DSNetax: a deep learning species annotation method based on a deep-shallow parallel framework

Microbial community analysis is an important field to study the composition and function of microbial communities. Microbial species annotation is crucial to revealing microorganisms' complex ecological functions in environmental, ecological and host interactions. Currently, widely used methods can suffer from issues such as inaccurate species-level annotations and time and memory constraints, and as sequencing technology advances and sequencing costs decline, microbial species annotation methods with higher quality classification effectiveness become critical. Therefore, we processed 16S rRNA gene sequences into k-mers sets and then used a trained DNABERT model to generate word vectors. We also design a parallel network structure consisting of deep and shallow modules to extract the semantic and detailed features of 16S rRNA gene sequences. Our method can accurately and rapidly classify bacterial sequences at the SILVA database's genus and species level. The database is characterized by long sequence length (1500 base pairs), multiple sequences (428,748 reads) and high similarity. The results show that our method has better performance. The technique is nearly 20% more accurate at the species level than the currently popular naive Bayes-dominated QIIME 2 annotation method, and the top-5 results at the species level differ from BLAST methods by <2%. In summary, our approach combines a multi-module deep learning approach that overcomes the limitations of existing methods, providing an efficient and accurate solution for microbial species labeling and more reliable data support for microbiology research and application.

Genome-wide identification of Avicennia marina aquaporins reveals their role in adaptation to intertidal habitats and their relevance to salt secretion and vivipary

Aquaporins (AQPs) regulate the transport of water and other substrates, aiding plants in adapting to stressful environments. However, the knowledge of AQPs in salt-secreting and viviparous Avicennia marina is limited. In this study, 46 AmAQPs were identified in A. marina genome, and their subcellular localisation and function in transporting H2 O2 and boron were assessed through bioinformatics analysis and yeast transformation. Through analysing their expression patterns via RNAseq and real-time quantitative polymerase chain reaction, we found that most AmAQPs were downregulated in response to salt and tidal flooding. AmPIP (1;1, 1;7, 2;8, 2;9) and AmTIP (1;5, 1;6) as salt-tolerant candidate genes may contribute to salt secretion together with Na+ /H+ antiporters. AmPIP2;1 and AmTIP1;5 were upregulated during tidal flooding and may be regulated by anaerobic-responsive element and ethylene-responsive element cis-elements, aiding in adaptation to tidal inundation. Additionally, we found that the loss of the seed desiccation and dormancy-related TIP3 gene, and the loss of the seed dormancy regulator DOG1 gene, or DOG1 protein lack heme-binding capacity, may be genetic factors contributing to vivipary. Our findings shed light on the role of AQPs in A. marina adaptation to intertidal environments and their relevance to salt secretion and vivipary.

Subzero saline chilling with or without prechilling in icy water improved chilling efficiency and meat tenderness of broiler carcasses

Freshly slaughtered carcasses need to be chilled to improve product quality, meat safety, and processing efficiency. This research investigated the effect of subzero saline chilling (SSC) on broiler carcasses with or without prechilling in icy water. Water immersion chilling at 0.5°C (WIC) or SSC at 4% NaCl/-2.41°C (SSC) was a major chilling step. For the combination of pre- and postchilling, the warm water immersion chilling (WWIC) at 10°C was used as prechilling and the WIC as postchilling (WWIC-WIC), and WIC was used as prechilling and the SSC as postchilling (WIC-SSC). The internal temperature of breast fillets was monitored during chilling. Carcasses in a prechiller were transported to a postchiller when their internal temperature reached 15°C. Chilling was completed when the carcass temperature reached 4.4°C or below, and breast fillets were harvested at 3-h postmortem to measure the pH and sarcomere length. Color (L*, a*, and b*) values were evaluated on both breast skin and skinless breast surfaces. Meat tenderness was evaluated using the breast fillets after overnight storage and cooking to an internal temperature of 76°C. The carcasses in the SSC and WIC-SSC showed shorter chilling times (85-91 min) than those (100-144 min) of WIC and WWIC-WIC. A higher chilling yield was observed for the carcasses in WIC-SSC, and a lower cooking yield was seen for the carcasses in WWIC-WIC than other chilling methods (P < 0.05). The breast fillets of broilers in the SSC and WIC-SSC showed lower shear forces and longer sarcomere length than the WIC and WWIC-WIC. No difference was found for L* and a* values, while lower b* value was observed in the SSC than the other chilling methods (P < 0.05). Based on these results, chilling of broiler carcasses in the SSC (4% NaCl/-2.41°C) with or without prechilling in WIC at 0.5°C significantly improved chilling efficiency and meat tenderness, with minor color changes on carcasses.

Chloroplast genome analysis of three Acanthus species reveal the adaptation of mangrove to intertidal habitats

Acanthus is a distinctive genus that covers three species with different ecological niches including Acanthus mollis (arid terrestrial), Acanthus leucostachyus (damp forest) and Acanthus ilicifolius (coastal intertidal). It is an intriguing question how these species evolved from terrestrial to coastal intertidal. In the present study, we assembled chloroplast genomes of A. ilicifolius, A. leucostachyus and A. mollis, which exhibited typical quadripartite structures. The sizes were 150,758, 154,686 and 150,339 bp that comprised a large single copy (LSC, 82,963, 86,461 and 82,612 bp), a small single copy (SSC, 17,191, 17,511 and 17,019 bp), and a pair of inverted repeats (IRs, 25,302, 25,357 and 25,354 bp), respectively. Gene annotation revealed that A. ilicifolius, A. leucostachyus and A. mollis contained 113, 112 and 108 unique genes, each of which contained 79, 79 and 74 protein-coding genes, 30, 29 and 30 tRNAs, and 4 rRNA genes, respectively. Differential gene analysis revealed plenty of ndhs gene deletions in the terrestrial plant A. mollis. Nucleotide diversity analysis showed that the psbK, ycf1, ndhG, and rpl22 have the highest nucleotide variability. Compared to A. leucostachyus and A. mollis, seven genes in A. ilicifolius underwent positive selection. Among them, the atpF gene showed a strong positive selection throughout terrestrial to marine evolution and was important for adaptation to coastal intertidal habitats. Phylogenetic analysis indicated that A. ilicifolius has a closer genetic relationship with A. leucostachyus than A. mollis which further confirmed the evolutionary direction of Acanthus going from terrestrial to coastal intertidal zones.

In silico analysis of NAC gene family in the mangrove plant Avicennia marina provides clues for adaptation to intertidal habitats

NAC (NAM, ATAF1/2, CUC2) transcription factors (TFs) constitute a plant-specific gene family. It is reported that NAC TFs play important roles in plant growth and developmental processes and in response to biotic/abiotic stresses. Nevertheless, little information is known about the functional and evolutionary characteristics of NAC TFs in mangrove plants, a group of species adapting coastal intertidal habitats. Thus, we conducted a comprehensive investigation for NAC TFs in Avicennia marina, one pioneer species of mangrove plants. We totally identified 142 NAC TFs from the genome of A. marina. Combined with NAC proteins having been functionally characterized in other organisms, we built a phylogenetic tree to infer the function of NAC TFs in A. marina. Gene structure and motif sequence analyses suggest the sequence conservation and transcription regulatory regions-mediated functional diversity. Whole-genome duplication serves as the driver force to the evolution of NAC gene family. Moreover, two pairs of NAC genes were identified as positively selected genes of which AmNAC010/040 may be imposed on less constraint toward neofunctionalization. Quite a few stress/hormone-related responsive elements were found in promoter regions indicating potential response to various external factors. Transcriptome data revealed some NAC TFs were involved in pneumatophore and leaf salt gland development and response to salt, flooding and Cd stresses. Gene co-expression analysis found a few NAC TFs participates in the special biological processes concerned with adaptation to intertidal environment. In summary, this study provides detailed functional and evolutionary information about NAC gene family in mangrove plant A. marina and new perspective for adaptation to intertidal habitats.

Microbial community succession patterns and drivers of Luxiang-flavor Jiupei during long fermentation

Luxiang-flavor Baijiu is the mainstream of Baijiu production and consumption in China, and the microbial composition has a great influence on the flavor and quality of Baijiu. In this study, we combined multi-omics sequencing technology to explore the microbial composition, dynamics and metabolite changes of Luxiang-flavor Jiupei during long fermentation periods. The results showed that based on the interaction between environmental constraints and microorganisms, Jiupei microorganisms formed different ecological niches and functional differentiation, which led to the formation of Jiupei stable core microorganisms. The bacteria were mainly Lactobacillus and Acetobacter, and the fungi were mainly Kazachstani and Issatchenkia. Most bacteria were negatively correlated with temperature, alcohol and acidity, and for the fungi, starch content, reducing sugar content and temperature had the most significant effects on community succession. Macroproteomic analysis revealed that Lactobacillus jinshani had the highest relative content; microbial composition, growth changes and functions were more similar in the pre-fermentation period (0-18 days); microorganisms stabilized in the late fermentation period (24-220 days). The metabolome analysis revealed that the metabolites of the Jiupei changed rapidly from 18 to 32 days of fermentation, with a significant increase in the relative content of amino acids, peptides and analogs and a significant decrease in the relative content of sugars; the metabolites of the Jiupei changed slowly from 32 to 220 days of fermentation, with a stabilization of the content of amino acids, peptides and analogs. This work provides insights into the microbial succession and microbial drivers during the long-term fermentation of Jiupei, which have potential implications for optimizing production and improving the flavor of Baijiu.

PlantPhoneDB: A manually curated pan-plant database of ligand-receptor pairs infers cell-cell communication

Ligand-receptor pairs play important roles in cell-cell communication for multicellular organisms in response to environmental cues. Recently, the emergence of single-cell RNA-sequencing (scRNA-seq) provides unprecedented opportunities to investigate cellular communication based on ligand-receptor expression. However, so far, no reliable ligand-receptor interaction database is available for plant species. In this study, we developed PlantPhoneDB (https://jasonxu.shinyapps.io/PlantPhoneDB/), a pan-plant database comprising a large number of high-confidence ligand-receptor pairs manually curated from seven resources. Also, we developed a PlantPhoneDB R package, which not only provided optional four scoring approaches that calculate interaction scores of ligand-receptor pairs between cell types but also provided visualization functions to present analysis results. At the PlantPhoneDB web interface, the processed datasets and results can be searched, browsed, and downloaded. To uncover novel cell-cell communication events in plants, we applied the PlantPhoneDB R package on GSE121619 dataset to infer significant cell-cell interactions of heat-shocked root cells in Arabidopsis thaliana. As a result, the PlantPhoneDB predicted the actively communicating AT1G28290-AT2G14890 ligand-receptor pair in atrichoblast-cortex cell pair in Arabidopsis thaliana. Importantly, the downstream target genes of this ligand-receptor pair were significantly enriched in the ribosome pathway, which facilitated plants adapting to environmental changes. In conclusion, PlantPhoneDB provided researchers with integrated resources to infer cell-cell communication from scRNA-seq datasets.

The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome

Ethiopian mustard (Brassica carinata) is an ancient crop with remarkable stress resilience and a desirable seed fatty acid profile for biofuel uses. Brassica carinata is one of six Brassica species that share three major genomes from three diploid species (AA, BB, and CC) that spontaneously hybridized in a pairwise manner to form three allotetraploid species (AABB, AACC, and BBCC). Of the genomes of these species, that of B. carinata is the least understood. Here, we report a chromosome scale 1.31-Gbp genome assembly with 156.9-fold sequencing coverage for B. carinata, completing the reference genomes comprising the classic Triangle of U, a classical theory of the evolutionary relationships among these six species. Our assembly provides insights into the hybridization event that led to the current B. carinata genome and the genomic features that gave rise to the superior agronomic traits of B. carinata. Notably, we identified an expansion of transcription factor networks and agronomically important gene families. Completion of the Triangle of U comparative genomics platform has allowed us to examine the dynamics of polyploid evolution and the role of subgenome dominance in the domestication and continuing agronomic improvement of B. carinata and other Brassica species.

[Trueness of 4 three-dimensional facial scanners: an in vitro study]

Objective: To investigate the trueness of 4 three-dimensional (3D) facial scanners and to evaluate the applicability of their clinical use. Methods: An art head model was used as the scanning object, and it was scanned by Handyscan 3D scanner in an enclosed environment with a fixed light source to obtain the reference digital model. Three fixed 3D facial scanners (A: 3dMDface; B: Facego Pro; C: RDS Facescan) and a portable hand-held 3D facial scanner (D: Revopoint POP 2) were used to scan the art head model 10 times, and 10 models of each scan group were obtained. The face of the reference model was divided into 16 regions according to anatomy and muscle distributions in the Geomagic Wrap software with saved boundary curves of whole face and each region. The test models were also divided into 16 regions through the curves above after registered with the reference model through "Best fit" function. The root-mean-square error (RMS) of the complete test models and their segmented regions compared with the reference model and its corresponding regions were calculated by 3D comparison function. The smaller the RMS, the higher the accuracy. One-way ANOVA and SNK post-test were used for statistical analysis. Results: RMS of complete test models scanned by A, B, C, D scanners were (0.295±0.005), (0.216±0.053), (0.059±0.012) and (0.103±0.026) mm (F=123.81, P<0.001), respectively. There was significant difference between any two groups (P<0.05). For each facial region, the group D had the best trueness in nasal region, lip region, left orbital region and right orbital region [RMS were (0.079±0.032), (0.061±0.019), (0.058±0.021), (0.081±0.032) mm, respectively], while the group C had the best trueness in frontal region, left buccal region, right buccal region, left zygomatic region, right zygomatic region, left parotideomasseteric region, right parotideomasseteric region, left temporofacial region, right temporofacial region, mental region, left infraorbital region and right infraorbital region [RMS were (0.039±0.011), (0.034±0.007), (0.033±0.007), (0.066±0.023), (0.038±0.022), (0.070±0.030), (0.067±0.024), (0.063±0.029), (0.045±0.023), (0.063±0.006), (0.039±0.010), (0.046±0.008) mm, respectively]. Conclusions: On the basis of art head model scanning, although the overall average deviation between the scanning model and the reference models obtained by the four kinds of 3D facial scanners were small, the portable handheld 3D facial scanner (D) has better accuracy than the fixed 3D facial scanners (A, B, C) in the orbital area, nasal area, lip area and areas with rich features.

Aging-based molecular classification and score system in ccRCC uncovers distinct prognosis, tumor immunogenicity, and treatment sensitivity

Objective

Aging is a complex biological process and a major risk factor for cancer development. This study was conducted to develop a novel aging-based molecular classification and score system in clear cell renal cell carcinoma (ccRCC).

Methods

Integrative analysis of aging-associated genes was performed among ccRCC patients in the TCGA and E-MTAB-1980 cohorts. In accordance with the transcriptional expression matrix of 173 prognostic aging-associated genes, aging phenotypes were clustered with the consensus clustering approach. The agingScore was generated to quantify aging phenotypes with principal component analysis. Tumor-infiltrating immune cells and the cancer immunity cycle were quantified with the ssGSEA approach. Immunotherapy response was estimated through the TIDE algorithm, and a series of tumor immunogenicity indicators were computed. Drug sensitivity analysis was separately conducted based on the GDSC, CTRP, and PRISM analyses.

Results

Three aging phenotypes were established for ccRCC, with diverse prognosis, clinical features, immune cell infiltration, tumor immunogenicity, immunotherapeutic response, and sensitivity to targeted drugs. The agingScore was developed, which enabled to reliably and independently predict ccRCC prognosis. Low agingScore patients presented more undesirable survival outcomes. Several small molecular compounds and three therapeutic targets, namely, CYP11A1, SAA1, and GRIK4, were determined for the low agingScore patients. Additionally, the high agingScore patients were more likely to respond to immunotherapy.

Conclusion

Overall, our findings introduced an aging-based molecular classification and agingScore system into the risk stratification and treatment decision-making in ccRCC.

[The opportunities and challenges of gynecologic cancer in precision medicine]

In recent years, the diagnosis and treatment of gynecologic cancer have entered a new era with the development of precision medicine. The diagnosis and treatment modes for ovarian cancer, cervical cancer, and endometrial cancer are constantly adjusted. The application of molecular targeted drugs and the progress of surgical concepts and technology have greatly improved the survival of patients with ovarian cancer. Immunotherapy and targeted therapy have become a new hot spot in the treatment of cervical cancer. More clinical research data have been accumulated on the comparison of laparoscopic and open radical hysterectomy in cervical cancer. The surgical management of endometrial cancer has been improved, and molecular diagnostics are increasingly used to guide the diagnosis and treatment of endometrial cancer. Meanwhile, it's necessary to realize the limitations and challenges of precision medicine in gynecologic cancer.

The genome of a mangrove plant, Avicennia marina, provides insights into adaptation to coastal intertidal habitats

Whole-genome duplication, gene family and lineage-specific genes analysis based on high-quality genome reveal the adaptation mechanisms of Avicennia marina to coastal intertidal habitats. Mangrove plants grow in a complex habitat of coastal intertidal zones with high salinity, hypoxia, etc. Therefore, it is an interesting question how mangroves adapt to the unique intertidal environment. Here, we present a chromosome-level genome of the Avicennia marina, a typical true mangrove with a size of 480.43 Mb, contig N50 of 11.33 Mb and 30,956 annotated protein-coding genes. We identified 621 Avicennia-specific genes that are mainly related to flavonoid and lignin biosynthesis, auxin homeostasis and response to abiotic stimulus. We found that A. marina underwent a novel specific whole-genome duplication, which is in line with a brief era of global warming that occurred during the paleocene-eocene maximum. Comparative genomic and transcriptomic analyses outline the distinct evolution and sophisticated regulations of A. marina adaptation to the intertidal environments, including expansion of photosynthesis and oxidative phosphorylation gene families, unique genes and pathways for antibacterial, detoxifying antioxidant and reactive oxygen species scavenging. In addition, we also analyzed salt gland secretion-related genes, and those involved in the red bark-related flavonoid biosynthesis, while significant expansions of key genes such as NHX, 4CL, CHS and CHI. High-quality genomes in future investigations will facilitate the understand of evolution of mangrove and improve breeding.

Genome-wide identification and characterization of aquaporins in mangrove plant Kandelia obovata and its role in response to the intertidal environment

Aquaporins (AQPs) play important roles in plant growth, development and tolerance to environmental stresses. To understand the role of AQPs in the mangrove plant Kandelia obovata, which has the ability to acquire water from seawater, we identified 34 AQPs in the K. obovata genome and analysed their structural features. Phylogenetic analysis revealed that KoAQPs are homologous to AQPs of Populus and Arabidopsis, which are evolutionarily conserved. The key amino acid residues were used to assess water-transport ability. Analysis of cis-acting elements in the promoters indicated that KoAQPs may be stress- and hormone-responsive. Subcellular localization of KoAQPs in yeast showed most KoAQPs function in the membrane system. That transgenic yeast with increased cell volume showed that some KoAQPs have significant water-transport activity, and the substrate sensitivity assay indicates that some KoAQPs can transport H₂ O₂ . The transcriptome data were used to analyze the expression patterns of KoAQPs in different tissues and developing fruits of K. obovata. In addition, real-time quantitative PCR analyses combined transcriptome data showed that KoAQPs have complex responses to environmental factors, including salinity, flooding and cold. Collectively, the transport of water and solutes by KoAQPs contributed to the adaptation of K. obovata to the coastal intertidal environment.

Identification, Characterization and Function of Orphan Genes Among the Current Cucurbitaceae Genomes

Orphan genes (OGs) that are missing identifiable homologs in other lineages may potentially make contributions to a variety of biological functions. The Cucurbitaceae family consists of a wide range of fruit crops of worldwide or local economic significance. To date, very few functional mechanisms of OGs in Cucurbitaceae are known. In this study, we systematically identified the OGs of eight Cucurbitaceae species using a comparative genomics approach. The content of OGs varied widely among the eight Cucurbitaceae species, ranging from 1.63% in chayote to 16.55% in wax gourd. Genetic structure analysis showed that OGs have significantly shorter protein lengths and fewer exons in Cucurbitaceae. The subcellular localizations of OGs were basically the same, with only subtle differences. Except for aggregation in some chromosomal regions, the distribution density of OGs was higher near the telomeres and relatively evenly distributed on the chromosomes. Gene expression analysis revealed that OGs had less abundantly and highly tissue-specific expression. Interestingly, the largest proportion of these OGs was significantly more tissue-specific expressed in the flower than in other tissues, and more detectable expression was found in the male flower. Functional prediction of OGs showed that (1) 18 OGs associated with male sterility in watermelon; (2) 182 OGs associated with flower development in cucumber; (3) 51 OGs associated with environmental adaptation in watermelon; (4) 520 OGs may help with the large fruit size in wax gourd. Our results provide the molecular basis and research direction for some important mechanisms in Cucurbitaceae species and domesticated crops.

Intraventricular pressure gradient: a promising tool to predict the post-infarction chronic congestive heart failure in rats

Funding Acknowledgements

Type of funding sources: None.

Background/Introduction: Congestive heart failure (CHF), the main reason for morbidity and mortality, is considered a serious consequence of myocardial infarction (MI). The use of left ventricular end-diastolic pressure (LVEDP) as a chief indicator of CHF becomes limited because of the possible impairment of cardiac function and induced aortic valve damage during its recording. Echocardiography is the gold standard approach to diagnose structural myocardial dysfunction. However, its ability to predict chronic CHF following MI is still limited. Recently, intraventricular pressure gradient (IVPG) was presented as a non-invasive, highly sensitive preload-independent diastolic function parameter to assess cardiac function, especially during cardiomyopathy. However, there have not been any investigations demonstrating the feasibility of IVPG in the evaluation of post-infarction chronic CHF.

Purpose

This study aimed to investigate the utility of IVPG to assess the heart function in a rat model with chronic CHF following MI with evaluating its capacity to predict these changes.

Methods

Fifty male rats were included. MI was induced via ligation of the left anterior descending artery (LAD) at the level of the atrioventricular junction (MI animals, n = 35). Sham animals were subjected to the same left thoracotomy procedure without LAD ligation (Sham animals, n = 15). Transthoracic conventional echocardiography and colour M-mode echocardiography (CMME) for IVPG were performed in all animals 6 months post-surgery. The next day, animals were anesthetized, ventilated, and euthanized after the recording of hemodynamics. The heart weight, and lung and liver wet-to-dry weight ratios were recorded. J-tree cluster-analysis was performed based on ten echocardiographic variables indicative of CHF.

Results

Based on the cluster analysis, animals were joined into two clusters; CHF+ (n = 22) and named MI/HF+, and CHF- (n = 28) that was joined from sham (n = 15), and MI/HF- (n = 13). MI/HF+ presented the most severe anatomical and echocardiographic changes indicative of CHF with significant reduction of all IVPG indices and impairment of the hemodynamics. The IVPG indices were significantly (P&lt; 0.0001) correlated with the anatomical and echocardiographic findings, LVDP, LVEDP, HR, -dP/dtmin, and Tau. Meanwhile, LVSP was only significantly correlated with apical IVPG (R = 0.677, P = 0.022). dP/dtmax was significantly correlated with total IVPG, basal IVPG, and apical IVPG (R = 0.797, P = 0.017, R = 0.724, P = 0.003, and R = 0.652, P = 0.026 ; respectively). Moreover, total, basal, mid-to-apical, mid-, and apical IVPG were significant (P&lt; 0.0001) predictors of chronic CHF following MI.

Conclusion

Compared to the structural, and functional indices of conventional echocardiography, IVPG derived from CMME could provide a substantial non-invasive tool to diagnose and predict CHF after long-term MI.

Genome-Wide Identification, Characterization and Function Analysis of Lineage-Specific Genes in the Tea Plant Camellia sinensis

Genes that have no homologous sequences with other species are called lineage-specific genes (LSGs), are common in living organisms, and have an important role in the generation of new functions, adaptive evolution and phenotypic alteration of species. Camellia sinensis var. sinensis (CSS) is one of the most widely distributed cultivars for quality green tea production. The rich catechins in tea have antioxidant, free radical elimination, fat loss and cancer prevention potential. To further understand the evolution and utilize the function of LSGs in tea, we performed a comparative genomics approach to identify Camellia-specific genes (CSGs). Our result reveals that 1701 CSGs were identified specific to CSS, accounting for 3.37% of all protein-coding genes. The majority of CSGs (57.08%) were generated by gene duplication, and the time of duplication occurrence coincide with the time of two genome-wide replication (WGD) events that happened in CSS genome. Gene structure analysis revealed that CSGs have shorter gene lengths, fewer exons, higher GC content and higher isoelectric point. Gene expression analysis showed that CSG had more tissue-specific expression compared to evolutionary conserved genes (ECs). Weighted gene co-expression network analysis (WGCNA) showed that 18 CSGs are mainly associated with catechin synthesis-related pathways, including phenylalanine biosynthesis, biosynthesis of amino acids, pentose phosphate pathway, photosynthesis and carbon metabolism. Besides, we found that the expression of three CSGs (CSS0030246, CSS0002298, and CSS0030939) was significantly down-regulated in response to both types of stresses (salt and drought). Our study first systematically identified LSGs in CSS, and comprehensively analyzed the features and potential functions of CSGs. We also identified key candidate genes, which will provide valuable assistance for further studies on catechin synthesis and provide a molecular basis for the excavation of excellent germplasm resources.

Male urethral diverticulum squamous cell carcinoma containing a calculus: a rare entity

Male urethral diverticula with calculi have a low incidence. It is extremely rare when the diverticulum accompanied with carcinoma. We report a case of diverticulum of the male urethra containing giant calculi which developed into squamous cell carcinoma. The patient initially presented with lower urinary tract symptoms and a hard, painless perineal mass. We believe that the process of diagnosis and treatment is of great significance in clinical practice.

[A comparative study of the retroperitoneal cavity established by the modified Hasson in urology]

Objective: To examine the safety and complications of two methods of establishing retroperitoneal cavity in urology. Methods: Totally 83 patients undergoing retroperitoneal laparoscopic surgery in Department of Urology, Shanxi Bethune Hospital from January 2020 to June 2021 were analyzed retrospectively. There were 47 males and 36 females, aged (48.3±11.3) years (range: 35 to 71 years). Forty-three cases in Hasson group(the first Trocar channel was selected at the junction of the 12^th rib and the posterior axillary line or lumbar triangle), 40 cases in modified Hasson group(the first Trocar channel is selected at 1.5 cm above the iliac crest on the mid-axillary line). The t test, χ² test, and Fisher exact test were used to compare the surgical safety indicators and complications of the two groups of patients. Results: There was no statistical difference between the two groups in gender, age, body mass index, waist length, and height (P>0.05). The comparison of safety indicators, included the time from skin incision to establishment of the retroperitoneal cavity and the amount of bleeding from the cavity were statistical difference between the two groups (P<0.05). Compared to that in Hasson group, the time from skin incision to establishment of the abdominal cavity in modified Hasson group was shorter ((8.56±2.64) minutes vs. (5.32±1.36) minutes, t=6.949, P<0.01), the blood loss of establishment was less ((15.32±6.09) ml vs. (9.85±3.55) ml, t=4.951, P<0.01). In terms of complication indicators, the incidence of Trocar hernia and the number of subcutaneous emphysema in modified Hasson group were lower than that in Hasson group (20.9% (9/43) vs. 2.5% (1/40), P=0.015, 18.6% (8/43) vs. 2.5% (1/40), P=0.030). Conclusions: The modified Hasson group is a safe method of establishing retroperitoneal cavity. The technique is simple and fast. It provides urologists with a more effective and easy-to-implement option with fewer complications.

RNA-seq analyses of Marine Medaka (Oryzias melastigma) reveals salinity responsive transcriptomes in the gills and livers

Increasing salinity levels in marine and estuarine ecosystems greatly influence developmental, physiological and molecular activities of inhabiting fauna. Marine medaka (Oryzias melastigma), a euryhaline research model, has extraordinary abilities to survive in a wide range of aquatic salinity. To elucidate how marine medaka copes with salinity differences, the responses of Oryzias melastigma after being transferred to different salt concentrations [0 practical salinity units (psu), 15 psu, 30 psu (control), 45 psu] were studied at developmental, histochemical and transcriptome levels in the gill and liver tissues. A greater number of gills differentially expressed genes (DEG) under 0 psu (609) than 15 psu (157) and 45 psu (312), indicating transcriptomic adjustments in gills were more sensitive to the extreme hypotonic environment. A greater number of livers DEGs were observed in 45 psu (1,664) than 0 psu (87) and L15 psu (512), suggesting that liver was more susceptible to hypertonic environment. Further functional analyses of DEGs showed that gills have a more immediate response, mainly in adjusting ion balance, immune and signal transduction. In contrast, DEGs in livers were involved in protein synthesis and processing. We also identified common DEGs in both gill and liver and found they were mostly involved in osmotic regulation of amino sugar and nucleotide sugar metabolism and steroid biosynthesis. Additionally, salinity stresses showed no significant effects on most developmental and histochemical parameters except increased heartbeat with increasing salinity and decreased glycogen after transferred from stable conditions (30 psu) to other salinity environments. These findings suggested that salinity-stress induced changes in gene expressions could reduce the effects on developmental and histochemical parameters. Overall, this study provides a useful resource for understanding the molecular mechanisms of fish responses to salinity stresses.

[Analysis of the clinical features and prognostic influencing factors of toxic epidermal necrolysis]

Objective: To investigate the clinical features and prognostic influencing factors of toxic epidermal necrolysis (TEN). Methods: A retrospective observational study was conducted. From January 2008 to March 2019, a total of 46 TEN patients who met the inclusion criteria were admitted to Guangdong Provincial People's Hospital. The gender, age, and hospital admission diagnosis of the 46 patients, the category of department admitted of patients complicated with sepsis, death ratio of the sepsis patients with or without treatment history in intensive care unit (ICU)/department of burns and wound repair, and the cause of death of the deceased patients were recorded. Depending on whether complicated with sepsis, the patients were divided into sepsis group (32 cases) and non-sepsis group (14 cases). According to whether died or not, the patients were divided into death group (9 cases) and survival group (37 cases). The specific conditions of suspected pathogenic agents and combined underlying diseases, the abnormality of transaminase/bilirubin, creatinine, and platelet count in blood on admission, and the detection of pathogenic microorganisms and drug resistance during the course of disease of patients were recorded in both sepsis group and non-sepsis group. The gender, age, lesion area, severity of illness score for TEN (SCORTEN) system score, combined underlying diseases on admission, and blood microbial culture positivity, hormone use, and gamma globulin use during the course of disease of patients between sepsis group and non-sepsis group, death group and survival group were compared respectively. Data were statistically analyzed with chi-square test, Fisher's exact probability test, and Mann-Whitney U test. The factors with statistically significant differences between sepsis group and non-sepsis group, death group and survival group were selected for binary multivariate logistic regression analysis, so as to screen the independent risk factors affecting sepsis and death in TEN patients. Results: Of the 46 TEN patients, 30 were male and 16 were female, aged from 8 months to 92.0 years, with 11 cases (23.91%) of epidermolysis bullosa, 9 cases (19.57%) of exfoliative dermatitis, 9 cases (19.57%) of TEN, 7 cases (15.22%) of epidermolysis bullosa, 6 cases (13.04%) of Stevens-Johnson syndrome, and 4 cases (8.70%) of severe drug rash for hospital admission diagnosis. The patients complicated with sepsis were admitted to 11 departments, and the death ratio of patients with treatment history in ICU/department of burns and wound repair was similar to that of patients without such department treatment history (P>0.05). All the deceased patients were complicated with sepsis, which was also the main cause of death. On admission, the suspected pathogenic agents of patients in sepsis group were mainly allopurinol (8 cases) and non-steroidal anti-inflammatory drugs (4 cases), while those in non-sepsis group were allopurinol (3 cases) and psychotropic drugs (3 cases). Patients in sepsis group combined as many as 10 underlying diseases, while those in non-sepsis group combined only 4 underlying diseases. The proportions of patients with increased creatinine (χ²=13.349, P<0.01) and decreased platelet count (P<0.01) in sepsis group were significantly higher than those in non-sepsis group, while the transaminase/bilirubin abnormality was similar to that in non-sepsis group (P>0.05). A wide variety of pathogens were detected in the blood, respiratory tract secretions, and skin secretions of 21 patients in sepsis group, and 14 patients were infected with drug-resistant bacteria; among the 9 strains cultured from the blood samples, 8 were drug-resistant bacteria and 6 were Gram-positive bacteria. In non-sepsis group, pathogens were detected in blood, respiratory tract secretions, and skin secretions of 8 patients, with fewer species, and 6 patients were infected with drug-resistant bacteria. The gender, age, lesion area, blood microbial culture positivity, hormone use, and gamma globulin use of patients in sepsis group were similar to those in non-sepsis group (P>0.05). The proportion of patients combined with underlying diseases (χ²=4.493, P<0.05) and the proportion of patients with SCORTEN system score of 4-6 points (P<0.01) of patients in sepsis group were significantly higher than those in non-sepsis group. The gender, combined underlying diseases, lesion area, blood microbial culture positivity, hormone use, and gamma globulin use of patients were similar between survival group and death group (P>0.05). The proportion of patients with age≥60 years and the proportion of patients with SCORTEN system score of 4-6 points of patients in death group were significantly higher than those in survival group (χ²=4.412, 11.627, P<0.05 or P<0.01). The SCORTEN system score was an independent risk factor affecting sepsis and death in TEN patients (odds ratio=3.025, 2.757, 95% confidence interval=1.352-6.769, 1.244-6.110, P<0.05 or P<0.01). Conclusions: The diagnosis of TEN is difficult on admission. Male population is susceptible to TEN, and allopurinol is the common pathogenic agent. The proportion of patients combined with underlying diseases is high in TEN patients complicated with sepsis, with mainly drug-resistant bacteria and mostly Gram-positive bacteria in blood-borne infections. The deceased patients are older than the survived, and the main cause of death is sepsis. The SCORTEN system score is an independent risk factor affecting sepsis and death in TEN patients.

Identification, characterization and expression analysis of lineage-specific genes within mangrove species Aegiceras corniculatum

Lineage-specific genes (LSGs) are the genes that have no recognizable homology to any sequences in other species, which are important drivers for the generation of new functions, phenotypic changes, and facilitating species adaptation to environment. Aegiceras corniculatum is one of major mangrove plant species adapted to waterlogging and saline conditions, and the exploration of aegiceras-specific genes (ASGs) is important to reveal its adaptation to the harsh environment. Here, we performed a systematic analysis on ASGs, focusing on their sequence characterization, origination and expression patterns. Our results reveal that there are 4823 ASGs in the genome, approximately 11.84% of all protein-coding genes. High proportion (45.78%) of ASGs originate from gene duplication, and the time of gene duplication of ASGs is consistent with the timing of two genome-wide replication (WGD) events that occurred in A. corniculatum, and also coincides with a short period of global warming during the Paleocene-Eocene Maximum (PETM, 55.5 million years ago). Gene structure analysis showed that ASGs have shorter protein lengths, fewer exons, and higher isoelectric point. Expression patterns analysis showed that ASGs had low levels of expression and more tissue-specific expression. Weighted gene co-expression network analysis (WGCNA) revealed that 86 ASGs co-expressed gene modules were primarily involved in pathways related to adversity stress, including plant hormone signal transduction, phenylpropanoid biosynthesis, photosynthesis, peroxisome and pentose phosphate pathway. This study provides a comprehensive analysis of the characteristics and potential functions of ASGs and identifies key candidate genes, which will contribute to the subsequent further investigation of the adaptation of A. corniculatum to intertidal coastal wetland habitats.

[Incidence and risk factors of anastomotic leak after transanal total mesorectal excision in China: a retrospective analysis based on national database]

Objective: Transanal total mesorectal excision (taTME) was a very hot topic in the first few years since its appearance, but now more introspections and controversies on this procedure have emerged. One of the reasons why the Norwegian Ministry of Health stopped taTME was the high incidence of postoperative anastomotic leak. In current study, the incidence and risk factors of anastomotic leak after taTME were analyzed based on the data registered in the Chinese taTME Registry Collaborative (CTRC). Methods: A case-control study was carried out. Between November 15, 2017 and December 31, 2020, clinical data of 1668 patients undergoing taTME procedure registered in the CTRC database from 43 domestic centers were collected retrospectively. After excluding 98 cases without anastomosis and 109 cases without complete postoperative complication data, 1461 patients were finally enrolled for analysis. There were 1036 males (70.9%) and 425 females (29.1%) with mean age of (58.2±15.6) years and mean body mass index of (23.6±3.8) kg/m(2). Anastomotic leak was diagnosed and classified according to the International Study Group of Rectal Cancer (ISREC) criteria. The risk factors associated with postoperative anastomotic leak cases were analyzed. The impact of the cumulative number of taTME surgeries in a single center on the incidence of anastomotic leak was evaluated. As for those centers with the number of taTME surgery ≥ 40 cases, incidence of anastomic leak between 20 cases of taTME surgery in the early and later phases was compared. Results: Of 1461 patients undergoing taTME, 103(7.0%) developed anastomotic leak, including 71 (68.9%) males and 32 (31.1%) females with mean age of (59.0±13.9) years and mean body mass index of (24.5±5.7) kg/m(2). The mean distance between anastomosis site and anal verge was (2.6±1.4) cm. Thirty-nine cases (37.9%) were classified as ISREC grade A, 30 cases (29.1%) as grade B and 34 cases (33.0%) as grade C. Anastomotic leak occurred in 89 cases (7.0%,89/1263) in the laparoscopic taTME group and 14 cases (7.1%, 14/198) in the pure taTME group. Multivariate analysis showed that hand-sewn anastomosis (P=0.004) and the absence of defunctioning stoma (P=0.013) were independently associated with anastomotic leak after taTME. In the 16 centers (37.2%) which performed ≥ 30 taTME surgeries with cumulative number of 1317 taTME surgeries, 86 cases developed anastomotic leak (6.5%, 86/1317). And in the 27 centers which performed less than 30 taTME surgeries with cumulative number of 144 taTME surgeries, 17 cases developed anastomotic leak (11.8%, 17/144). There was significant difference between two kinds of center (χ(2)=5.513, P=0.019). Thirteen centers performed ≥ 40 taTME surgeries. In the early phase (the first 20 cases in each center), 29 cases (11.2%, 29/260) developed anastomotic leak, and in the later phase, 12 cases (4.6%, 12/260) developed anastomotic leak. The difference between the early phase and the later phase was statistically significant (χ(2)=7.652, P=0.006). Conclusion: The incidence of anastomotic leak after taTME may be reduced by using stapler and defunctioning stoma, or by accumulating experience.

Genus-Wide Characterization of Bumblebee Genomes Provides Insights into Their Evolution and Variation in Ecological and Behavioral Traits

Bumblebees are a diverse group of globally important pollinators in natural ecosystems and for agricultural food production. With both eusocial and solitary life-cycle phases, and some social parasite species, they are especially interesting models to understand social evolution, behavior, and ecology. Reports of many species in decline point to pathogen transmission, habitat loss, pesticide usage, and global climate change, as interconnected causes. These threats to bumblebee diversity make our reliance on a handful of well-studied species for agricultural pollination particularly precarious. To broadly sample bumblebee genomic and phenotypic diversity, we de novo sequenced and assembled the genomes of 17 species, representing all 15 subgenera, producing the first genus-wide quantification of genetic and genomic variation potentially underlying key ecological and behavioral traits. The species phylogeny resolves subgenera relationships, whereas incomplete lineage sorting likely drives high levels of gene tree discordance. Five chromosome-level assemblies show a stable 18-chromosome karyotype, with major rearrangements creating 25 chromosomes in social parasites. Differential transposable element activity drives changes in genome sizes, with putative domestications of repetitive sequences influencing gene coding and regulatory potential. Dynamically evolving gene families and signatures of positive selection point to genus-wide variation in processes linked to foraging, diet and metabolism, immunity and detoxification, as well as adaptations for life at high altitudes. Our study reveals how bumblebee genes and genomes have evolved across the Bombus phylogeny and identifies variations potentially linked to key ecological and behavioral traits of these important pollinators.

Role of diesel exhaust particles in the induction of allergic asthma to low doses of soybean

INTRODUCTION

Exposure to environmental pollutants such as diesel exhaust particles (DEP) increases the risk of asthma and asthma exacerbation. However, the exact mechanisms inducing asthma to low doses of allergens remain poorly understood. The present study aimed to analyse the immunomodulatory effect of the inhalation of DEP in a mouse model exposed to non-asthmagenic doses of soybean hull extract (SHE).

MATERIAL AND METHODS

BALB/c ByJ mice were randomly divided into four experimental groups. Two groups received nasal instillations of saline and the other two groups received 3 mg ml-1 SHE during 5 days per week for 3 weeks. One group in each pair also received 150 μg of DEP in the same instillations 3 days per week. SHE-specific IgE levels, oxidative stress, leukocyte pattern and optical projection tomography (OPT) imaging studies were assessed.

RESULTS

Inhalation of SHE and/or DEP increased levels of H2O2 in BAL, while coexposure to SHE and DEP increased SHE-specific IgE levels in serum. Inhalation of SHE alone increased eosinophils, B cells, total and resident monocytes and decreased levels of NK cells, while inhalation of DEP increased neutrophils and decreased total monocytes. Regarding dendritic cells (DC), the inhalation of SHE and/or DEP increased the total population, while the inhalation of SHE alone increased Th2-related DCs (CD11b + Ly6C-) and decreased tolerogenic DCs (CD11b-Ly6C-). However, coexposure to SHE and DEP increased oxidative stress-sensitive DCs (CD11b-Ly6C+) and decreased Th1-related DCs (CD11b + Ly6C+). As regards macrophages, inhalation of SHE and DEP decreased total and alveolar populations. DEP deposition in lung tissue did not differ between groups.

CONCLUSION

Coexposure to DEP activates the asthmatic response to low doses of soy by triggering the immune response and oxidative stress.

Twenty-year changes in mortality rates and underlying causes of death in patients with rheumatoid arthritis-associated interstitial lung disease

Objectives: Despite recent advances in the treatment of rheumatoid arthritis (RA), few population-based studies have assessed the mortality rates and the underlying causes of death (UCDs) among patients with RA and RA-associated interstitial lung disease (RA-ILD). This study evaluated the trends in mortality rates, demographic characteristics, and UCDs among patients with RA-ILD.Method: Using data from death certificates (1999-2018) from the US Centers for Disease Control and Prevention Multiple Cause of Death files, we explored the trends in mortality rates and UCD for patients with RA and RA-ILD. Moreover, we examined the crude and age-standardized mortality rates (ASMRs) for such patients.Results: Among patients with RA or RA-ILD, ASMR variation decreased over 20 years. The ASMR ratio of RA-ILD to RA decreased by 5.84%. The ASMR for RA and RA-ILD stratified by gender or age group also decreased. The change in the ASMR ratio of RA-ILD to RA trended downwards in women and upwards in men. Arthropathies and ILD were the most frequent UCDs for RA-ILD, while arthropathies and ischaemic heart disease were the most frequent UCDs for RA.Conclusions: Although RA and RA-ILD presented a downward trend in mortality, RA combined with ILD may reduce life expectancy. Specifically, the mortality rate for patients with RA-ILD remained relatively stable during the study period when ILD was the UCD, suggesting the need for active prevention, early diagnosis, and effective management of RA-ILD.

Shear stress-induced MMP1 and PDE2A expressions in coronary atherosclerosis

AIM

Biomechanical stress plays an essential role in coronary atherosclerosis (CAS), however, inter-relations between mechanical conditions and gene expressions remain unclear.

METHODS

We constructed finite element model of CAS to map human wall shear stress (WSS). Biopsy aortic tissue samples were obtained from 3 CAS patients. Gene expression pattern in CAS was analyzed by GEO datasets. Immunofluorescence staining and western blot confirmed protein expression and localization.

RESULTS

Peak WSS was significantly increased in the vessel stenosis of CAS at 0.25 s (mean 55.1 Pa). Analyses results of GSE76275 showed matrix metalloproteinases1 (MMP1) and phosphodiesterase-2A (PDE2A) up-regulation in endothelial shear responsiveness, which was further validated and localized in vascular endothelial cells, smooth muscle cells and other cells by double immunofluorescence staining. Western blotting assay demonstrated up-regulation of MMP1 and PDE2A expression dependent on the WSS.

CONCLUSIONS

MMP1 and PDE2A up-regulations rely on increased WSS in development and risk of CAS, suggesting that their elevation may be potential target for diagnosis and treatment (Fig. 3, Ref. 28).

Chromosome-level assembly of the mangrove plant Aegiceras corniculatum genome generated through Illumina, PacBio and Hi-C sequencing technologies

Aegiceras corniculatum is a major mangrove plant species adapted to waterlogging and saline conditions, grows in the coastal intertidal zone of tropical and subtropical regions. Here, we present a chromosome-level genome assembly of A. corniculatum by incorporating PacBio long-read sequencing and Hi-C technology. The results showed that the PacBio draft genome size is 906.63 Mb. Hi-C scaffolding anchored 885.06 Mb contigs (97.62% of draft assembly) onto 24 pseudochromosomes. The contig N50 and scaffold N50 were 7.1 Mb and 37.74 Mb, respectively. Out of 40,727 protein-coding genes predicted in the study, 89% have functional annotations in public databases. We also showed that of the 603.93 Mb repetitive sequences predicted in the assembled genome, long terminal repeat retrotransposons constitute 41.52%. The genome evolution analysis showed that the A. corniculatum genome experienced two whole-genome duplication events and shared the ancient γ whole-genome triplication event. A comparative genomic analysis revealed an incidence of expansion in 1,488 gene families associated with essential metabolism and biosynthetic pathways, including photosynthesis, oxidative phosphorylation, phenylalanine, glyoxylate, dicarboxylate metabolism, and DNA replication, which probably constitute adaptation traits that allow the A. corniculatum to survive in the intertidal zone. Also, the systematic characterization of genes associated with flavonoid biosynthesis pathway and the AcNHX gene family conducted in this study will provide insight into the adaptation mechanism of A. corniculatum to intertidal environments. The high-quality genome reported here can provide historical insights into genomic transformations that support the survival of A. corniculatum under harsh intertidal habitats.

Genomic evidence of prevalent hybridization throughout the evolutionary history of the fig-wasp pollination mutualism

Ficus (figs) and their agaonid wasp pollinators present an ecologically important mutualism that also provides a rich comparative system for studying functional co-diversification throughout its coevolutionary history (~75 million years). We obtained entire nuclear, mitochondrial, and chloroplast genomes for 15 species representing all major clades of Ficus. Multiple analyses of these genomic data suggest that hybridization events have occurred throughout Ficus evolutionary history. Furthermore, cophylogenetic reconciliation analyses detect significant incongruence among all nuclear, chloroplast, and mitochondrial-based phylogenies, none of which correspond with any published phylogenies of the associated pollinator wasps. These findings are most consistent with frequent host-switching by the pollinators, leading to fig hybridization, even between distantly related clades. Here, we suggest that these pollinator host-switches and fig hybridization events are a dominant feature of fig/wasp coevolutionary history, and by generating novel genomic combinations in the figs have likely contributed to the remarkable diversity exhibited by this mutualism.

High-Quality Genome of the Medicinal Plant Strobilanthes cusia Provides Insights Into the Biosynthesis of Indole Alkaloids

Strobilanthes cusia (Nees) Kuntze is an important plant used to process the traditional Chinese herbal medicines "Qingdai" and "Nanbanlangen". The key active ingredients are indole alkaloids (IAs) that exert antibacterial, antiviral, and antitumor pharmacological activities and serve as natural dyes. We assembled the S. cusia genome at the chromosome level through combined PacBio circular consensus sequencing (CCS) and Hi-C sequencing data. Hi-C data revealed a draft genome size of 913.74 Mb, with 904.18 Mb contigs anchored into 16 pseudo-chromosomes. Contig N50 and scaffold N50 were 35.59 and 68.44 Mb, respectively. Of the 32,974 predicted protein-coding genes, 96.52% were functionally annotated in public databases. We predicted 675.66 Mb repetitive sequences, 47.08% of sequences were long terminal repeat (LTR) retrotransposons. Moreover, 983 Strobilanthes-specific genes (SSGs) were identified for the first time, accounting for ~2.98% of all protein-coding genes. Further, 245 putative centromeric and 29 putative telomeric fragments were identified. The transcriptome analysis identified 2,975 differentially expressed genes (DEGs) enriched in phenylpropanoid, flavonoid, and triterpenoid biosynthesis. This systematic characterization of key enzyme-coding genes associated with the IA pathway and basic helix-loop-helix (bHLH) transcription factor family formed a network from the shikimate pathway to the indole alkaloid synthesis pathway in S. cusia. The high-quality S. cusia genome presented herein is an essential resource for the traditional Chinese medicine genomics studies and understanding the genetic underpinning of IA biosynthesis.

Chromosome-level reference genome assembly provides insights into aroma biosynthesis in passion fruit (Passiflora edulis)

Passion fruit, native to tropical America, is an agriculturally, economically and ornamentally important fruit plant that is well known for its acid pulp, rich aroma and distinctive flavour. Here, we present a chromosome-level genome assembly of passion fruit by incorporating PacBio long HiFi reads and Hi-C technology. The assembled reference genome is 1.28 Gb size with a scaffold N50 of 126.4 Mb and 99.22% sequences anchored onto nine pseudochromosomes. This genome is highly repetitive, accounting for 86.61% of the assembled genome. A total of 39,309 protein-coding genes were predicted with 93.48% of those being functionally annotated in the public databases. Genome evolution analysis revealed a core eudicot-common γ whole-genome triplication event and a more recent whole-genome duplication event, possibly contributing to the expansion of certain gene families. The 33 rapidly expanded gene families were significantly enriched in the pathways of isoflavone biosynthesis, galactose metabolism, diterpene biosynthesis and fatty acid metabolism, which might be responsible for the formation of featured flavours in the passion fruit. Transcriptome analysis revealed that genes related to ester and ethylene biosynthesis were significantly upregulated in the mature fruit and the expression levels of those genes were consistent with the accumulation of volatile lipid compounds. The passion fruit genome analysis improves our understanding of the genome evolution of this species and sheds new lights into the molecular mechanism of aroma biosynthesis in passion fruit.

Effects of ET-1 and TNF-α levels on the cardiac function and prognosis in rats with chronic heart failure

OBJECTIVE

To investigate the effects of ET-1 and TNF-α levels on cardiac function and prognosis in rats with chronic heart failure (CHF), to provide reference for clinical practice.

MATERIALS AND METHODS

120 SD rats were randomly divided into healthy group (n=60) and heart failure group (n=60). Rats from heart failure group were made into CHF models by an intraperitoneal injection of adriamycin. According to the average serum levels of ET-1 and TNF-α, 30 rats with higher level were enrolled in high expression subgroup, while 30 rats with lower level were enrolled in low expression subgroup. The sandwich enzyme-linked immunosorbent assay (ELISA) was employed to determine the ET-1 and TNF-α in rats from healthy group and heart failure group. Doppler echocardiography was used to measure the left ventricular ejection fraction, heart rate, and aortic diameter. After the death of heart failure rats, the total heart mass and left ventricle mass were measured and compared with those of the healthy rats. The serum levels of ET-1 and TNF-α were monitored to explore the influence of ET-1 and TNF-α levels on the prognosis of rats from study group.

RESULTS

The total heart mass and left ventricle mass of the heart failure group were higher than those of healthy group (p<0.05). The total heart mass and left ventricle mass of the low expression subgroup were lower than those of high expression subgroup (p<0.05).

CONCLUSIONS

The serum levels of ET-1 and TNF-α are higher than those in healthy rats. CHF rats with higher serum levels of ET-1 and TNF-α have a worse heart function and survival. Serum levels of ET-1 and TNF-α can be used as predictors of cardiac function and prognosis in CHF rats, providing references for clinical practice.

Microtubule organization defects in Arabidopsis thaliana

Microtubules (MT) are critical cytoskeletal filaments that have several functions in cell morphogenesis, cell division, vesicle transport and cytoplasmic separation in the spatiotemporal regulation of eukaryotic cells. Formation of MT requires the co-interaction of MT nucleation and α-β-tubulins, as well as MT-associated proteins (MAP). Many key MAP contributing to MT nucleation and elongation are essential for MT nucleation and regulation of MT dynamics, and are conserved in the plant kingdom. Therefore, the deletion or decrease of γ-tubulin ring complex (γTuRC) components and related MAP, such as the augmin complex, NEDD1, MZT1, EB1, MAP65, etc., in Arabidopsis thaliana results in MT organizational defects in the spindle and phragmoplast MT, as well as in chromosome defects. In addition, similar defects in MT organization and chromosome structure have been observed in plants under abiotic stress conditions, such as under high UV-B radiation. The MT can sense the signal from UV-B radiation, resulting in abnormal MT arrangement. Further studies are required to determine whether the abnormal chromosomes induced by UV-B radiation can be attributed to the involvement of abnormal MT arrays in chromosome migration after DNA damage.

One Case of Soil and Groundwater Environmental Forensics Caused by Illegal Landfill Waste

Abstract

Grape-seed polyphenols inhibit AAA in mice via regulation of macrophage polarization

AIM

Abdominal aortic aneurysm (AAA) is characterized by macrophage polarization, and at present, no drug therapy is available. Although grape-seed polyphenols (GSP) showed an anti-AAA effect, the role of GSP in the phenotype shift in macrophages remains unknown.

METHOD

The main phenolic compounds in GSP were determined by LC-MS. Male C57BL/6 mice were divided into four equal groups, namely sham group, CaPO4 group, CaPO4+GSP low-dose group, and CaPO4+GSP high-dose group. GSP was administered intragastrically after CaPO4 application. Molecular expressions were histologically evaluated and analyzed by various staining assays and FACS.

RESULTS

GSP administration inhibited CaPO4-induced AAA formation, which correlated with a decrease in macrophage infiltration and retainment of vascular smooth muscle layer as compared to those in the CaPO4 group. FACS assay showed that the GSP administration dose-dependently decreased the CD54 expression (low-dose group: 11.4 ± 2.1 % and high-dose group: 4.8 ± 1.4 % vs 23.2 ± 3.6 %; p < 0.05 and p < 0.01, respectively) and increased the CD206 expression of F4/80-positive cells in GSP-administered groups as compared with that in CaPO4-injured aortas in the CaPO4 group (low-dose group: 22.4 ± 3.3 % and high-dose group: 26.7 ± 4.2 % vs 8.1 ± 1.3 %; p < 0.05 and p < 0.01, respectively).

CONCLUSIONS

GSP could be a pharmacologically potent agent in the treatment of AAA (Tab. 1, Fig. 3,Ref. 20). Text in PDF www.elis.sk Keywords: grape-seed polyphenols, abdominal aortic aneurysm, macrophage, inflammatory, polarization.

Immunorelated gene polymorphisms associated with acute myeloid leukemia

Although the pathogenesis of acute myeloid leukemia (AML) is still unknown, accumulating evidence has revealed that immune response plays a vital part in the pathogenesis. Here, we investigated the involvement of 21 single nucleotide polymorphisms (SNPs) of immunorelated genes, including cytokines [interleukin (IL)-2, IL-4, IL-9, IL-12A, IL-22, interferon (IFN-α) and transforming growth factor (TGF)-β1], transcriptional regulatory genes (TBX21, STAT1, STAT3, STAT5B, STAT6, GATA3, FOXP3 and IRF4) and others (IL2RA, IL6R, NFKBIA) in 269 AML in-patients and 200 healthy controls. Furthermore, we analyzed the relationship between the SNPs and clinical characteristics. Immunorelated SNP genotyping was performed on the Sequenom MassARRAY iPLEX platform. All the SNPs in healthy controls were consistent with Hardy-Weinberg equilibrium. All final P-values were adjusted by Bonferroni multiple testing. Our results showed that IL-22 (rs2227491) was significantly associated with the white blood cell (WBC) counts. Signal transducer and activator of transcription 5B (STAT-5B) (rs6503691) showed a close relationship with the recurrent genetic abnormalities in patients with AML. We verified the negatively independent effect of age and risk of cytogenetics on overall survival (OS). More importantly, the GG genotype of IL-12A (rs6887695) showed a negative impact on AML prognosis independently. Furthermore, the relative expression of IL-12 was decreased in GG genotype, no matter under a co-dominant or recessive model. However, no correlation was observed between the SNPs mentioned above and disease susceptibility, risk stratification and survival. Our findings suggest that immunorelated gene polymorphisms are associated with prognosis in AML, which may perform as novel inspection targets for AML patients.