki beans. Compared with the variety 17033, 87 and 80 DEPs were increased and decreased accumulation in variety 17235 under drought, respectively. Meanwhile, in the control group, a few DEPs, including 9 up-regulated and 21 down-regulated proteins, were detected in variety 17235, respectively. GO, KEGG, and PPI analysis revealed that the DEPs related to carbohydrate metabolism and energy production were significantly increased in response to drought stresses. To validate the proteomic function, the ectopic overexpression of V-ATPase in tobacco was performed and the result showed that V-ATPase upregulation could enhance the drought tolerance of tobacco. The results provide valuable insights into genetic response to drought stress in adzuki bean, and the DEPs could be applied to develop biomarkers related to drought tolerant in adzuki bean breeding projects.

The Immune Subtypes and Landscape of Gastric Cancer and to Predict Based on the Whole-Slide Images Using Deep Learning.

Background: Gastric cancer (GC) is a highly heterogeneous tumor with different responses to immunotherapy. Identifying immune subtypes and landscape of GC could improve immunotherapeutic strategies. Methods: Based on the abundance of tumor-infiltrating immune cells in GC patients from The Cancer Genome Atlas, we used unsupervised consensus clustering algorithm to identify robust clusters of patients, and assessed their reproducibility in an independent cohort from Gene Expression Omnibus. We further confirmed the feasibility of our immune subtypes in five independent pan-cancer cohorts. Finally, functional enrichment analyses were provided, and a deep learning model studying the pathological images was constructed to identify the immune subtypes. Results: We identified and validated three reproducible immune subtypes presented with diverse components of tumor-infiltrating immune cells, molecular features, and clinical characteristics. An immune-inflamed subtype 3, with better prognosis and the highest immune score, had the highest abundance of CD8+ T cells, CD4+ T-activated cells, follicular helper T cells, M1 macrophages, and NK cells among three subtypes. By contrast, an immune-excluded subtype 1, with the worst prognosis and the highest stromal score, demonstrated the highest infiltration of CD4+ T resting cells, regulatory T cells, B cells, and dendritic cells, while an immune-desert subtype 2, with an intermediate prognosis and the lowest immune score, demonstrated the highest infiltration of M2 macrophages and mast cells, and the lowest infiltration of M1 macrophages. Besides, higher proportion of EVB and MSI of TCGA molecular subtyping, over expression of CTLA4, PD1, PDL1, and TP53, and low expression of JAK1 were observed in immune subtype 3, which consisted with the results from Gene Set Enrichment Analysis. These subtypes may suggest different immunotherapy strategies. Finally, deep learning can predict the immune subtypes well. Conclusion: This study offers a conceptual frame to better understand the tumor immune microenvironment of GC. Future work is required to estimate its reference value for the design of immune-related studies and immunotherapy selection.

Insights into Temperature and Hypoxia Tolerance in Cowpea Weevil via HIF-1.

Cowpea weevil (Callosobruchus maculatus) is a major pest that leads to severe damage of the stored leguminous grains. Several management approaches, including physical barriers, biological or chemical methods, are used for controlling bruchid in cowpea. These methods usually target the metabolically active state of weevil. However, it becomes less effective at early stages as egg, larva, or pupa under low temperature and oxygen conditions. Since hypoxia-inducible factor-1 (HIF-1) is known to coordinate multiple gene responses to low oxygen or low temperature signals, we examined the HIF-1α gene expression under low temperature and hypoxic treatments. At -20 °C, it took 4 h to reduce the survival rate for eggs, larvae, and pupae down to 10%, while at 4 °C and 15 °C, the survival rate remained higher than 50% even after 128 h as HIF-1α gene expression peaked at 15 °C. Moreover, HIF-1 protein offers a valuable target for early stage pest control complementary to traditional methods. In particular, HIF-1 inhibitor camptothecin (CPT), one of the five HIF-1 inhibitors examined, achieved a very significant reduction of 96.2% and 95.5% relative to the control in weevil survival rate into adult at 4 °C and 30 °C, respectively. Our study can be used as one model system for drug development in virus infections and human cancer.