Association Between the Serum α-Klotho Level and Insulin Resistance in Adults: NHANES 2007-2016.

OBJECTIVE: This study aimed to investigate the relationship between serum α-Klotho levels and insulin resistance (IR), a precursor to type 2 diabetes. METHODS: The study analyzed data from 4,758 adult participants in the National Health and Nutrition Examination Survey (NHANES) spanning from 2007 to 2016. The relationship between α-Klotho concentration and IR was assessed using the Homeostatic Model Assessment of Insulin Resistance (HOMA-IR) and odds ratios (OR) derived from logistic regression models. RESULTS: Results showed that every 1-ln increase in α-Klotho concentration raised the HOMA-IR value by 0.55 (95% confidence interval 0.35-0.74) and the odds of IR by 64% (odds ratio 1.64; 95% confidence interval 1.28-2.1). The odds of IR was 40% greater in highest tertile than in the lowest tertile. CONCLUSION: The findings of this study underscore a significant correlation between increased serum α-Klotho levels and the prevalence of IR.

Genome assembly of Melilotus officinalis provides a new reference genome for functional genomics.

BACKGROUND: Sweet yellow clover (Melilotus officinalis) is a diploid plant (2n = 16) that is native to Europe. It is an excellent legume forage. It can both fix nitrogen and serve as a medicine. A genome assembly of Melilotus officinalis that was collected from Best corporation in Beijing is available based on Nanopore sequencing. The genome of Melilotus officinalis was sequenced, assembled, and annotated. RESULTS: The latest PacBio third generation HiFi assembly and sequencing strategies were used to produce a Melilotus officinalis genome assembly size of 1,066 Mbp, contig N50 = 5 Mbp, scaffold N50 = 130 Mbp, and complete benchmarking universal single-copy orthologs (BUSCOs) = 96.4%. This annotation produced 47,873 high-confidence gene models, which will substantially aid in our research on molecular breeding. A collinear analysis showed that Melilotus officinalis and Medicago truncatula shared conserved synteny. The expansion and contraction of gene families showed that Melilotus officinalis expanded by 565 gene families and shrank by 56 gene families. The contacted gene families were associated with response to stimulus, nucleotide binding, and small molecule binding. Thus, it is related to a family of genes associated with peptidase activity, which could lead to better stress tolerance in plants. CONCLUSIONS: In this study, the latest PacBio technology was used to assemble and sequence the genome of the Melilotus officinalis and annotate its protein-coding genes. These results will expand the genomic resources available for Melilotus officinalis and should assist in subsequent research on sweet yellow clover plants.

Illumina and Nanopore sequencing in culture-negative samples from suspected lower respiratory tract infection patients.

Objective: To evaluate the diagnostic value of metagenomic sequencing technology based on Illumina and Nanopore sequencing platforms for patients with suspected lower respiratory tract infection whose pathogen could not be identified by conventional microbiological tests. Methods: Patients admitted to the Respiratory and Critical Care Medicine in Shanghai Ruijin Hospital were retrospectively studied from August 2021 to March 2022. Alveolar lavage or sputum was retained in patients with clinically suspected lower respiratory tract infection who were negative in conventional tests. Bronchoalveolar lavage fluid (BALF) samples were obtained using bronchoscopy. Sputum samples were collected, while BALF samples were not available due to bronchoscopy contraindications. Samples collected from enrolled patients were simultaneously sent for metagenomic sequencing on both platforms. Results: Thirty-eight patients with suspected LRTI were enrolled in this study, consisting of 36 parts of alveolar lavage and 2 parts of sputum. According to the infection diagnosis, 31 patients were confirmed to be infected with pathogens, while 7 patients were diagnosed with non-infectious disease. With regard to the diagnosis of infectious diseases, the sensitivity and specificity of Illumina and Nanopore to diagnose infection in patients were 80.6% vs. 93.5% and 42.9 vs. 28.6%, respectively. In patients diagnosed with bacterial, Mycobacterium, and fungal infections, the positive rates of Illumina and Nanopore sequencer were 71.4% vs. 78.6%, 36.4% vs. 90.9%, and 50% vs. 62.5%, respectively. In terms of pathogen diagnosis, the sensitivity and specificity of pathogens detected by Illumina and Nanopore were 55.6% vs. 77.8% and 42.9% vs. 28.6%, respectively. Among the patients treated with antibiotics in the last 2 weeks, 61.1% (11/18) and 77.8% (14/18) cases of pathogens were accurately detected by Illumina and Nanopore, respectively, among which 8 cases were detected jointly. The consistency between Illumina and diagnosis was 63.9% (23/36), while the consistency between Nanopore and diagnosis was 83.3% (30/36). Between Illumina and Nanopore sequencing methods, the consistency ratio was 55% (22/42) based on pathogen diagnosis. Conclusion: Both platforms play a certain value in infection diagnosis and pathogen diagnosis of CMT-negative suspected LRTI patients, providing a theoretical basis for clinical accurate diagnosis and symptomatic treatment. The Nanopore platform demonstrated potential advantages in the identification of Mycobacterium and could further provide another powerful approach for patients with suspected Mycobacterium infection.

High-quality chromosome-level de novo assembly of the Trifolium repens.

BACKGROUND: White clover (Trifolium repens L.), an excellent perennial legume forage, is an allotetraploid native to southeastern Europe and southern Asia. It has high nutritional, ecological, genetic breeding, and medicinal values and exhibits excellent resistance to cold, drought, trample, and weed infestation. Thus, white clover is widely planted in Europe, America, and China; however, the lack of reference genome limits its breeding and cultivation. This study generated a white clover de novo genome assembly at the chromosomal level and annotated its components. RESULTS: The PacBio third-generation Hi-Fi assembly and sequencing methods generated a 1096 Mb genome size of T. repens, with contigs of N50 = 14 Mb, scaffolds of N50 = 65 Mb, and BUSCO value of 98.5%. The newly assembled genome has better continuity and integrity than the previously reported white clover reference genome; thus provides important resources for the molecular breeding and evolution of white clover and other forage. Additionally, we annotated 90,128 high-confidence gene models from the genome. White clover was closely related to Trifolium pratense and Trifolium medium but distantly related to Glycine max, Vigna radiata, Medicago truncatula, and Cicer arietinum. The expansion, contraction, and GO functional enrichment analysis of the gene families showed that T. repens gene families were associated with biological processes, molecular function, cellular components, and environmental resistance, which explained its excellent agronomic traits. CONCLUSIONS: This study reports a high-quality de novo assembly of white clover genome obtained at the chromosomal level using PacBio Hi-Fi sequencing, a third-generation sequencing. The generated high-quality genome assembly of white clover provides a key basis for accelerating the research and molecular breeding of this important forage crop. The genome is also valuable for future studies on legume forage biology, evolution, and genome-wide mapping of quantitative trait loci associated with the relevant agronomic traits.

Islet function changes of post-glucose-challenge relate closely to 15 years mortality of elderly men with a history of hyperglycemia.

Aims: We aimed to investigate the relationship between islet function changes during a glucose challenge and 15-year mortality in elderly men. Methods: Elderly men who did the oral glucose tolerance test in 2005 owing to an abnormal glucose history without diabetes were included. Changes in insulin resistance and secretion were evaluated using the homeostasis model assessment (HOMA) of fast, post-load, and ratios. Comparisons between the dead and the survival groups were analyzed using the Student's t-test (continuous variables) or χ2 test (Categorical variables). Single-factor logistic regression was used to identify the possible affecting factors. Multifactorial logistic regression was used to identify the independent risk factors in total population and in the subgroups. ROC curve was used to assess the predictive ability of risk factor and to determine the cut-off value. Results: Of the 220 elderly men, 67 died according to 15-year retrospection. Age (OR = 1.243, P = 0.000), diastolic pressure (OR = 0.958, P = 0.027), and HOMA-IR (2 h/0 h) (OR = 1.040, P = 0.010) were independent risk factors for 15-year mortality. Subgroup analysis showed that HOMA-IR (2 h/0 h) was an obvious risk factor, especially for normal glucose tolerance (OR = 1.060, P = 0.030), age 60-70 years (OR = 1.068, P = 0.005), and hypertension (OR = 1.048, P = 0.013); HOMA-ß (2 h/0 h) showed some protective effects in the impaired glucose regulation subgroup (OR = 0.779, P = 0.057). HOMA-IR (2 h/0 h) cut-off value was 15. Conclusions: HOMA-IR (2 h/0 h) higher than 15 was an independent risk factor for 15-year mortality in elderly men with hyperglycemia history.

Reversible Transformation and Distribution Determination of Diverse Pt Single-Atom Species.

In single-atom catalysts (SACs), the complexity of the support anchoring sites creates a vast diversity of single-atom species with varied coordination environments. To date, the quantitative distribution of these diverse single-atom species in a given SAC has remained elusive. Recently, CeO2-supported metal SACs have been extensively studied by modulating their local environments via numerous synthetic strategies. However, owing to the absence of a quantitative description, unraveling the site-specific reactivity and regulating their transformation remain challenging. Here, we show that two distinct Pt/CeO2 SACs can be reversibly generated by oxidative and nonoxidative dispersions, which contain varied Pt1On-Ceδ+ single-atom species despite similar Pt charge states and coordination numbers. By means of Raman spectroscopy and computational studies, we semiquantitatively reveal the distribution of diverse Pt1On-Ceδ+ species in each specific SACs. Remarkably, the minority species of Pt1O4-Ce3+-Ov accounting for only 14.2% affords the highest site-specific reactivity for low-temperature CO oxidation among the other abundant counterparts, i.e., Pt1O4-Ce4+ and Pt1O6-Ce4+. The second nearest oxygen vacancy (Ov) not only acts synergistically with the nearby active metal sites to lower the reaction barrier but also facilitates the dynamic transformation from six-coordinated to four-coordinated sites during cyclic nonoxidative and oxidative dispersions. This work elucidates the quantitative distribution and dynamic transformation of varied single-atom species in a given SAC, offering a more intrinsic descriptor and quantitative measure to depict the inhomogeneity of SACs.

The bidirectional association of C-peptide with cardiovascular risk in nondiabetic adults and patients with newly diagnosed type 2 diabetes mellitus: a retrospective cohort study.

BACKGROUND: Recent literature reported the biological role of C-peptide, but this role is still controversial and unclear. The primary aim of this study was to investigate associations between C-peptide and cardiovascular biomarkers as well as events. METHODS: A total of 55636 participants who had a health examination from 2017 to 2021 were included. Of them, 6727 participants visited the hospital at least twice. Cardiovascular biomarkers like high-sensitivity C-reactive protein (hs-CRP) and high-sensitivity cardiac troponin T (hs-cTnT) were measured and their relationships with fasting C-peptide were evaluated for all participants. Cardiovascular events were obtained during the last visit and their associations with C-peptide were evaluated for those participants who visited the hospital at least twice. RESULTS: Among the included participants, 11.1% had a previous type 2 diabetes mellitus (T2DM). In the participants without previous T2DM, the relationships between fasting C-peptide and hs-CRP and hs-cTnT were negative if the value of fasting C-peptide was < 1.4 ng/mL and positive if the value was ≥ 1.4 ng/mL. These relationships remained significant after adjusting for hemoglobin A1c, insulin resistance index, and its interaction with C-peptide, even if the participants were stratified by glucose metabolism status or levels of insulin resistance index. Hazard ratios of cardiovascular events were first decreased and then increased with the increasing of baseline C-peptide levels, though these associations became unsignificant using the multivariate Cox regression model. Unlike the participants without previous T2DM, the associations of C-peptide with cardiovascular biomarkers and events were not significant in the patients with previous T2DM. CONCLUSIONS: The associations of C-peptide with cardiovascular biomarkers and events were different between the participants without previous T2DM and those with previous T2DM. The effect of C-peptide on cardiovascular risk may be bidirectional, play a benefit role at a low level, and play a harmful role at a high level in the nondiabetic adults and the patients with newly diagnosed T2DM.

Screening of universal DNA barcodes for identifying grass species of Gramineae.

There is currently international interest in applying DNA barcoding as a tool for plant species discrimination and identification. In this study, we evaluated the utility of four candidate plant DNA barcoding regions [rbcL, matK, trnL-F, and internal transcribed spacer (ITS)] in seven genera of Gramineae including Agropyron, Bromus, Elymus, Elytrigia, Festuca, Leymus, and Lolium. Fourteen accessions were analyzed, and matK and ITS showed the highest species, subspecies, and variety discriminatory power, each resolving 11 accessions. Species discrimination using rbcL and trnL-F was lower, resolving 7 and 8 accessions, respectively. Subspecies and variety discrimination using rbcL and trnL-F could not identify 4 accessions of Agropyron. A technical system can be established using the proposed DNA barcode to rapidly and reliably identify the seven genera of Gramineae. This study serves as a "useful reference" for identifying the genetic diversity of grass germplasm resources. DNA barcoding can be utilized to uncover the relatives of different species within the same family or between different families. It can also be used to determine the related groups of important herbage, turfgrass, and crops and provide crucial background information for discovering excellent genes and improving existing crop varieties.

A High-Quality Genome Assembly of Sorghum dochna.

Sweet sorghum (Sorghum dochna) is a high-quality bio-energy crop that also serves as food for humans and animals. However, there is little information on the genomic characteristics of S. dochna. In this study, we presented a high-quality assembly of S. dochna with PacBio long reads, Illumina short reads, high-throughput chromosome capture technology (Hi-C) sequencing data, gene annotation, and a comparative genome analysis. The results showed that the genome of S. dochna was assembled to 777 Mb with a contig N50 of 553.47 kb and a scaffold N50 of 727.11 kb. In addition, the gene annotation predicted 37,971 genes and 39,937 transcripts in the genome of S. dochna. A Venn analysis revealed a set of 7,988 common gene annotations by integrating five databases. A Cafe software analysis showed that 191 gene families were significantly expanded, while 3,794 were significantly contracted in S. dochna. A GO enrichment analysis showed that the expanded gene families were primarily clustered in the metabolic process, DNA reconstruction, and DNA binding among others. The high-quality genome map constructed in this study provides a biological basis for the future analysis of the biological characteristics of S. dochna, which is crucial for its breeding.

A de novo assembled high-quality chromosome-scale Trifolium pratense genome and fine-scale phylogenetic analysis.

BACKGROUND: Red clover (Trifolium pratense L.) is a diploid perennial temperate legume with 14 chromosomes (2n = 14) native to Europe and West Asia, with high nutritional and economic value. It is a very important forage grass and is widely grown in marine climates, such as the United States and Sweden. Genetic research and molecular breeding are limited by the lack of high-quality reference genomes. In this study, we used Illumina, PacBio HiFi, and Hi-C to obtain a high-quality chromosome-scale red clover genome and used genome annotation results to analyze evolutionary relationships among related species. RESULTS: The red clover genome obtained by PacBio HiFi assembly sequencing was 423 M. The assembly quality was the highest among legume genome assemblies published to date. The contig N50 was 13 Mb, scaffold N50 was 55 Mb, and BUSCO completeness was 97.9%, accounting for 92.8% of the predicted genome. Genome annotation revealed 44,588 gene models with high confidence and 52.81% repetitive elements in red clover genome. Based on a comparison of genome annotation results, red clover was closely related to Trifolium medium and distantly related to Glycine max, Vigna radiata, Medicago truncatula, and Cicer arietinum among legumes. Analyses of gene family expansions and contractions and forward gene selection revealed gene families and genes related to environmental stress resistance and energy metabolism. CONCLUSIONS: We report a high-quality de novo genome assembly for the red clover at the chromosome level, with a substantial improvement in assembly quality over those of previously published red clover genomes. These annotated gene models can provide an important resource for molecular genetic breeding and legume evolution studies. Furthermore, we analyzed the evolutionary relationships among red clover and closely related species, providing a basis for evolutionary studies of clover leaf and legumes, genomics analyses of forage grass, the improvement of agronomic traits.

Genomic characterization and expression analysis of TCP transcription factors in Setaria italica and Setaria viridis.

The plant-specific TCP transcription factor plays important roles in plant development and environment adaptation. Setaria italica and Setaria viridis, the C4 model plants, can grow on drought or arid soils. However, there is no systematic information about the genomic dissection and the expression of Setaria TCP genes. A total of 22 TCP genes were both identified from S. italica and S. viridis genomes. They all contained bHLH domain and were grouped into three main clades (PCF, CIN, and CYC/TB1). The TCP genes in the same clades shared similar gene structures. Cis-element in the TCP promoter regions were analyzed and associated with hormones and stress responsiveness. Ten TCP genes were predicted to be targets of miRNA319. Moreover, gene ontology analysis indicated three SiTCP and three SvTCP genes were involved in the regulation of shoot development, and SiTCP16/SvTCP16 were clustered together with tillering controlling gene TB1. The TCP genes were differentially expressed in the organs, but SiTCP/SvTCP orthologs shared similar expression patterns. Ten SiTCP members were downregulated under drought or salinity stresses, indicating they may play regulatory roles in abiotic stresses. The study provides detailed information regarding Setaria TCP genes, providing the theoretical basis for agricultural applications.

High-quality chromosome-scale de novo assembly of the Paspalum notatum 'Flugge' genome.

BACKGROUND: Paspalum notatum 'Flugge' is a diploid with 20 chromosomes (2n = 20) multi-purpose subtropical herb native to South America and has a high ecological significance. It is currently widely planted in tropical and subtropical regions. Despite the gene pool of P. notatum 'Flugge' being unearthed to a large extent in the past decade, no details about the genomic information of relevant species in Paspalum have been reported. In this study, the complete genome information of P. notatum was established and annotated through sequencing and de novo assembly of its genome. RESULTS: The latest PacBio third-generation HiFi assembly and sequencing revealed that the genome size of P. notatum 'Flugge' is 541 M. The assembly result is the higher index among the genomes of the gramineous family published so far, with a contig N50 = 52Mbp, scaffold N50 = 49Mbp, and BUSCOs = 98.1%, accounting for 98.5% of the estimated genome. Genome annotation revealed 36,511 high-confidence gene models, thus providing an important resource for future molecular breeding and evolutionary research. A comparison of the genome annotation results of P. notatum 'Flugge' with other closely related species revealed that it had a close relationship with Zea mays but not close compared to Brachypodium distachyon, Setaria viridis, Oryza sativa, Puccinellia tenuiflora, Echinochloa crusgalli. An analysis of the expansion and contraction of gene families suggested that P. notatum 'Flugge' contains gene families associated with environmental resistance, increased reproductive ability, and molecular evolution, which explained its excellent agronomic traits. CONCLUSION: This study is the first to report the high-quality chromosome-scale-based genome of P. notatum 'Flugge' assembled using the latest PacBio third-generation HiFi sequencing reads. The study provides an excellent genetic resource bank for gramineous crops and invaluable perspectives regarding the evolution of gramineous plants.

Change of vitamin D status and all-cause mortality among Chinese older adults: a population-based cohort study.

BACKGROUND: The association of vitamin D with all-cause mortality remains controversial and longitudinal evidence exploring the potential effects of change in vitamin D status is limited in the oldest old (aged ≥ 80 years old). We aimed to study the relationship between vitamin D change and all-cause mortality among older Chinese adults including the oldest old. METHODS: The data of Chinese Longitudinal and Health Longevity Study in 2012 and 2014 wave was used for baseline data. Mortality was assessed in the subsequent 2018 survey waves. Cox proportional hazard regression models were used to calculate hazard ratios (HRs) and 95% confidence interval (CI) of all-cause mortality related to vitamin D change, including maintaining deficiency or no deficiency, deficiency to no deficiency, and no deficiency to deficiency, using below 50 nmol/L as definition of deficiency. RESULTS: The mean age of the total 1362 participants was 84.4 ± 12.1(60-113) years. The prevalence of vitamin D deficiency was 67.5% and 68.4% in 2012 and 2014 wave respectively, and significantly differed by sex and age at baseline. Cox regression showed that participants with deficiency to no deficiency and maintaining no deficiency of vitamin D status had decreased HR for all-cause mortality, compared to the maintaining deficiency group. The HRs for mortality were 0.70(95%CI: 0.50-0.96, p = 0.028) and 0.47(95%CI: 0.33-0.68, p < 0.001) respectively in the adjusted model. Also, females and the oldest old had a greatest reduction in mortality risk. And no significant difference in mortality in the no deficiency to deficiency group. CONCLUSIONS: Not only maintaining no deficiency, but also the change from deficiency to no deficiency of vitamin D status were associated with lower risk of all-cause mortality, especially in the female and oldest-old participants initially with low vitamin D level.

Effects of a prolonged diet regimen on autophagic function in rat islets with aging.

The prevalence of type 2 diabetes increases with age-associated increased susceptibility of islet ß-cells and altered dietary patterns, in part because of insufficient compensation of ß-cell functional mass in the face of increasing insulin resistance. However, the underlying mechanisms have not been fully elucidated. In the present study, we investigated the effects of a long-term calorie-restricted (CR) or high-fat (HF) diet compared to a normal ad libitum diet on ß-cell structure-function relationships and autophagy in the islets of 3- and 24-month-old Fischer 344 rats. Aging and the HF diet decreased the ß-cell-to-islet area ratio, disorganized the islet structure, and increased the expression of senescence markers. Aging and the long-term HF diet also decreased autophagy-related proteins, which suggests compromised autophagic function. These findings were further corroborated by increased p62 accumulation and polyubiquitin aggregates observed with aging and the HF diet intervention; these are cardinal markers of attenuated autophagic function. It is important to note that the 24-month-old rats maintained on the CR diet closely mimicked the 3-month-old rats, which indicates that a long-term CR diet can delay islet aging and prevent the decline in the autophagic function of islets during the aging process. Taken together, our results indicate an autophagy-dependent mechanism responsible for islet function in older people or those with altered dietary patterns and lay the foundations for future research leading to novel therapeutic strategies for treating diabetes.

Integrative analysis of the metabolome and transcriptome reveal the phosphate deficiency response pathways of alfalfa.

Understanding the mechanisms underlying the responses to inorganic phosphate (Pi) deficiency in alfalfa will help enhance Pi acquisition efficiency and the sustainable use of phosphorous resources. Integrated global metabolomic and transcriptomic analyses of mid-vegetative alfalfa seedlings under 12-day Pi deficiency were conducted. Limited seedling growth were found, including 13.24%, 16.85% and 33.36% decreases in height, root length and photosynthesis, and a 24.10% increase in root-to-shoot ratio on day 12. A total of 322 and 448 differentially abundant metabolites and 1199 and 1061 differentially expressed genes were identified in roots and shoots. Increased (>3.68-fold) inorganic phosphate transporter 1;4 and SPX proteins levels in the roots (>2.15-fold) and shoots (>2.50-fold) were related to Pi absorption and translocation. The levels of phospholipids and Pi-binding carbohydrates and nucleosides were decreased, while those of phosphatases and pyrophosphatases in whole seedlings were induced under reduced Pi. In addition, nitrogen assimilation was affected by inhibiting high-affinity nitrate transporters (NRT2.1 and NRT3.1), and nitrate reductase. Increased delphinidin-3-glucoside might contribute to the gray-green leaves induced by Pi limitation. Stress-induced MYB, WRKY and ERF transcription factors were identified. The responses of alfalfa to Pi deficiency were summarized as local systemic signaling pathways, including root growth, stress-related responses consisting of enzymatic and nonenzymatic systems, and hormone signaling and systemic signaling pathways including Pi recycling and Pi sensing in the whole plant, as well as Pi recovery, and nitrate and metal absorption in the roots. This study provides important information on the molecular mechanism of the response to Pi deficiency in alfalfa.

Genomic Insight into the Antimicrobial Resistance of Streptococcus Suis - Six Countries, 2011-2019.

WHAT IS ALREADY KNOWN ON THIS TOPIC?: Streptococcus suis (S. suis) is a zoonotic pathogen causing disease in humans and animals, and the emergence of its increased resistance to antimicrobial agents has become a significant challenge in many countries. WHAT IS ADDED BY THIS REPORT?: Using whole genome sequencing data to accurately predict antimicrobial resistance determinants, it was found that the prevalence of antimicrobial resistance genes was higher in the pig isolates of S. suis than in the human isolates and that the prevalence of these genes varied with serotype. WHAT ARE THE IMPLICATIONS FOR PUBLIC HEALTH PRACTICE?: The data regarding S. suis antimicrobial resistance will help guide rational drug use in the clinic to better protect the health of humans and animals.

De novo hydroponics system efficiency for the cuttings of alfalfa (Medicago sativa L.).

The legume plant alfalfa (Medicago sativa L.) is a widely cultivated perennial forage due to its high protein content, palatability, and strong adaptability to diverse agro-ecological zones. Alfalfa is a self-incompatible cross-pollinated autotetraploid species with tetrasomic inheritance. Therefore, maintaining excellent traits through seed reproduction is a prime challenge in alfalfa. However, the cutting propagation technology could enable consistent multiplication of quality plants that are genetically identical to the parent plant. The current study aimed to develop a simple, cost-effective, reproducible, and efficient hydroponic cutting method to preserve alfalfa plants and for molecular research. In this study, alfalfa landrace 'Wudi' was grown in hydroponics for 30 days and used as source material for cuttings. The top, middle and bottom sections of its stem were used as cuttings. The rooting rate, root length, and stem height of the different stem sections were compared to determine the best segment for alfalfa propagation in four nutrient treatments (HM, HM + 1/500H, HM + 1/1000H and d HM + 1/2000H). After 21 days of culture, the rooting rates of all the three stem types under four cutting nutrient solutions were above 78%. The rooting rate of the middle and bottom parts in HM + 1/1000 H and HM + 1/2000 H nutrient solutions reached more than 93%, with a higher health survey score (> 4.70). In conclusion, this study developed a de novo cutting propagation method that can be used to conserve and propagate germplasm in breeding programs and research. This method is a new report on the cutting propagation of alfalfa by hydroponics, which could supplement the existing cutting propagation methods.

Comprehensive analysis of coding sequence architecture features and gene expression in Arachis duranensis.

Coding sequence (CDS) architecture affects gene expression levels in organisms. Codon optimization can increase the gene expression level. Therefore, understanding codon usage patterns has important implications for research on genetic engineering and exogenous gene expression. To date, the codon usage patterns of many model plants have been analyzed. However, the relationship between CDS architecture and gene expression in Arachis duranensis remains poorly understood. According to the results of genome sequencing, A. duranensis has many resistant genes that can be used to improve the cultivated peanut. In this study, bioinformatic approaches were used to estimate A. duranensis CDS architectures, including frequency of the optimal codon (Fop), polypeptide length and GC contents at the first (GC1), second (GC2) and third (GC3) codon positions. In addition, Arachis RNA-seq datasets were downloaded from PeanutBase. The relationships between gene expression and CDS architecture were assessed both under normal growth as well as nematode and drought stress conditions. A total of 26 codons with high frequency were identified, which preferentially ended with A or T in A. duranensis CDSs under the above-mentioned three conditions. A similar CDS architecture was found in differentially expressed genes (DEGs) under nematode and drought stresses. The GC1 content differed between DEGs and non-differentially expressed genes (NDEGs) under both drought and nematode stresses. The expression levels of DEGs were affected by different CDS architectures compared with NDEGs under drought stress. In addition, no correlation was found between differential gene expression and CDS architecture neither under nematode nor under drought stress. These results aid the understanding of gene expression in A. duranensis.

Characterization of Two New brown midrib1 Mutations From an EMS-Mutagenic Maize Population for Lignocellulosic Biomass Utilization.

Gene mutations linked to lignin biosynthesis are responsible for the brown midrib (bm) phenotypes. The bm mutants have a brown-reddish midrib associated with changes in lignin content and composition. Maize bm1 is caused by a mutation of the cinnamyl alcohol dehydrogenase gene ZmCAD2. Here, we generated two new bm1 mutant alleles (bm1-E1 and bm1-E2) through EMS mutagenesis, which contained a single nucleotide mutation (Zmcad2-1 and Zmcad2-2). The corresponding proteins, ZmCAD2-1 and ZmCAD2-2 were modified with Cys103Ser and Gly185Asp, which resulted in no enzymatic activity in vitro. Sequence alignment showed that CAD proteins have high similarity across plants and that Cys103 and Gly185 are conserved in higher plants. The lack of enzymatic activity when Cys103 was replaced for other amino acids indicates that Cys103 is required for its enzyme activity. Enzymatic activity of proteins encoded by CAD genes in bm1-E plants is 23-98% lower than in the wild type, which leads to lower lignin content and different lignin composition. The bm1-E mutants have higher saccharification efficiency in maize and could therefore provide new and promising breeding resources in the future.

Prevalence of pathogens harbouring mobile antimicrobial resistance genes and virulence factors in retail beef and mutton.

Food safety is always a global issue, due to the increased dissemination of antimicrobial resistance and food poisoning related to foodborne bacterial pathogens. The purpose of this study was to assess the risk of potential foodborne bacteria of beef and mutton in retail stores. A total of 134 samples were collected from 24 local markets in Beijing, including raw and cooked beef or mutton, as well as samples derived from the corresponding environment and human beings. We obtained 674 isolates, of which Klebsiella spp. and Staphylococcus spp. were the dominant bacterial species in the meat samples and the environmental samples, respectively. Additionally, environmental bacteria are common in samples from different sources. Based on the results of antimicrobial sensitivity testing, resistance to tetracycline (with a resistance rate of 47.40%), amoxicillin + clavulanate (47.13%) and erythromycin (28.03%) were the major resistant phenotypes. According to the whole genome analysis, the extended spectrum beta-lactamase genes harboured by two K. pneumoniae strains isolated from cooked and raw beef were located on mobile elements. The major toxin genes of Bacillus cereus and adhesion- or invasion-related virulence factors were also shared among isolates from different sources. These factors pose potential risks to public health and need attention.