Chromosome-level genome and multi-omics analyses provide insights into the geo-herbalism properties of Alpinia oxyphylla

IntroductionAlpinia oxyphylla Miquel (A. oxyphylla), one of the “Four Famous South Medicines” in China, is an essential understory cash crop that is planted widely in the Hainan, Guangdong, Guangxi, and Fujian provinces. Particularly, A. oxyphylla from Hainan province is highly valued as the best national product for geo-herbalism and is an important indicator of traditional Chinese medicine efficacy. However, the molecular mechanism underlying the formation of its quality remains unspecified.MethodsTo this end, we employed a multi-omics approach to investigate the authentic quality formation of A. oxyphylla.ResultsIn this study, we present a high-quality chromosome-level genome assembly of A. oxyphylla, with contig N50 of 76.96 Mb and a size of approximately 2.08Gb. A total of 38,178 genes were annotated, and the long terminal repeats were found to have a high frequency of 61.70%. Phylogenetic analysis demonstrated a recent whole-genome duplication event (WGD), which occurred before A. oxyphylla’s divergence from W. villosa (~14 Mya) and is shared by other species from the Zingiberaceae family (Ks, ~0.3; 4DTv, ~0.125). Further, 17 regions from four provinces were comprehensively assessed for their metabolite content, and the quality of these four regions varied significantly. Finally, genomic, metabolic, and transcriptomic analyses undertaken on these regions revealed that the content of nootkatone in Hainan was significantly different from that in other provinces.DiscussionOverall, our findings provide novel insights into germplasm conservation, geo-herbalism evaluation, and functional genomic research for the medicinal plant A. oxyphylla

The dynamic effects of maternal high-calorie diet on glycolipid metabolism and gut microbiota from weaning to adulthood in offspring mice

Dysbiosis of gut microbiota can contribute to the progression of diabetes and obesity. Previous studies have shown that maternal high-fat (HF) diet during the perinatal period can alter the microbiota and induce metabolic disorders at weaning. However, whether dysbiosis of gut microbiota and metabolism could be recovered by a normal diet after weaning and the dynamic changes of gut microbiota have not been fully studied. In this study, C57BL/6J female mice were fed with a normal chow (NC) or HF diet for 4 weeks preconception, during gestation, and until pup weaning. After weaning, male offspring were fed with an NC diet until 9 weeks of age. The microbiota of offspring at weaning and 9 weeks of age was collected for 16S rRNA gene amplicon sequencing. We found that dams fed with an HF diet showed glucose intolerance after lactation. Compared with the offspring from NC dams, the offspring from HF dams exhibited a higher body weight, hyperglycemia, glucose intolerance, hyperinsulinemia, hypercholesterolemia, and leptin resistance and lower adiponectin at weaning. Fecal analysis indicated altered microbiota composition between the offspring of the two groups. The decrease in favorable bacteria (such as norank f Bacteroidales S24-7 group) and increase in unfavorable bacteria (such as Lachnoclostridium and Desulfovibrio) were strongly associated with a disturbance of glucose and lipid metabolism. After 6 weeks of normal diet, no difference in body weight, glucose, and lipid profiles was observed between the offspring of the two groups. However, the microbiota composition of offspring in the HF group was still different from that in the NC group, and microbiota diversity was lower in offspring of the HF group. The abundance of Lactobacillus was lower in the offspring of the HF group. In conclusion, a maternal HF diet can induce metabolic homeostasis and gut microbiota disturbance in offspring at weaning. Gut microbiota dysbiosis can persist into adulthood in the offspring, which might have a role in the promotion of susceptibility to obesity and diabetes in the later life of the offspring

Identification of hub genes in airway epithelial cells of asthma patients by WGCNA and PPI network

258-267Bronchial asthma is a common chronic disease of airway inflammation, high mucus secretion and airway hyper responsiveness. The pathogenetic mechanisms of asthma remain unclear. In this study, we aimed at identifying genes playing an import role in disease-related pathways in airway epithelial cells of asthma patients. Microarray data GSE41861 of asthma airway epithelial cells was used to screen differentially expressed genes (DEGs) through GEO2R analysis. The weighted gene co-expression network analysis (WGCNA) was performed to identify gene co-expression network modules in bronchial asthma. The DAVID database was then used to perform functional and pathway enrichment analysis of these DEGs. In addition, we have conducted protein-protein interaction (PPI) network of DEGs by STRING, and eventually found key genes and significant modules. A total of 315 DEGs (111 up-regulated and 204 down-regulated) were identified between severe asthma and healthy individual, which were mainly involved in pathways of cilium assembly, cilium morphogenesis, axon guidance, positive regulation of fat cell differentiation, and positive regulation of cell substrate adhesion. A total of 60 genes in the black module and green module were considered to be correlated with the severity of asthma. Combining PPI network, several key genes were identified, such as BP2RY14, PTGS1, SLC18A2, SIGLEC6, RGS13, CPA3, and HPGDS. Our findings revealed several genes that may be involved in the process of development of bronchial asthma and potentially be candidate targets for diagnosis or therapy of bronchial asthma

Clinical manifestations and imaging and pathological features of giant cell angioblastoma: Report of four cases and literature review

Giant cell angioblastoma is a relatively rare vasogenic tumour. To date, studies on its clinical manifestations, imaging characteristics, pathological features, and prognosis are extremely limited and unknown, with only a few cases recorded. In this study, four cases of giant cell angioblastoma confirmed by pathological examination were reported to improve our understanding and deep exploration of the tumour spectrum. All cases in our study were male, including two adults and two boys. The lesions were located in the lower segment of the femur, medial condyle of the femur, knee joint, and popliteal fossa. Regarding the imaging characteristics, two patients with lesions in bone showed bone destruction, while the other two had lesions that invaded soft tissues, showing irregular, abnormal signal shadows and obvious enhancement. Histopathological analysis revealed that the nodular tumour tissue was mainly composed of oval and spindle cells, with varying numbers of osteoclast-like multinucleated giant cells, and the interstitial tissues were often filled with blood vessels of different sizes. The immunophenotype demonstrates that endothelial cells of small vessels in nodules expressed CD31, SMA, and ERG, while osteoclast-like multinucleated giant cells and histiocytes expressed CD68 and CD163, and the surrounding cells expressed SMA. All four patients were treated with surgical resection. One of them relapsed 1 month after surgery and received a second surgical resection. No distant metastasis or death occurred during the follow-up period. This study indicates that giant cell angioblastoma is a local invasive vascular tumour that can develop both in children and adults with skin, mucous membrane, soft tissue, and bone involvement. Imaging characteristics show bone destruction and irregular, abnormal signal shadows; in addition, obvious pathological morphological features can be observed. Currently, the treatment is mainly surgical resection, and interferons may be used as adjuvant chemotherapy

Autologous CIK cells combined with chemotherapy as the first-line treatment for locally advanced or metastatic gastric cancer is safe and feasible

AimTo evaluate the safety and initial efficacy of autologous cytokine-induced killer (CIK) cells combined with S-1+oxaliplatin (SOX) as the first-line treatment for locally advanced or metastatic gastric cancer (GC).Materials and methodsIn this two-arm, single-center exploratory trial, patients with locally advanced or metastatic GC were randomly assigned (1:1) to receive autologous CIK cells in combination with SOX (CIK-SOX) or SOX alone. The primary endpoint was the incidence of adverse events (AEs). Progression-free survival (PFS), overall survival (OS), objective response rate (ORR), and disease control rate (DCR) served as the secondary endpoints.ResultsFifty-nine patients were enrolled in the study between November 20, 2014 and September 6, 2017. A total of 31 patients received CIK-SOX and 28 patients received SOX. The most common AEs in both groups were gastrointestinal reaction, leucopenia, neutropenia, anemia, thrombocytopenia, hyperbilirubinemia, and elevated aspartate transaminase concentration, with a higher incidence of these conditions in the SOX group. The median PFS for the CIK-SOX and SOX groups was 6.9 and 4.9 months, respectively (hazard ratio (HR) 0.80, p=0.45). The respective median OS values were 17.8 and 9.75 months (HR 0.76, p=0.34). Patients who received more than three injections of specific lymphocyte subsets benefited the most from this combination therapy. Cox univariate and multivariate analyses showed that tumor metastasis to more than two organs was the main risk factor for PFS and OS. A total of 29 patients in the CIK-SOX group and 25 in the SOX group had measurable lesions. The ORR for the CIK-SOX and SOX groups was 55.2% and 32.0%, while the DCR was 93.1% and 88.0%, respectively.ConclusionThe safety of CIK-SOX as the first-line treatment for patients with locally advanced or metastatic GC was good. Although the PFS and OS in the CIK-SOX group were not statistically significantly different compared to the values in the SOX alone group, this treatment increased the PFS and OS duration, with the absolute improvement in OS of about 8.05 months. Continuous benefit from the CIK-SOX treatment was observed during long-term follow-up.Clinical trial registrationhttps://clinicaltrials.gov/study/NCT02504229?term=NCT02504229&rank=1, identifier ChiCTR-IPR-15005923; NCT02504229

The diploid genome sequence of an Asian individual

Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.97% coverage, and guided by the reference genome, we used uniquely mapped reads to assemble a high-quality consensus sequence for 92% of the Asian individual's genome. We identified approximately 3 million single-nucleotide polymorphisms (SNPs) inside this region, of which 13.6% were not in the dbSNP database. Genotyping analysis showed that SNP identification had high accuracy and consistency, indicating the high sequence quality of this assembly. We also carried out heterozygote phasing and haplotype prediction against HapMap CHB and JPT haplotypes (Chinese and Japanese, respectively), sequence comparison with the two available individual genomes (J. D. Watson and J. C. Venter), and structural variation identification. These variations were considered for their potential biological impact. Our sequence data and analyses demonstrate the potential usefulness of next-generation sequencing technologies for personal genomics

Comparison and correction of element measurements using qualitative and quantitative X-ray fluorescence in lacustrine sediments: A case study of Lake Hurleg

Using an X-ray Fluorescence (XRF) core scanner with nondestructive and successive, the chemistry features of lacustrine sediment can be measured directly. This method of XRF core scanner measurements has been widely applied to core sediment analysis but uncertain of the precision and accuracy. Comparison of intensities obtained by XRF core scanning and the concentration measured by conventional X-ray Fluorescence, indicates effects of physical properties varied from different elements on elemental intensities in the lacustrine sediments of a core from Lake Hurleg in the northeastern Tibetan Plateau. Correlation among elements Ti and Sr between the two measurement methods of the XRF and the conventional XRF is high. Using the intensity of Cl as an indicator of water content, the element intensities of Ti and Sr in the core samples is corrected. But the correlation coefficients of Ti and Sr is litter raised. The results show that XRF core scanning is a very useful tool for measuring element concentration in sediments particularly for high intensities elements

The dust storm events recorded in DaQaidam region of Qaidam Basin since Late Glacial period: evidence from the grain size of lake sediment

The paper focused on the study of detrital yellow layer from sediment profile D3 of DaQaidam Salt Lake, based on AMS 14C chronologic and mineralogical methods, aimed to discuss the dust storm events recorded by detrital yellow layer of DaQaidam region since Late Glacial period. The results showed that the grain-size distribution curve displayed double kurtosis, the main peak (10 µm in average) reflected the fine-grained fractions into lake by fluviation, and the secondary peak (> 32 µm) reflected the coarse silt fractions into lake by wind effect and fluviation. Finally, the coarse-grained fractions (> 64 µm) from sediment profile D3 probably recorded the dust storm events since Late Glacial period

Lithostratigraphy, mineralogy and the boron-bearing brine evolution of DaQaidam Salt Lake in Qaidam Basin since Holocene period, northern Qinghai-Tibet Plateau

Little attention has been paid to the study of sedimentary records from DaQaidam Salt Lake regarding brine evolution and hydro-climate change. Here we report the results of AMS 14C dating and mineralogical investigation on a sediment profile D4 from the south central of perennial saline water-body. The result revealed that pinnoite deposit in the lakebed was formed in early Holocene, the lake underwent three stages of lake-level and brine evolution in Holocene period, which were determined mainly by precipitation-controlled catchment inflow. The mineralogical records also depicted fluctuations in lake level and hydrochemistry on decadal and centennial scales