Genotype selection identified elite lines through quantitative trait loci mapping of agronomically important traits in wheat.

Wheat is one of the most important staple foods in the world. Genetic characterization of wheat agronomically important traits is crucial for yield improvement through molecular breeding. In this study, a recombinant inbred line (RIL) population was developed by crossing a local adapted high yield variety Jimai 22 (JM22) with an external variety Cunmai no.1 (CM1). A high-density genetic map containing 7,359 single nucleotide polymorphism (SNP) markers was constructed. Quantitative trait loci (QTL) mapping identified 61 QTL for eight yield-related traits under six environments (years). Among them, 17 QTL affecting spike number per plant, grain number per spike and thousand grain weight showed high predictability for theoretical yield per plant (TYP), of which, 12 QTL alleles positively contributed to TYP. Nine promising candidate genes for seven of the 12 QTL were identified including three known wheat genes and six rice orthologs. Four elite lines with TYP increased by 5.6%-15.2% were identified through genotype selection which carried 7-9 favorable alleles from JM22 and 2-3 favorable alleles from CM1 of the 12 QTL. Moreover, the linked SNPs of the 12 QTL were converted to high-throughput kompetitive allele-specific PCR (KASP) markers and validated in the population. The mapped QTL, identified promising candidate genes, developed elite lines and KASP markers are highly valuable in future genotype selection to improve wheat yield. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-024-01496-3.

Allostatic load and chronic pain: a prospective finding from the national survey of midlife development in the United States, 2004-2014.

BACKGROUND: Previous research has demonstrated a correlation between chronic stress and chronic pain (CP). However, there have been few studies examining the prospective association of allostatic load (AL)-the biological processes related to stress-with CP. METHODS: We firstly conducted latent class analysis to identify phenotypes of AL using a community-dwelling sample, the Midlife in the United States. Multinomial logistic regression models were used to examine the prospective association between phenotypes of AL at MIDUS 2 biomarker project and the presence of CP, CP interference and the number of CP sites at MIDUS 3. RESULTS: Three phenotypes of AL, low biological dysregulation, parasympathetic dysregulation and metabolic dysregulation, were identified. Compared to low biological dysregulation group, participants experiencing metabolic dysregulation phenotype of AL at MIDUS 2 had higher risks of having high-interference CP (RRR = 2.00, 95% CI: 1.06, 3.79, P < 0.05) and 3 or more CP sites (RRR = 2.03, 95% CI: 1.08, 3.83, P < 0.05) at MIDUS 3. CONCLUSION: The findings indicate that focusing on mitigating the metabolic dysfunction phenotype of AL has the potential to be an efficacious strategy for alleviating future CP bodily widespreadness and high CP interference.

Ultrasound Sonosensitizers for Tumor Sonodynamic Therapy and Imaging: A New Direction with Clinical Translation.

With the rapid development of sonodynamic therapy (SDT), sonosensitizers have evolved from traditional treatments to comprehensive diagnostics and therapies. Sonosensitizers play a crucial role in the integration of ultrasound imaging (USI), X-ray computed tomography (CT), and magnetic resonance imaging (MRI) diagnostics while also playing a therapeutic role. This review was based on recent articles on multifunctional sonosensitizers that were used in SDT for the treatment of cancer and have the potential for clinical USI, CT, and MRI applications. Next, some of the shortcomings of the clinical examination and the results of sonosensitizers in animal imaging were described. Finally, this paper attempted to inform the future development of sonosensitizers in the field of integrative diagnostics and therapeutics and to point out current problems and prospects for their application.

High-resolution genome-wide association study and genomic prediction for disease resistance and cold tolerance in wheat.

KEY MESSAGE: High-resolution genome-wide association study (GWAS) facilitated QTL fine mapping and candidate gene identification, and the GWAS based genomic prediction models were highly predictive and valuable in wheat genomic breeding. Wheat is a major staple food crop and provides more than one-fifth of the daily calories and dietary proteins for humans. Genome-wide association study (GWAS) and genomic selection (GS) for wheat stress resistance and tolerance related traits are critical to understanding their genetic architecture for improvement of breeding selection efficiency. However, the insufficient marker density in previous studies limited the utility of GWAS and GS in wheat genomic breeding. Here, we conducted a high-resolution GWAS for wheat leaf rust (LR), yellow rust (YR), powdery mildew (PM), and cold tolerance (CT) by genotyping a panel of 768 wheat cultivars using genotyping-by-sequencing. Among 153 quantitative trait loci (QTLs) identified, 81 QTLs were delimited to ≤ 1.0 Mb intervals with three validated using bi-parental populations. Furthermore, 837 stress resistance-related genes were identified in the QTL regions with 12 showing induced expression by YR and PM pathogens. Genomic prediction using 2608, 4064, 3907, and 2136 pre-selected SNPs based on GWAS and genotypic correlations between the SNPs showed high prediction accuracies of 0.76, 0.73, and 0.78 for resistance to LR, YR, and PM, respectively, and 0.83 for resistance to cold damage. Our study laid a solid foundation for large-scale QTL fine mapping, candidate gene validation and GS in wheat.

Development of a highly thermostable immunoassay based on a nanobody-alkaline phosphatase fusion protein for carcinoembryonic antigen detection.

Carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM-5) assays are employed in routine clinical settings to diagnose tumor. We selected two nanobodies with high-affinity to CEACAM-5, termed Nb11C12 and Nb2D5, using phage-display technology. The Nb2D5 fused with calf intestinal alkaline phosphatase (CAP), human placental alkaline phosphatase (HAP), or Pyrococcus abyssi alkaline phosphatase (PAP) were expressed in human embryonic kidney (HEK293) cells. The enzymatic activity of Nb2D5-HAP fusion protein was the best and remained stable at 60 °C for 7 days. The affinity of Nb2D5-HAP fusion protein to CEACAM-5 reached 42 pM. A chemiluminescent enzyme immunoassay (CLEIA) based on Nb2D5-HAP fusion protein was established for quantitative CEACAM-5 assay in clinical settings. The CLEIA exhibited a wide linear range of 0.31-640 ng/mL toward CEACAM-5, with a limit of detection (LOD) of 0.85 ng/mL. No cross-reactivity occurred with CEACAM-1, CEACAM-3, CEACAM-6, or CEACAM-8, and no interference was observed with rheumatoid factors. The CLEIA based on Nb2D5-HAP fusion protein was stable for 8 weeks at 37 °C and 50% relative humidity. The CLEIA developed from Nb2D5-HAP fusion protein had much better stability and linearity with similar reproducibility compared with the enzyme-linked immunosorbent assay developed from conventional monoclonal antibodies, which have been widely used in clinics over the past several decades. Graphical abstract.

Life course socioeconomic status, chronic pain, and the mediating role of allostatic load: findings from the midlife in the United States.

Introduction: Low socioeconomic status (SES) has been linked to chronic pain (CP); however, the mechanisms by which SES over the life course influences downstream CP outcomes remain unclear. Methods: This study utilizes data from the Midlife in the United States (MIDUS) survey, a prospective sample of community-dwelling individuals (N=781), to investigate the chain of risk additive model of SES in relation to CP. Additionally, the study examines the mediating role of allostatic load (AL) in the relationship between life course SES and CP. Confirmatory factor analysis was employed to capture the multidimensionality of life course SES and path analysis was used to examine the direct and indirect effects on CP. AL was computed by quartile-based summation and by latent class analysis. Results: Results indicated lower SES in MIDUS 2 was associated with greater high-interference CP odds in MIDUS 3 (OR=1.069, 95% CI=1.006-1.136, P < 0.05) and no association was found between distal SES and levels of CP interference. Similarly, no significant relationship was observed between SES and the number of CP locations. Additionally, no additive effects of SES were found, and AL did not present mediation effects on the association between life course SES and CP. Discussion: The present study emphasizes the importance of directly proximal effects of SES on CP, underscoring the need for equitable distribution of health resources and the implementation of policies focused on diminishing socioeconomic inequalities. Further research is needed to examine alternative pathways by which proximal SES impact CP.

Transcriptional and genetic characteristic of chimera pea generation via double ethyl methanesulfonate-induced mutation revealed by transcription analysis.

Ethyl methanesulfonate (EMS)-induced mutagenesis is a prominent method for generating plant mutants, often resulting in chimera plants; however, their transcriptional and genetic characteristic remain elusive. In this investigation, chimera pea (Pisum sativum L.) specimens, labeled GY1 and GY2, exhibiting a distinctive phenotype with yellow and green leaves were meticulously cultivated via sequential double EMS mutagenesis. The observed color disparity between the yellow and green leaves was attributed to a significant reduction in chlorophyll content coupled with heightened lutein levels in both chimeric variants. Transcriptome profiling revealed the enrichment of differentially expressed genes in both GY1 and GY2, specifically implicating Kyoto Encyclopedia of Genes and Genomes pathways linked to amino acid biosynthesis and ribosome development, alongside Gene Ontology (GO) biological processes linked with stress response mechanisms. Few structural genes associated with chlorophyll and lutein biosynthesis exhibited discernible differential expression. Despite these functional similarities, distinctive nuances were evident between specimens, with GY1 exhibiting enrichment in GO pathways related to chloroplast development and GY2 showing enrichment for ribosome development pathways. Single-nucleotide polymorphism (SNP) analysis uncovered a shared pool of 599 and 598 polymorphisms in the yellow and green leaves of GY1 and GY2, respectively, likely stemming from the initial EMS mutagenesis step. Further investigation revealed an increased number of unique SNPs in the yellow leaves following the second EMS application, whereas the green leaves exhibited sparse and unique SNP occurrences, suggestive of potential evasion from secondary mutagenesis. This inherent genetic variability underpins the mechanism underlying the formation of chimera plants. Predominant base mutations induced by EMS were characterized by G/A and C/T transitions, constituting 74.1% of the total mutations, aligning with established EMS mutation induction paradigms. Notably, genes encoding the eukaryotic translation initiation factor eIIso4G and the ubiquitin ligase RKP, known to modulate leaf color in model plants, harbored two SNPs in the yellow leaves of both GY1 and GY2, implicating their putative role in the yellow leaf phenotype. Collectively, this study provides novel insights into the transcriptional and genetic characteristics of chimera plants via EMS-induced mutagenesis.

The mediating effect of allostatic load on the association between life course socioeconomic disadvantage and chronic pain: a prospective finding from the National Survey of Midlife Development in the United States.

Background: Socioeconomic disadvantages (SEDs) are associated with chronic pain (CP) and allostatic load (AL). Few prospective population-based studies have examined the relationship between life course SED, CP interference, and CP widespreadness, and there is no prospective population-based study on whether AL mediates the association between SED and CP. Objective: In this study, we investigated whether the prospective effect of SED on CP at Midlife in the United States (MIDUS) 3 is consistent with the accumulation of risk model and social mobility model, using the National Survey of MIDUS (n = 593). To prepare for the mediation analysis, we tested (1) whether SED would be prospectively associated with AL in the MIDUS 2 biomarker project, (2) whether AL would be prospectively associated with CP, and (3) whether childhood, as a critical period, moderated the association between AL and CP. In addition, the mediating effect of AL on the association between SED and CP was examined. Method: SED was measured using cumulative scores and disadvantage trajectories derived from latent class trajectory modeling (LCTM). After multiple imputations, analyses were conducted using multinomial logistic regression for CP and negative binomial regression for AL, respectively. Finally, mediation analyses and moderated mediation analyses were performed. Results: LCTM identified three SED trajectories, namely, constant low, high to low, and medium to high. The results showed that proximal cumulative SED was associated with high-interference CP. Furthermore, compared with the group with constant low SED, the group with medium-to-high SED was significantly associated with high-interference pain and experienced pain in at least three different sites. Cumulative SED and deteriorating SED trajectories were associated with higher AL, consistent with previous studies. Furthermore, childhood SED moderated the effect of AL on CP widespreadness and unexpectedly demonstrated a protective effect, while other associations between AL and CP were not significant. Subsequent mediation analysis did not yield statistically significant evidence. Conclusions: People who experienced more recent SED or increasing disadvantage throughout their lives were more likely to suffer from CP, and this association was not mediated by physiological system dysregulation caused by chronic stress. Therefore, measures to alleviate AL may not be effective in protecting socioeconomically disadvantaged populations from CP.

A Multi-Task Multi-Stage Transitional Training Framework for Neural Chat Translation.

Neural chat translation (NCT) aims to translate a cross-lingual chat between speakers of different languages. Existing context-aware NMT models cannot achieve satisfactory performances due to the following inherent problems: 1) limited resources of annotated bilingual dialogues; 2) the neglect of modelling conversational properties; 3) training discrepancy between different stages. To address these issues, in this paper, we propose a multi-task multi-stage transitional (MMT) training framework, where an NCT model is trained using the bilingual chat translation dataset and additional monolingual dialogues. We elaborately design two auxiliary tasks, namely utterance discrimination and speaker discrimination, to introduce the modelling of dialogue coherence and speaker characteristic into the NCT model. The training process consists of three stages: 1) sentence-level pre-training on large-scale parallel corpus; 2) intermediate training with auxiliary tasks using additional monolingual dialogues; 3) context-aware fine-tuning with gradual transition. Particularly, the second stage serves as an intermediate phase that alleviates the training discrepancy between the pre-training and fine-tuning stages. Moreover, to make the stage transition smoother, we train the NCT model using a gradual transition strategy, i.e., gradually transiting from using monolingual to bilingual dialogues. Extensive experiments on two language pairs demonstrate the effectiveness and superiority of our proposed training framework.

Integrating genomic and multiomic data for Angelica sinensis provides insights into the evolution and biosynthesis of pharmaceutically bioactive compounds.

Angelica sinensis roots (Angelica roots) are rich in many bioactive compounds, including phthalides, coumarins, lignans, and terpenoids. However, the molecular bases for their biosynthesis are still poorly understood. Here, an improved chromosome-scale genome for A. sinensis var. Qinggui1 is reported, with a size of 2.16 Gb, contig N50 of 4.96 Mb and scaffold N50 of 198.27 Mb, covering 99.8% of the estimated genome. Additionally, by integrating genome sequencing, metabolomic profiling, and transcriptome analysis of normally growing and early-flowering Angelica roots that exhibit dramatically different metabolite profiles, the pathways and critical metabolic genes for the biosynthesis of these major bioactive components in Angelica roots have been deciphered. Multiomic analyses have also revealed the evolution and regulation of key metabolic genes for the biosynthesis of pharmaceutically bioactive components; in particular, TPSs for terpenoid volatiles, ACCs for malonyl CoA, PKSs for phthalide, and PTs for coumarin biosynthesis were expanded in the A. sinensis genome. These findings provide new insights into the biosynthesis of pharmaceutically important compounds in Angelica roots for exploration of synthetic biology and genetic improvement of herbal quality.

Enhanced anticoagulant activity of hirudin-i analogue co-expressed with arylsulfotransferase in periplasm of E. coli BL21(DE3).

Hirudin, a blood anticoagulant, is the most potent natural thrombin inhibitor of leech origin. Its application is limited because it is difficult to obtain abundant natural hirudin directly from the leech. Although some bioengineering methods can significantly increase the production of hirudin, the reduced efficacy of recombinant hirudin (rH) remains a critical shortcoming. The lack of sulfation of tyrosine 63 in rH is an important cause of its inadequate performance. This article is the first report of periplasmic co-expression of an rH-I analogue with arylsulfotransferase (ASST) in E. coli BL21(DE3). Co-expressed rH-I analogue with sulfate donor substrate (p-nitrophenyl sulfate potassium) showed anticoagulant (rabbit and goat serum) activity twice more than rH-I analogue expressed without ASST, indicating its potential periplasmic sulfation. Moreover, purified rH-I analogue showed above 4.5 times higher anticoagulant activity compared to therapeutic anti-thrombotic heparin (HE). At the same time, pH-dependent differential solubility was employed to purify rH analogues from fermentation broth, which is a simple, fast and inexpensive purification technology, and can potentially be used for larger scale purification. This will also greatly improve the application of rH in clinical treatment.

Development of tilapia collagen and chitosan composite hydrogels for nanobody delivery.

Recently, injectable hydrogels have shown great potential in cell therapy and drug delivery. They can easily fill in any irregular-shaped defects and remain in desired positions after implantation using minimally invasive strategies. Here, we developed hydrogels prepared from tilapia skin collagen and chitosan (HCC). The residual mass rate of HCC was affected by the pH at the time of preparation, which was 29.1 % at pH 7 in 36 h. By comparison, the residual mass ratios of HCC at pH values of 6 and 5 were only approximately 8.4 % and 0, respectively. In addition, the stability of HCC was also affected by the concentration of these two components. HCC10 catalyzed by 10 mg mL-1 tilapia skin collagen and 10 mg mL-1 chitosan was more stable than HCC5 catalyzed by 5 mg mL-1 tilapia skin collagen and 10 mg mL-1 chitosan; therefore, we studied that ability of HCC10 to deliver two model nanobodies: 2D5 and KPU. As the concentration of nanobodies increased, the cumulative release rate of 2D5 decreased, and the release rate of KPU increased. Meanwhile, the cumulative release rate of 2D5 was the highest (68.3 %) at pH 5.5, followed by pH 6.8 (56.4 %) and 7.4 (28.4 %). However, the cumulative release rates of KPU were similar at pH 5.5 (45.1 %), 6.8 (46.5 %), and 7.4 (44.9 %). HCC is biodegradable, and can facilitate the release nanobodies; thus, HCC could be developed into an intelligent responsive tumor treatment matrix for use in cancer therapy.

High-Resolution Genome-wide Association Study Identifies Genomic Regions and Candidate Genes for Important Agronomic Traits in Wheat.

Wheat (Triticum aestivum) is a major staple food crop worldwide. Genetic dissection of important agronomic traits is essential for continuous improvement of wheat yield to meet the demand of the world's growing population. We conducted a large-scale genome-wide association study (GWAS) using a panel of 768 wheat cultivars that were genotyped with 327 609 single-nucleotide polymorphisms generated by genotyping-by-sequencing and detected 395 quantitative trait loci (QTLs) for 12 traits under 7 environments. Among them, 273 QTLs were delimited to ≤1.0-Mb intervals and 7 of them are either known genes (Rht-D, Vrn-B1, and Vrn-D1) that have been cloned or known QTLs (TaGA2ox8, APO1, TaSus1-7B, and Rht12) that were previously mapped. Eight putative candidate genes were identified for three QTLs that enhance spike seed setting and grain size using gene expression data and were validated in three bi-parental populations. Protein sequence analysis identified 33 putative wheat orthologs that have high identity with rice genes in QTLs affecting similar traits. Large r2 values for additive effects observed among the QTLs for most traits indicated that the phenotypes of these identified QTLs were highly predictable. Results from this study demonstrated that significantly increasing GWAS population size and marker density greatly improves detection and identification of candidate genes underlying a QTL, solidifying the foundation for large-scale QTL fine mapping, candidate gene validation, and developing functional markers for genomics-based breeding in wheat.

A strategy for L-isoleucine dioxygenase screening and 4-hydroxyisoleucine production by resting cells.

L-Isoleucine dioxygenase (IDO) specifically converts L-isoleucine(L-Ile) to 4-hydroxyisoleucine(4-HIL). To obtain IDO with improved activity, a strategy was developed that is dependent on the restoration of succinate-minus E. coli cell growth by the coupling of L-Ile hydroxylation and the oxidation of α-ketoglutarate(α-KGA) to succinate. Five mutants were obtained with this strategy, and the characteristics of IDOM3, which exhibited the highest activity, were studied. The catalytic efficiency, thermal stability and catalytic rate of IDOM3 were significantly improved compared with those of wild-type IDO. Moreover, an efficient method for the biotransformation of 4-HIL by resting cells expressing IDOM3 was developed, with which 151.9 mmol of 4-HIL/L (22.4 g/L) was synthesized in 12 h while the substrates seldom exhibited additional consumption.

Overproduction, Purification and Characterization of Adenylate Deaminase from Aspergillus oryzae.

Adenylate deaminase (AMPD, EC 3.5.4.6) is an aminohydrolase that widely used in the food and medicine industries. In this study, the gene encoding Aspergillus oryzae AMPD was cloned and expressed in Escherichia coli. Induction with 0.75 mM isopropyl ß-D-l-thiogalactopyranoside resulted in an enzyme activity of 1773.9 U/mL. Recombinant AMPD was purified to electrophoretic homogeneity using nickel affinity chromatography, and its molecular weight was calculated as 78.6 kDa. Purified AMPD exhibited maximal activity at 35 °C, pH 6.0 and 30 mM K+, with apparent K m and V max values of 2.7 × 10-4 M and 77.5 µmol/mg/min under these conditions. HPLC revealed that recombinant AMPD could effectively catalyse the synthesis of inosine-5'-monophosphate (IMP) with minimal by-products, indicating high specificity and suggesting that it could prove useful for IMP production.