Posterior open wound healing in immediate implant placement using reactive soft tissue versus absorbable collagen sponge: a retrospective cohort study

The soft and hard tissue healing of open wounds in immediate implant placement are yet to be explored. The aim of this study was to compare the clinical outcomes of open wound healing using reactive soft tissue (RST) and absorbable collagen sponge (ACS). Forty implants placed immediately in posterior sockets were included; autologous RST was used in 20 and ACS substitute was used in 20. Soft tissue healing was primarily assessed through a novel scoring system and the evaluation of gingival recession. The horizontal bone width (HBW) and interproximal marginal bone level (MBL) were measured on radiographs to observe the hard tissue healing. No significant difference in total soft tissue healing score was observed at 2 weeks postoperatively. Notably, the ACS group showed better tissue colour (P = 0.016) but worse fibrous repair (P = 0.043) scores than the RST group. Gingival recession levels were comparable in the two groups, both before tooth extraction and after placement of the restoration. Regarding hard tissue, HBW and MBL changes showed no intergroup differences. Within the limitations of this study, both RST and ACS seemed effective for open wound closure, achieving ideal soft and hard tissue healing in immediate implant placement.

Simplified integration of optimal self-management behaviors is associated with improved HbA1c in patients with type 1 diabetes

PURPOSE

Living with type 1 diabetes requires burdensome and complex daily diabetes self-management behaviors. This study aimed to determine the association between integrated behavior performance and HbA1c, while identifying the behavior with the most significant impact on HbA1c.

METHODS

A simple and feasible questionnaire was used to collect diabetes self-management behavior in patients with type 1 diabetes (n = 904). We assessed six dimensions of behavior performance: continuous glucose monitor (CGM) usage, frequent glucose testing, insulin pump usage, carbohydrate counting application, adjustment of insulin doses, and usage of apps for diabetes management. We evaluated the association between these behaviors and HbA1c.

RESULTS

In total, 21.3% of patients performed none of the allotted behavior, while 28.5% of patients had a total behavior score of 3 or more. 63.6% of patients with a behavior score ≥ 3 achieved HbA1c goal, contrasting with only 30.4% of patients with a behavior score of 0-1. There was a mean 0.54% ± 0.05% decrease in HbA1c for each 1-unit increase in total behavior score after adjustment for age, family education and diabetes duration. Each behavior was independently correlated with a lower HbA1c level, with CGM having the most significant effect on HbA1c levels.

CONCLUSIONS

Six optimal self-management behaviors, especially CGM usage, were associated with improved glycemic control, emphasizing the feasibility of implementing a simplified version of DSMES in the routine clinical care.

REGISTRATION NUMBER

ClinicalTrials.gov Identifier: NCT03610984.

Constitutive expression of apple endo-POLYGALACTURONASE1 in fruit induces early maturation, alters skin structure and accelerates softening

During fruit ripening, polygalacturonases (PGs) are key contributors to the softening process in many species. Apple is a crisp fruit that normally exhibits only minor changes to cell walls and limited fruit softening. Here, we explore the effects of PG overexpression during fruit development using transgenic apple lines overexpressing the ripening-related endo-POLYGALACTURONASE1 gene. MdPG1-overexpressing (PGox) fruit displayed early maturation/ripening with black seeds, conversion of starch to sugars and ethylene production occurring by 80 days after pollination (DAP). PGox fruit exhibited a striking, white-skinned phenotype that was evident from 60 DAP and most likely resulted from increased air spaces and separation of cells in the hypodermis due to degradation of the middle lamellae. Irregularities in the integrity of the epidermis and cuticle were also observed. By 120 DAP, PGox fruit cracked and showed lenticel-associated russeting. Increased cuticular permeability was associated with microcracks in the cuticle around lenticels and was correlated with reduced cortical firmness at all time points and extensive post-harvest water loss from the fruit, resulting in premature shrivelling. Transcriptomic analysis suggested that early maturation was associated with upregulation of genes involved in stress responses, and overexpression of MdPG1 also altered the expression of genes involved in cell wall metabolism (e.g. β-galactosidase, MD15G1221000) and ethylene biosynthesis (e.g. ACC synthase, MD14G1111500). The results show that upregulation of PG not only has dramatic effects on the structure of the fruit outer cell layers, indirectly affecting water status and turgor, but also has unexpected consequences for fruit development.

[The life and works of Li Shouxian, a medical doctor in the Qing Dynasty]

Li Shouxian, styled as Shanshu, was a medical doctor in the Qing Dynasty. His work Zhenjiu Yixue (Easy Study of Acupuncture and Moxibustion) has numerous versions, with the most refined one being the self-engraved edition from the third year of Jiaqing's reign, housed in the Jilin Province Library. While most content of the book was drawn from Zhenjiu Dacheng (Great Compendium of Acupuncture and Moxibustion), Li's condensation and arrangement of the material achieved the purpose of making it simple and easy to learn. The book has been widely spread and holds certain academic and historical value. This paper makes a textual research on Li's life, family, and his works, clarifies the content, structure and origin of the version of Zhenjiu Yixue and corrects errors in the version records of this book in the General Catalogue of Chinese Ancient Medical Books.

A multiplexed plant-animal SNP array for selective breeding and species conservation applications

Reliable and high-throughput genotyping platforms are of immense importance for identifying and dissecting genomic regions controlling important phenotypes, supporting selection processes in breeding programs, and managing wild populations and germplasm collections. Amongst available genotyping tools, single nucleotide polymorphism arrays have been shown to be comparatively easy to use and generate highly accurate genotypic data. Single-species arrays are the most commonly used type so far; however, some multi-species arrays have been developed for closely related species that share single nucleotide polymorphism markers, exploiting inter-species cross-amplification. In this study, the suitability of a multiplexed plant-animal single nucleotide polymorphism array, including both closely and distantly related species, was explored. The performance of the single nucleotide polymorphism array across species for diverse applications, ranging from intra-species diversity assessments to parentage analysis, was assessed. Moreover, the value of genotyping pooled DNA of distantly related species on the single nucleotide polymorphism array as a technique to further reduce costs was evaluated. Single nucleotide polymorphism performance was generally high, and species-specific single nucleotide polymorphisms proved suitable for diverse applications. The multi-species single nucleotide polymorphism array approach reported here could be transferred to other species to achieve cost savings resulting from the increased throughput when several projects use the same array, and the pooling technique adds another highly promising advancement to additionally decrease genotyping costs by half.

[Application of the Chinese Expert Consensus on Diabetes Classification in clinical practice]

Objective: To evaluate the diagnostic for classification of newly diagnosed diabetes patients and assess the application of the screening tests recommended by the 2022 Chinese Expert Consensus on Diabetes Classification. Methods: Retrospective case series study. The data from the electronic medical record system of patients with new-onset diabetes mellitus (within 1 year of disease onset) who attending the Diabetes Specialist Outpatient Clinic at the Second Xiangya Hospital of Central South University from January 1, 2018 to December 31, 2021 were collected for the analysis. Based on the consensus, patients were categorized according their age of onset, body mass index (BMI), and suspicion of type 1 diabetes mellitus (T1DM). The chi-square statistic was used to compare key classifier indicators, including C-peptide, islet autoantibodies, and genetic markers, in the subgroups. The diagnosis in suspected T1DM patients was also evaluated. The screening strategy recommended in the consensus was further assessed using a logistic regression model and the area under the receiver-operating curve (AUC). Results: A total of 3 384 patients with new-onset diabetes were included. The average age of disease onset was (46.3±13.9) years, and 61.0% (2 065/3 384) of the patients were male. The proportions of patients who completed C-peptide and glutamic acid decarboxylase antibody (GADA) tests were 36.6% (1 238/3 384) and 37.5% (1 269/3 384), respectively. There were no significant differences in C-peptide test results among the subgroups (all P>0.05). In contrast, the GADA detection rate was higher in patients with young age of onset (<30 years old), in those who were non-obese (BMI<24 kg/m2), and in those clinically suspected of T1DM (all P<0.05). According to the diagnostic pathway proposed by the consensus, only 57.4% (1 941/3 384) of patients could be subtyped. For a definitive diagnosis, the remaining patients needed completion of C-peptide, islet autoantibody, genetic testing, or follow-up. Furthermore, among patients with clinical features of suspected T1DM, the antibody positivity rate was higher than in non-suspected T1DM patients [24.5% (154/628) vs. 7.1% (46/646), P<0.001]. When the clinical features of suspected T1DM defined in the consensus were taken as independent variables and antibody positivity was considered the outcome variable in the logistic regression model, young onset, non-obese onset, and ketosis onset could enter the model. Based on AUC analysis, the accuracy of the diagnostic model was 0.77 (95%CI 0.73-0.81), suggesting that the clinical features of suspected T1DM in the consensus have good clinical diagnostic value for this patient subgroup. Conclusions: There was a significant discrepancy between the clinical practice of diabetes classification and the process recommended by the consensus, which was specifically reflected in the low proportions of both subtyping indicator testing and definitively subtyped diabetes patients. Attention should be pay to the classification diagnosis process proposed in the consensus and the clinical detection rate of key diabetes subtyping indicators such as C-peptide and islet autoantibodies for diabetes classification should be improved. Noteworthy, the screening strategy for T1DM proposed by the consensus showed good clinical application value.

Multi-omics analysis reveals the mechanism of bHLH130 responding to low-nitrogen stress of apple rootstock

Nitrogen is critical for plant growth and development. With the increase of nitrogen fertilizer application, nitrogen use efficiency decreases, resulting in wasted resources. In apple (Malus domestica) rootstocks, the potential molecular mechanism for improving nitrogen uptake efficiency to alleviate low-nitrogen stress remains unclear. We utilized multi-omics approaches to investigate the mechanism of nitrogen uptake in two apple rootstocks with different responses to nitrogen stress, Malus hupehensis and Malus sieversii. Under low-nitrogen stress, Malus sieversii showed higher efficiency in nitrogen uptake. Multi-omics analysis revealed substantial differences in the expression of genes involved in flavonoid and lignin synthesis pathways between the two materials, which were related to the corresponding metabolites. We discovered that basic helix-loop-helix 130 (bHLH130) transcription factor was highly negatively associated with the flavonoid biosynthetic pathway. bHLH130 may directly bind to the chalcone synthase gene (CHS) promoter and inhibit its expression. Overexpressing CHS increased flavonoid accumulation and nitrogen uptake. Inhibiting bHLH130 increased flavonoid biosynthesis while decreasing lignin accumulation, thus improving nitrogen uptake efficiency. These findings revealed the molecular mechanism by which bHLH130 regulates flavonoid and lignin biosyntheses in apple rootstocks under low-nitrogen stress.

Development and initial results of 320 GHz interferometer system in Heliotron J

A new 320 GHz solid-state source interferometer is installed in the Heliotron J helical device to explore the physics of high-density plasmas (ne > 2-3 × 10¹⁹ m^-3, typically) realized with advanced fueling techniques. This interferometry system is of the Michelson type and is based on the heterodyne principle, with two independent solid-state sources that can deliver an output power of up to 50 mW. A high time resolution measurement of <1 µs can be derived by tuning the frequency of one source in the frequency range of 312-324 GHz on the new system, which can realize the fluctuation measurement. We successfully measured the line-averaged electron density in high-density plasma experiments. The measured density agreed well with a microwave interferometer measurement using a different viewing chord, demonstrating that the new system can be used for routine diagnostics of electron density in Heliotron J.

Observed coupling between air mass history, secondary growth of nucleation mode particles and aerosol pollution levels in Beijing

Atmospheric aerosols have significant effects on the climate and on human health. New particle formation (NPF) is globally an important source of aerosols but its relevance especially towards aerosol mass loadings in highly polluted regions is still controversial. In addition, uncertainties remain regarding the processes leading to severe pollution episodes, concerning e.g. the role of atmospheric transport. In this study, we utilize air mass history analysis in combination with different fields related to the intensity of anthropogenic emissions in order to calculate air mass exposure to anthropogenic emissions (AME) prior to their arrival at Beijing, China. The AME is used as a semi-quantitative metric for describing the effect of air mass history on the potential for aerosol formation. We show that NPF events occur in clean air masses, described by low AME. However, increasing AME seems to be required for substantial growth of nucleation mode (diameter < 30 nm) particles, originating either from NPF or direct emissions, into larger mass-relevant sizes. This finding assists in establishing and understanding the connection between small nucleation mode particles, secondary aerosol formation and the development of pollution episodes. We further use the AME, in combination with basic meteorological variables, for developing a simple and easy-to-apply regression model to predict aerosol volume and mass concentrations. Since the model directly only accounts for changes in meteorological conditions, it can also be used to estimate the influence of emission changes on pollution levels. We apply the developed model to briefly investigate the effects of the COVID-19 lockdown on PM_2.5 concentrations in Beijing. While no clear influence directly attributable to the lockdown measures is found, the results are in line with other studies utilizing more widely applied approaches.

The genome of low-chill Chinese plum 'Sanyueli' (Prunus salicina Lindl.) provides insights into the regulation of the chilling requirement of flower buds

Chinese plum (Prunus salicina Lindl.) is a stone fruit that belongs to the Prunus genus and plays an important role in the global production of plum. In this study, we report the genome sequence of the Chinese plum 'Sanyueli', which is known to have a low-chill requirement for flower bud break. The assembled genome size was 282.38 Mb, with a contig N50 of 1.37 Mb. Over 99% of the assembly was anchored to eight pseudochromosomes, with a scaffold N50 of 34.46Mb. A total of 29,708 protein-coding genes were predicted from the genome and 46.85% (132.32 Mb) of the genome was annotated as repetitive sequence. Bud dormancy is influenced by chilling requirement in plum and partly controlled by DORMANCY ASSOCIATED MADS-box (DAM) genes. Six tandemly arrayed PsDAM genes were identified in the assembled genome. Sequence analysis of PsDAM6 in 'Sanyueli' revealed the presence of large insertions in the intron and exon regions. Transcriptome analysis indicated that the expression of PsDAM6 in the dormant flower buds of 'Sanyueli' was significantly lower than that in the dormant flower buds of the high chill requiring 'Furongli' plum. In addition, the expression of PsDAM6 was repressed by chilling treatment. The genome sequence of 'Sanyueli' plum provides a valuable resource for elucidating the molecular mechanisms responsible for the regulation of chilling requirements, and it is also useful for the identification of the genes involved in the control of other important agronomic traits and molecular breeding in plum.

Sleep Duration and Frailty Risk among Older Adults: Evidence from a Retrospective, Population-Based Cohort Study

OBJECTIVES

Frailty and sleep duration complaints are both prevalent and often coexist among older adults. The purpose of this study was to examine the prospective association between sleep duration and frailty risk in a nationally representative cohort study.

DESIGN

Prospective cohort study, ten-year follow-up.

SETTING

Community-based setting in 23 provinces of China.

PARTICIPANTS

A total of 7623 older adults age 65 and over without frailty at baseline were included in the analysis.

MEASUREMENTS

The participants were divided into three groups according to self-reported sleep duration: short (≤6 hours per day), middle (>6 but <10 hours per day) and long (≥10 hours per day). Frailty was measured according to the accumulation of health deficits by the construction of a frailty index of 38 items with 0.25 as the cutoff. A Cox proportional hazard model, a competing risk model and a generalized estimating equation (GEE) model with multiple adjustments were performed to evaluate the association between sleep duration and frailty risk.

RESULTS

During a median follow-up period of 4.4 years (IQR 2.9-9.0), 2531 (33.2%) individuals developed frailty. Compared with participants with middle sleep duration, the risk of frailty was increased among participants with long sleep duration (HR 1.26, 95% CI 1.14-1.38) in the fully adjusted Cox proportional hazard model. However, short sleep duration was insignificantly associated with frailty risk. The competing risk model and the GEE model yielded similar results.

CONCLUSION

Long sleep duration is significantly associated with frailty incidence among older adults even after adjustment for confounding factors. This study provides reinforcing longitudinal evidence for the need to design sleep quality improvement interventions in health care programs to prevent frailty among older adults.

Resolving the developmental distribution patterns of polyphenols and related primary metabolites in bilberry (Vaccinium myrtillus) fruit

Bilberry (Vaccinium myrtillus) is a commercially important wild berry species, which accumulates high amounts of polyphenols, particularly anthocyanins, in the skin and flesh. Whilst a number of studies have quantified these phytochemicals in intact ripe bilberry fruit, we extend the current knowledge by investigating the spatial distribution of anthocyanin-associated polyphenols in fruit tissue, and study their links with primary metabolism during ripening. To address this, we used LC-MS and mass spectrometry imaging to measure and map primary and secondary metabolites in fruit. Correlation analysis showed that five sugars displayed strong positive correlations with anthocyanin accumulation, whereas all amino acids were negatively correlated. The accumulation patterns of polyphenols correlated in fruit skin and flesh, but altered with development. Finally, spatial segmentation analysis revealed that the chemical signatures of ripening first appear at defined regions under the skin and rapidly expand to encompass the entire fruit at the eating-ripe stage.

The Efficacy of Pyrotinib as a Third- or Higher-Line Treatment in HER2-Positive Metastatic Breast Cancer Patients Exposed to Lapatinib Compared to Lapatinib-Naive Patients: A Real-World Study

Background: Pyrotinib is a novel irreversible pan-ErbB receptor tyrosine kinase inhibitor. Evidence of the efficacy of pyrotinib-based treatments for HER2-positive metastatic breast cancer (MBC) in patients exposed to lapatinib is limited.

Methods: Ninety-four patients who received pyrotinib as a third- or higher-line treatment for HER2-positive MBC were included in this retrospective study. The primary and secondary endpoints were overall survival (OS) and progression‐free survival (PFS). Propensity score matching (PSM) and inverse probability of treatment weighting (IPTW) analysis were implemented to balance important patient characteristics between groups.

Results: Thirty (31.9%) patients were pretreated with lapatinib and subsequently received pyrotinib as an anti-HER2 treatment, and 64 (68.1%) patients did not receive this treatment. The OS and PFS indicated a beneficial trend in lapatinib-naive group compared to lapatinib-treated group in either the original cohort (PFS: 9.02 vs 6.36 months, p = 0.05; OS: 20.73 vs 14.35 months, p = 0.08) or the PSM (PFS: 9.02 vs 6.08 months, p = 0.07; OS: 19.07 vs 18.00 months, p = 0.61) or IPTW (PFS: 9.90 vs 6.17 months, p = 0.05; OS: 19.53 vs 15.10 months, p = 0.08) cohorts. Subgroup analyses demonstrated lapatinib treatment-related differences in PFS in the premenopausal subgroup and the no prior trastuzumab treatment subgroup, but no significant differences were observed in OS.

Conclusion: Pyrotinib-based therapy demonstrated promising effects in HER2-positive MBC patients in a real-world study, especially in lapatinib-naive patients, and also some activity in lapatinib-treated patients.

O-044 Chinese Society of Reproductive Medicine 2018 annual report on ART

Objective

To analysis the Chinese ART data in 2018 to provide evidence for utilization of various ART.

Methods

The data of ART of 263 Reproductive Centers in the mainland of China in 2018 were collected by CSRM ART Data Reporting System. A cross-sectional survey of the use of ART technology was performed.

Results

In 2018, the CSRM data reporting system reported 105 610 AID/AIH cycles, 323 938 oocyte retrieval cycles, 147 129 fresh embryo transfer cycles, 254 012 frozen-thawed embryo transfer (FET) cycles, and 204 688 newborn . The patient's age was mainly concentrated in the group &lt;35 years old, accounting for 63.75%. The pregnancy rate and live birth rate of retrieval cycles were 52.49% and 42.23% respectively. The pregnancy rate and live birth rate of FET cycles were 48.71% and 37.68% respectively. Among ART complications, the incidence of moderate to severe OHSS was 1.42%, 0.03% postoperative bleeding, 0.01% postoperative pelvic infection, and 0.04% the other complications. The incidence of birth defects of IVF was 0.87%.

Conclusions

This study uses "CSRM data reporting system" data to describe and analyze the current status of ART, basically consistent with the comparison in 2016 and 2017 that most cycles with good outcomes. However, no clear conclusions have been drawn on the changes of PGD/PGS cycle, all-freeze cycle and comprehensive analysis should be conducted by combining with laboratory data.

Trial registration number:

Study funding:

Funding source:

A chromosome-scale assembly of the bilberry genome identifies a complex locus controlling berry anthocyanin composition

Bilberry (Vaccinium myrtillus L.) belongs to the Vaccinium genus, which includes blueberries (Vaccinium spp.) and cranberry (V. macrocarpon). Unlike its cultivated relatives, bilberry remains largely undomesticated, with berry harvesting almost entirely from the wild. As such, it represents an ideal target for genomic analysis, providing comparisons with the domesticated Vaccinium species. Bilberry is prized for its taste and health properties and has provided essential nutrition for Northern European indigenous populations. It contains high concentrations of phytonutrients, with perhaps the most important being the purple colored anthocyanins, found in both skin and flesh. Here, we present the first bilberry genome assembly, comprising 12 pseudochromosomes assembled using Oxford Nanopore (ONT) and Hi-C Technologies. The pseudochromosomes represent 96.6% complete BUSCO genes with an assessed LAI score of 16.3, showing a high conservation of synteny against the blueberry genome. Kmer analysis showed an unusual third peak, indicating the sequenced samples may have been from two individuals. The alternate alleles were purged so that the final assembly represents only one haplotype. A total of 36,404 genes were annotated after nearly 48% of the assembly was masked to remove repeats. To illustrate the genome quality, we describe the complex MYBA locus, and identify the key regulating MYB genes that determine anthocyanin production. The new bilberry genome builds on the genomic resources and knowledge of Vaccinium species, to help understand the genetics underpinning some of the quality attributes that breeding programs aspire to improve. The high conservation of synteny between bilberry and blueberry genomes means that comparative genome mapping can be applied to transfer knowledge about marker-trait association between these two species, as the loci involved in key characters are orthologous.

Development of a multi-channel 320 GHz interferometer for high density plasma measurement in Heliotron J

We report the development of a new interferometer with two stable, high-power, 320 GHz solid-state sources in Heliotron J. A heterodyne Michelson interferometer optical scheme is employed. Two solid-state oscillators are utilized as sources with a fixed frequency at 320 GHz and frequency tunable of 312-324 GHz. Quasi-optical techniques are used for beam transmission. The beam is elongated in the vertical direction with two off-axis parabolic mirrors and injected into the plasma as a sheet beam for the multi-channel measurement (>5 ch.). Passing through the plasma, the beam is reflected at a retroreflector-array installed at the vacuum chamber wall. The retroreflector-array is a bunch of retroreflector structures, which can suppress the beam refraction caused by plasma without much space inside a vacuum chamber unlike a single retroreflector and can facilitate the system design. The source, detectors, and the retroreflector-array are tested to evaluate their basic performance on a tabletop experiment.

Differential regulation of triterpene biosynthesis induced by an early failure in cuticle formation in apple

Waxy apple cuticles predominantly accumulate ursane-type triterpenes, but the profile shifts with the induction of skin russeting towards lupane-type triterpenes. We previously characterised several key enzymes in the ursane-type and lupane-type triterpene pathways, but this switch in triterpene metabolism associated with loss of cuticle integrity is not fully understood. To analyse the relationship between triterpene biosynthesis and russeting, we used microscopy, RNA-sequencing and metabolite profiling during apple fruit development. We compared the skin of three genetically-close clones of 'Golden Delicious' (with waxy, partially russeted and fully russeted skin). We identified a unique molecular profile for the russet clone, including low transcript abundance of multiple cuticle-specific metabolic pathways in the early stages of fruit development. Using correlation analyses between gene transcription and metabolite concentration we found MYB transcription factors strongly associated with lupane-type triterpene biosynthesis. We showed how their transcription changed with the onset of cuticle cracking followed by russeting and that one factor, MYB66, was able to bind the promoter of the oxidosqualene cyclase OSC5, to drive the production of lupeol derivatives. These results provide insights into the breakdown of cuticle integrity leading to russet and how this drives MYB-regulated changes to triterpene biosynthesis.

Reduced expression of a subunit gene of sucrose non-fermenting 1 related kinase, PpSnRK1βγ, confers flat fruit abortion in peach by regulating sugar and starch metabolism

BACKGROUND

Fruit abortion is a major limiting factor for fruit production. In flat peach, fruit abortion is present in the whole tree of some accessions during early fruit development. However, the physiological factors and genetic mechanism underlying flat fruit abortion remain largely elusive.

RESULTS

In this study, we have revealed that the fertilization process was accomplished and the reduction of sucrose and starch contents might result in flat fruit abortion. By combining association and gene expression analysis, a key candidate gene, PpSnRK1βγ, was identified. A 1.67-Mb inversion co-segregated with flat fruit shape altered the promoter activity of PpSnRK1βγ, resulting in much lower expression in aborting flat peach. Ectopic transformation in tomato and transient overexpression in peach fruit have shown that PpSnRK1βγ could increase sugar and starch contents. Comparative transcriptome analysis further confirmed that PpSnRK1βγ participated in carbohydrate metabolism. Subcellular localization found that PpSnRK1βγ was located in nucleus.

CONCLUSIONS

This study provides a possible reason for flat fruit abortion and identified a critical candidate gene, PpSnRK1βγ, that might be responsible for flat fruit abortion in peach. The results will provide great help in peach breeding and facilitate gene identification for fruit abortion in other plant species.

An integrated peach genome structural variation map uncovers genes associated with fruit traits

BACKGROUND

Genome structural variations (SVs) have been associated with key traits in a wide range of agronomically important species; however, SV profiles of peach and their functional impacts remain largely unexplored.

RESULTS

Here, we present an integrated map of 202,273 SVs from 336 peach genomes. A substantial number of SVs have been selected during peach domestication and improvement, which together affect 2268 genes. Genome-wide association studies of 26 agronomic traits using these SVs identify a number of candidate causal variants. A 9-bp insertion in Prupe.4G186800, which encodes a NAC transcription factor, is shown to be associated with early fruit maturity, and a 487-bp deletion in the promoter of PpMYB10.1 is associated with flesh color around the stone. In addition, a 1.67 Mb inversion is highly associated with fruit shape, and a gene adjacent to the inversion breakpoint, PpOFP1, regulates flat shape formation.

CONCLUSIONS

The integrated peach SV map and the identified candidate genes and variants represent valuable resources for future genomic research and breeding in peach.

Comparison of contrast-enhanced ultrasound and contrast-enhanced computed tomography for the diagnosis of cervical lymph node metastasis in squamous cell carcinoma of the oral cavity

Early detection of cervical lymph node metastasis (CLNM) from squamous cell carcinoma (SCC) of the oral cavity remains challenging. This prospective study was performed to evaluate the ability of contrast-enhanced ultrasound (CEUS) to detect CLNM from oral cavity SCC. Additionally, its diagnostic value was compared with that of contrast-enhanced computed tomography (CECT). Forty-eight consecutive patients with SCC of the oral cavity were enrolled. All subjects were examined preoperatively with both CEUS and CECT. Subsequently, neck dissections were performed for these patients, and cervical lymph nodes separated from the surgical specimens were assessed histologically. The diagnostic performance of these two examinations was compared based on the results of histopathology. The sensitivity, specificity, accuracy, positive predictive value, negative predictive value, and Youden index for CEUS and CECT were 69.39% vs. 44.90%, 94.71% vs. 97.12%, 89.88%% vs. 87.16%, 75.56% vs. 78.57%, 92.92% vs. 88.21%, and 64.10% vs. 42.02%, respectively. A significant difference was observed in terms of sensitivity (P=0.024) and Youden index (rate difference 22.08%, 95% confidence interval 2.72-41.44%). Therefore, CEUS appears to be a promising diagnostic tool that is superior to CECT for detecting CLNM from SCC of the oral cavity, with a higher sensitivity.

CRISPR-dCas9-mediated knockdown of prtR, an essential gene in Pseudomonas aeruginosa

Pseudomonas aeruginosa is a widely distributed non-fermentative Gram-negative opportunistic pathogen that is often responsible for nosocomial infections. Gene interference is a potentially valuable tool for investigating essential genes in P. aeruginosa. To establish a gene interference platform in P. aeruginosa, CRISPR system was used with an inactive Cas9 protein. The CRISPR-dCas9 system was cloned into pHERD20T, a shuttle vector with arabinose inducible promoter, and was further modified to target a regulatory gene prtR that is essential for the viability of P. aeruginosa. Cells expressing the prtR-targeting CRISPR interference (CRISPRi) showed growth defect in an arabinose dose-dependent manner. A high-throughput RNA sequencing analysis of bacterial cells with or without the CRISPRi-mediated prtR inhibition indicated that prtRis a global regulator affecting multiple biological processes. In conclusion, the CRISPR-dCas9-based gene knockdown system has been successfully implemented in P. aeruginosa and demonstrated to be an effective tool in the investigation of essential or difficult-to-inactivate genes in this species.

Spatiotemporal Modulation of Flavonoid Metabolism in Blueberries

Blueberries are distinguished by their purple-blue fruit color, which develops during ripening and is derived from a characteristic composition of flavonoid-derived anthocyanin pigments. The production of anthocyanins is confined to fruit skin, leaving the colorless fruit flesh devoid of these compounds. By linking accumulation patterns of phenolic metabolites with gene transcription in Northern Highbush (Vaccinium corymbosum) and Rabbiteye (Vaccinium virgatum) blueberry, we investigated factors limiting anthocyanin production in berry flesh. We find that flavonoid production was generally lower in fruit flesh compared with skin and concentrations further declined during maturation. A common set of structural genes was identified across both species, indicating that tissue-specific flavonoid biosynthesis was dependent on co-expression of multiple pathway genes and limited by the phenylpropanoid pathway in combination with CHS, F3H, and ANS as potential pathway bottlenecks. While metabolite concentrations were comparable between the blueberry genotypes when fully ripe, the anthocyanin composition was distinct and depended on the degree of hydroxylation/methoxylation of the anthocyanidin moiety in combination with genotype-specific glycosylation patterns. Co-correlation analysis of phenolic metabolites with pathway structural genes revealed characteristic isoforms of O-methyltransferases and UDP-glucose:flavonoid-3-O-glycosyltransferase that were likely to modulate anthocyanin composition. Finally, we identified candidate transcriptional regulators that were co-expressed with structural genes, including the activators MYBA, MYBPA1, and bHLH2 together with the repressor MYBC2, which suggested an interdependent role in anthocyanin regulation.

The genomic pool of standing structural variation outnumbers single nucleotide polymorphism by threefold in the marine teleost Chrysophrys auratus

Recent studies have highlighted an important role of structural variation (SV) in ecological and evolutionary processes, but few have studied nonmodel species in the wild. As part of our long-term research programme on the nonmodel teleost fish Australasian snapper (Chrysophrys auratus), we aim to build one of the first catalogues of genomic variants (SNPs and indels, and deletions, duplications and inversions) in fishes and evaluate overlap of genomic variants with regions under putative selection (Tajima's D and π), and coding sequences (genes). For this, we analysed six males and six females from three locations in New Zealand and generated a high-resolution genomic variation catalogue. We characterized 20,385 SVs and found they intersected with almost a third of all annotated genes. Together with small indels, SVs account for three times more variation in the genome in terms of bases affected compared to SNPs. We found that a sizeable portion of detected SVs was in the upper and lower genomic regions of Tajima's D and π, indicating that some of these have an effect on the phenotype. Together, these results shed light on the often neglected genomic variation that is produced by SVs and highlights the need to go beyond the mere measure of SNPs when investigating evolutionary processes, such as species diversification and adaptation.

[Characteristics and clinical significance of body composition in gout patients]

Objective: To investigate the characteristics of body composition (BC) in gout patients and its clinical significance. Methods: Consecutive gout patients were recruited between August 2017 and December 2018. Demographic information, clinical characteristics and comorbidities were collected. BC was assessed by bioelectric impedance analysis including body fat percentage (BF%), trunk and limb BF%, appendicular skeletal muscle index. Overfat was defined by BF% ≥25% for male and ≥35% for female. The association between BC and serum uric acid (sUA) was evaluated by multiple linear regression. Results: A total of 362 gout patients were recruited with median age 38 (30, 52) years, 96.1% (348/362) were male. Mean sUA was (551±133) μmol/L. The mean BF% was (25.8±6.4)% with 53.6%(194/362) patients overfat. Male gout patients with overfat showed more affected joints [4(2, 6) vs. 2(2, 5)], higher sUA [(576±126)μmol/L vs. (523±134) μmol/L], higher prevalence of dyslipidemia [70.1%(131/187) vs. 54.0%(87/161)], metabolic syndrome [60.8%(118/187) vs. 28.0%(47/161)], fatty liver [58.2%(113/187) vs. 35.1%(59/161)] and hypertension [44.4%(83/187) vs. 25.5%(41/161)] than male patients with normal fat (all P<0.05). Their BF%, trunk BF% and limb BF% were positively correlated with the numbers of affected joints, sUA, metabolic syndrome, fatty liver, and hypertension, respectively (r=0.154-0.435, all P<0.05). Multivariable linear regression suggested that BF% (β=4.29, P=0.020) and trunk BF% (β=9.11, P=0.007), but not limb BF%, were positively correlated with sUA. Conclusion: Overfat is very common in gout patients. The proportion of trunk fat in male patients is positively correlated with sUA. When assessing obesity in gout patients clinically, body composition analysis should be performed simultaneously.

Probiotics maintain intestinal secretory immunoglobulin A levels in healthy formula-fed infants: a randomised, double-blind, placebo-controlled study

Formula-fed infants are more susceptible to infectious diseases because they lack the maternal immune factors transferred from breast milk, while their own immune system is still immature. As timely probiotic administration was suggested to promote immune system development in formula-fed infants, this study aimed at assessing the safety and the effects of a probiotic supplement (Bifidobacterium infantis R0033, Bifidobacterium bifidum R0071, and Lactobacillus helveticus R0052) on mucosal immune competence and digestive function in formula-fed infants. Healthy infants (3.5-6 months old) were randomised to receive either probiotic- (n=66) or placebo-supplemented (n=66) formula once a day for four weeks. In the probiotics group, faecal secretory immunoglobulin A (SIgA) levels remained similar between visit 2 (baseline; V2) and visit 3 (end-of-treatment; V3), but decreased in the placebo group. Changes in SIgA levels following treatment (log₁₀ΔV3-V2 [95%CI]) between the probiotic and placebo groups were statistically significant (23 ng/dl [-57;102] and -137 ng/dl [-212;-62], respectively (P=0.0044; ANCOVA)). While log₁₀ΔV3-V2 [95%CI] for salivary SIgA levels increased in both groups, this trend was more pronounced in the probiotics than in the placebo group with an increase of 123 ng/dl [9;236] and 37 ng/dL [-72;147], respectively (P=0.2829; ANCOVA). The weekly average number of stools/day was significantly higher in the probiotics group compared to placebo during the last week of treatment for the per protocol population. There was no difference in microbiota composition or anthropometric parameters between groups. No serious adverse event was reported, and all adverse events were mild and unrelated to the product or study. Our results show that formula-fed infants receiving probiotics maintained higher faecal SIgA levels at the end of the four-week treatment period, suggesting a positive effect of probiotics on SIgA production. This study demonstrates the safety of this probiotic formulation in infants. Formula-fed infants may benefit from probiotics supplementation to sustain the development of mucosal immunity.

Genetic and cytological analyses reveal the recombination landscape of a partially differentiated plant sex chromosome in kiwifruit

BACKGROUND

Angiosperm sex chromosomes, where present, are generally recently evolved. The key step in initiating the development of sex chromosomes from autosomes is the establishment of a sex-determining locus within a region of non-recombination. To better understand early sex chromosome evolution, it is important to determine the process by which recombination is suppressed around the sex determining genes. We have used the dioecious angiosperm kiwifruit Actinidia chinensis var. chinensis, which has an active-Y sex chromosome system, to study recombination rates around the sex locus, to better understand key events in the development of sex chromosomes.

RESULTS

We have confirmed the sex-determining region (SDR) in A. chinensis var. chinensis, using a combination of high density genetic mapping and fluorescent in situ hybridisation (FISH) of Bacterial Artificial Chromosomes (BACs) linked to the sex markers onto pachytene chromosomes. The SDR is a subtelomeric non-recombining region adjacent to the nucleolar organiser region (NOR). A region of restricted recombination of around 6 Mbp in size in both male and female maps spans the SDR and covers around a third of chromosome 25.

CONCLUSIONS

As recombination is suppressed over a similar region between X chromosomes and between and X and Y chromosomes, we propose that recombination is suppressed in this region because of the proximity of the NOR and the centromere, with both the NOR and centromere suppressing recombination, and this predates suppressed recombination due to differences between X and Y chromosomes. Such regions of suppressed recombination in the genome provide an opportunity for the evolution of sex chromosomes, if a sex-determining locus develops there or translocates into this region.

Multiple quantitative trait loci contribute to resistance to bacterial canker incited by Pseudomonas syringae pv. actinidiae in kiwifruit (Actinidia chinensis)

Pseudomonas syringae pv. actinidiae (Psa) biovar 3, a virulent, canker-inducing pathogen is an economic threat to the kiwifruit (Actinidia spp.) industry worldwide. The commercially grown diploid (2×) A. chinensis var. chinensis is more susceptible to Psa than tetraploid and hexaploid kiwifruit. However information on the genetic loci modulating Psa resistance in kiwifruit is not available. Here we report mapping of quantitative trait loci (QTLs) regulating resistance to Psa in a diploid kiwifruit population, derived from a cross between an elite Psa-susceptible 'Hort16A' and a resistant male breeding parent P1. Using high-density genetic maps and intensive phenotyping, we identified a single QTL for Psa resistance on Linkage Group (LG) 27 of 'Hort16A' revealing 16-19% phenotypic variance and candidate alleles for susceptibility and resistance at this loci. In addition, six minor QTLs were identified in P1 on distinct LGs, exerting 4-9% variance. Resistance in the F1 population is improved by additive effects from 'Hort16A' and P1 QTLs providing evidence that divergent genetic pathways interact to combat the virulent Psa strain. Two different bioassays further identified new QTLs for tissue-specific responses to Psa. The genetic marker at LG27 QTL was further verified for association with Psa resistance in diploid Actinidia chinensis populations. Transcriptome analysis of Psa-resistant and susceptible genotypes in field revealed hallmarks of basal defense and provided candidate RNA-biomarkers for screening for Psa resistance in greenhouse conditions.

A novel FGFR1-binding peptide attenuates the degeneration of articular cartilage in adult mice

OBJECTIVE

We previously reported that genetic ablation of (Fibroblast Growth Factors Receptors) FGFR1 in knee cartilage attenuates the degeneration of articular cartilage in adult mice, which suggests that FGFR1 is a potential targeting molecule for osteoarthritis (OA). Here, we identified R1-P1, an inhibitory peptide for FGFR1 and investigated its effect on the pathogenesis of OA in mice induced by destabilization of medial meniscus (DMM).

DESIGN

Binding ability between R1-P1 and FGFR1 protein was evaluated by enzyme-linked immuno sorbent assay (ELISA) and molecular docking. Alterations in cartilage were evaluated histologically. The expression levels of molecules associated with articular cartilage homeostasis and FGFR1 signaling were analyzed by quantitative real-time polymerase chain reaction (qRT-PCR), Western blotting and immunohistochemistry (IHC). The chondrocyte apoptosis was detected by terminal-deoxynucleoitidyl transferase mediated nick end labeling (TUNEL) assay.

RESULTS

R1-P1 had highly binding affinities to human FGFR1 protein, and efficiently inhibited extracellular signal-regulated kinase (ERK)1/2 pathway in mouse primary chondrocytes. In addition, R1-P1 attenuated the IL-1β induced significant loss of proteoglycan in full-thickness cartilage tissue from human femur head. Moreover, this peptide can significantly restore the IL-1β mediated loss of proteoglycan and type II collagen (Col II) and attenuate the expression of matrix metalloproteinase-13 (MMP13) in mouse primary chondrocytes. Finally, intra-articular injection of R1-P1 remarkably attenuated the loss of proteoglycan and the destruction of articular cartilage and decreased the expressions of extracellular matrix (ECM) degrading enzymes and apoptosis in articular chondrocytes of mice underwent DMM surgery.

CONCLUSIONS

R1-P1, a novel inhibitory peptide for FGFR1, attenuates the degeneration of articular cartilage in adult mice, which is a potential leading molecule for the treatment of OA.

Phase transitions in a programmable quantum spin glass simulator

Understanding magnetic phases in quantum mechanical systems is one of the essential goals in condensed matter physics, and the advent of prototype quantum simulation hardware has provided new tools for experimentally probing such systems. We report on the experimental realization of a quantum simulation of interacting Ising spins on three-dimensional cubic lattices up to dimensions 8 × 8 × 8 on a D-Wave processor (D-Wave Systems, Burnaby, Canada). The ability to control and read out the state of individual spins provides direct access to several order parameters, which we used to determine the lattice's magnetic phases as well as critical disorder and one of its universal exponents. By tuning the degree of disorder and effective transverse magnetic field, we observed phase transitions between a paramagnetic, an antiferromagnetic, and a spin-glass phase.

A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

Background

Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) ‘Hongyang’ draft genome has 164 Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models.

Results

A second genome of an A. chinensis (genotype Red5) was fully sequenced. This new sequence resulted in a 554.0 Mb assembly with all but 6 Mb assigned to pseudo-chromosomes. Pseudo-chromosomal comparisons showed a considerable number of translocation events have occurred following a whole genome duplication (WGD) event some consistent with centromeric Robertsonian-like translocations. RNA sequencing data from 12 tissues and ab initio analysis informed a genome-wide manual annotation, using the WebApollo tool. In total, 33,044 gene loci represented by 33,123 isoforms were identified, named and tagged for quality of evidential support. Of these 3114 (9.4%) were identical to a protein within ‘Hongyang’ The Kiwifruit Information Resource (KIR v2). Some proportion of the differences will be varietal polymorphisms. However, as most computationally predicted Red5 models required manual re-annotation this proportion is expected to be small. The quality of the new gene models was tested by fully sequencing 550 cloned ‘Hort16A’ cDNAs and comparing with the predicted protein models for Red5 and both the original ‘Hongyang’ assembly and the revised annotation from KIR v2. Only 48.9% and 63.5% of the cDNAs had a match with 90% identity or better to the original and revised ‘Hongyang’ annotation, respectively, compared with 90.9% to the Red5 models.

Conclusions

Our study highlights the need to take a cautious approach to draft genomes and computationally predicted genes. Our use of the manual annotation tool WebApollo facilitated manual checking and correction of gene models enabling improvement of computational prediction. This utility was especially relevant for certain types of gene families such as the EXPANSIN like genes. Finally, this high quality gene set will supply the kiwifruit and general plant community with a new tool for genomics and other comparative analysis.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4656-3) contains supplementary material, which is available to authorized users.