Chromosome-scale assembly of the Dendrobium chrysotoxum genome enhances the understanding of orchid evolution

As one of the largest families of angiosperms,the Orchidaceae family is diverse.Dendrobium represents the second largest genus of the Orchidaceae.However,an assembled high-quality genome of species in this genus is lacking.Here,we report a chromosome-scale reference genome of Dendrobium chrysotoxum,an important ornamental and medicinal orchid species.The assembled genome size of D.chrysotoxum was 1.37 Gb,with a contig N50 value of 1.54 Mb.Of the sequences,95.75%were anchored to 19 pseudochromosomes.There were 30,044 genes predicted in the D.chrysotoxum genome.Two whole-genome polyploidization events occurred in D.chrysotoxum.In terms of the second event,whole-genome duplication(WGD)was also found to have occurred in other Orchidaceae members,which diverged mainly via gene loss immediately after the WGD event occurred;the first duplication was found to have occurred in most monocots(tau event).We identified sugar transporter(SWEET)gene family expansion,which might be related to the abundant medicinal compounds and fleshy stems of D.chrysotoxum.MADS-box genes were identified in D.chrysotoxum,as well as members of TPS and Hsp90 gene families,which are associated with resistance,which may contribute to the adaptive evolution of orchids.We also investigated the interplay among carotenoid,ABA,and ethylene biosynthesis in D.chrysotoxum to elucidate the regulatory mechanisms of the short flowering period of orchids with yellow flowers.The reference D.chrysotoxum genome will provide important insights for further research on medicinal active ingredients and breeding and enhances the understanding of orchid evolution.

果糖饮食致大鼠肠内菌群的变迁及双歧杆菌干预作用的研究

目的探究果糖饮食致大鼠代谢异常中拟杆菌属、乳杆菌属和梭杆菌属丰度变化及双歧杆菌干预对3种菌属和代谢的影响。方法将SD雄性大鼠随机分为对照组(NC组)、果糖组(HFD组)和双歧杆菌组(B组),每组各10只。NC组,普通饲料+自来水喂养;HFD组,普通饲料+10%果糖水喂养;B组,普通饲料+10%果糖水+双歧杆菌水(1 ml/d,1×109 cfu/ml)灌胃。其他饲养条件相同,每周检测大鼠体重。于16周末空腹抽血检测谷丙转氨酶(ALT)、谷草转氨酶(AST)、三酰甘油(TG)、脂多糖(LPS)、肿瘤坏死因子α(TNF-α)及空腹胰岛素(FINS)水平,计算胰岛素抵抗指数(HOMA-IR);实时聚合酶链反应(real-time PCR)检测大鼠粪便中3种菌属丰度变化;镜下观察肝组织病理学变化。结果与NC组比较,HFD组血浆LPS、ALT、AST、TG、TNF-α、空腹血糖及FINS差异有统计学意义(P <0.05),HFD组升高;粪便中拟杆菌属、乳杆菌属丰度下降,梭杆菌属丰度升高,差异有统计学意义(P <0.05);双歧杆菌干预对HFD组上述指标有一定程度的改善。结论果糖饮食引起3种菌属失调参与机体代谢异常的发生,双歧杆菌通过调节其失调对机体代谢紊乱发挥改善作用。

Effect of endogenous insulin-like growth factor and stem cell factor on diabetic colonic dysmotility

AIM: To investigate whether the reduction of stem cell factor (SCF) is mediated by decreased endogenous insulin-like growth factor (IGF)-1 in diabetic rat colon smooth muscle. METHODS: Sixteen Sprague-Dawley rats were randomly divided into two groups: control group and streptozotocin-induced diabetic group. After 8 wk of streptozotocin administration, colonic motility function and contractility of circular muscle strips were measured. The expression of endogenous IGF-1 and SCF was tested in colonic tissues. Colonic smooth muscle cells were cultured from normal adult rats. IGF-1 siRNA transfection was used to investigate whether SCF expression was affected by endogenous IGF-1 expression in smooth muscle cells, and IGF-1 induced SCF expression effects were studied. The effect of high glucose on the expression of endogenous IGF-1 and SCF was also investigated. RESULTS: Diabetic rats showed prolonged colonic transit time (252 ± 16 min vs 168 ± 9 min, P < 0.01) and weakness of circular muscle contraction (0.81 ± 0.09 g vs 2.48 ± 0.23 g, P < 0.01) compared with the control group. Endogenous IGF-1 and SCF protein expression was significantly reduced in the diabetic colonic muscle tissues. IGF-1 and SCF mRNA expression also showed a paralleled reduction in diabetic rats. In the IGF-1 siRNA transfected smooth muscle cells, SCF mRNA and protein expression was significantly decreased. IGF-1 could induce SCF expression in a concentration and time-dependent manner, mainly through the extracellular-signal-regulated kinase 1/2 signal pathway. High glucose inhibited endogenous IGF-1 and SCF expression and the addition of IGF-1 to the medium reversed the SCF expression. CONCLUSION: Myopathy may resolve in colonic motility dysfunction in diabetic rats. Deficiency of endogenous IGF-1 in colonic smooth muscle cells leads to reduction of SCF expression.

Age-related symptom and life quality changes in women with irritable bowel syndrome

AIM:To explore age-related changes in symptoms and quality of life(QoL) of women with irritable bowel syndrome(IBS).METHODS:Two-hundred and fifty-four female adult outpatients with IBS attending the Department of Gastroenterology at the First Affiliated Hospital of Nanjing Medical University between January,2008 and October,2008 were approached.Patients with a history of abdominal surgery,mental illness or those who had recently taken psychotropic drugs were excluded.A physician obtained demographic and abdominal symptom data.All patients were asked to complete the Zung Self-Rated Anxiety and Depression Scale(SDS/SAS) and the IBS-specific QoL questionnaire.The patients were divided into six groups according to age,in 10-year increments:18-27 years,28-37 years,38-47 years,48-57 years,58-67 years and 68-75 years(maximum 75 years).Age-related differences of abdominal pain or discomfort were analyzed using ranksum tests.Differences in SDS/SAS and IBS-QoL scores between age groups were analyzed using one-way analysis of variance.Pearson's correlations evaluated potential associations between IBS symptoms,psychological factors and QoL in each age group.RESULTS:There were no differences in the distribution of IBS subtypes between age groups(χ2 = 20.516,P = 0.153).Differences in the severity of abdominal pain/discomfort with age were statistically significant(χ2 = 25.638,P < 0.001);patients aged 48-57 years,58-67 years or 68-75 years had milder abdominal pain/discomfort than those in the younger age groups.The severity of anxiety or depressive symptoms did not differ between age groups(SDS,χ2 = 390.845,P = 0.110;SAS,χ 2 = 360.071,P = 0.220).Differences of IBSQoL scores were statistically significant between age groups(χ2 = 1098.458,P = 0.011).The scores of patients in the 48-57-year group were lower than those in the 18-27-year and 28-37-year groups(48-57-year group vs 18-27-year group,74.88 ± 8.76 vs 79.76 ± 8.63,P = 0.021;48-57-year group vs 28-37-year group,74.88 ± 8.76 vs 79.04 ± 8.32,P = 0.014).The scores in the 68-75-year group were lower than those in the 18-27-year,28-37-year and 38-47-year groups(68-75-year group vs 18-27-year group,71.98 ± 9.83 vs 79.76 ± 8.63,P = 0.003;68-75-year group vs 28-37-year group,71.98 ± 9.83 vs 79.04 ± 8.32,P = 0.002;68-75-year group vs 38-47-year group,71.98 ± 9.83 vs 76.44 ± 8.15,P = 0.039).Anxiety and depression were negatively correlated with QoL in all age groups(SDS and QoL:18-27-year group,r =-0.562,P = 0.005;28-37-year group,r =-0.540,P < 0.001;38-47-year group,r =-0.775,P < 0.001;48-57-year group,r =-0.445,P = 0.001;58-67-year group,r =-0.692,P < 0.001;68-75-year group,r =-0.732,P < 0.001.SAS and QoL:18-27-year group,r =-0.600,P = 0.002;28-37-year group,r =-0.511,P < 0.001;38-47-year group,r =-0.675,P < 0.001;48-57-year group,r =-0.558,58-67-year group,P = 0.001;r =-0.588,P < 0.001;68-75-year group,r =-0.811,P < 0.001).A negative correlation between abdominal pain severity and QoL was found in patients aged more than 58 years(58-67-year group,r =-0.366,P = 0.017;68-75-year group,r =-0.448,P = 0.048),but not in younger patients(18-27-year group,r = 0.080,P = 0.716;28-37-year group,r =-0.063,P = 0.679;38-47-year group,r =-0.029,P = 0.812;48-57-year group,r =-0.022,P = 0.876).CONCLUSION:Factors affecting QoL should always be treated in IBS,especially emotional problems in young adults.Even mild abdominal pain should be controlled in elderly patients.

Estimation of sea clutter inherent Doppler spectrum from shipborne S-band radar sea echo

Measurement of shipborne radar sea echo is instrumental in collecting the sea clutter data in open sea areas.However,the ship movement would introduce an extra Doppler component into the spectrum of the sea clutter,so the sea clutter inherent spectrum must be estimated prior to investigating the sea clutter Doppler characteristics from the shipborne radar sea echo.In this paper we show some results about a shipborne sea clutter measurement experiment that was conducted in the South China Sea in a period between 2017 and 2018;abundant clutter data have been collected by using a shipborne S-band clutter measurement radar.To obtain the sea clutter inherent Doppler spectrum from these data,an estimation method,based on the mapping relationship between the shipborne clutter spectrum and the inherent clutter spectrum,is proposed.This method is validated by shipborne clutter data sets under the same measuring conditions except for the ship speed.Using this method,the characteristics of the Doppler spectrum lineshapes in the South China Sea are calculated and analyzed according to different sea states,wave directions,and radar resolutions,which can be instrumental in designing the radar target detection algorithms.

Correction: The Cymbidium genome reveals the evolution of unique morphological traits

After online publication of the article 1 the author noticed minor typo in Fig.4c.CeSEP1/2/3/4 should be read as CeSEP1/3/4.Revised figure supplied during the proof correction was inadvertently not reproduced in the final version.In addition,the affiliation numbers of the authors revised in the original article during proof correction,but not reflected in the title page in Supplementary Information.

The Cymbidium genome reveals the evolution of unique morphological traits

The marvelously diverse Orchidaceae constitutes the largest family of angiosperms.The genus Cymbidium in Orchidaceae is well known for its unique vegetation,floral morphology,and flower scent traits.Here,a chromosomescale assembly of the genome of Cymbidium ensifolium(Jianlan)is presented.Comparative genomic analysis showed that C.ensifolium has experienced two whole-genome duplication(WGD)events,the most recent of which was shared by all orchids,while the older event was the t event shared by most monocots.The results of MADS-box genes analysis provided support for establishing a unique gene model of orchid flower development regulation,and flower shape mutations in C.ensifolium were shown to be associated with the abnormal expression of MADS-box genes.The most abundant floral scent components identi fied included methyl jasmonate,acacia alcohol and linalool,and the genes involved in the floral scent component network of C.ensifolium were determined.Furthermore,the decreased expression of photosynthesis-antennae and photosynthesis metabolic pathway genes in leaves was shown to result in colorful striped leaves,while the increased expression of MADS-box genes in leaves led to perianth-like leaves.Our results provide fundamental insights into orchid evolution and diversi fication.

Label-Free Microscopic Imaging Based on the Random Matrix Theory in Wavefront Shaping

Wavefront shaping technology has mainly been applied to microscopic fluorescence imaging through turbid media,with the advantages of high resolution and imaging depth beyond the ballistic regime. However, fluorescence needs to be introduced extrinsically and the field of view is limited by memory effects. Here we propose a new method for microscopic imaging light transmission through turbid media, which has the advantages of label-free and discretional field of view size, based on transmission-matrix-based wavefront shaping and the random matrix theory. We also verify that a target of absorber behind the strong scattering media can be imaged with high resolution in the experiment. Our method opens a new avenue for the research and application of wavefront shaping.

Elemental mercury removal from coal gas by CeMnTi sorbents and their regeneration performance

Ce and Mn modified TiO_(2) sorbents(CeMnTi) were prepared by a co-precipitation method,and their ability to remove elemental mercury from coal gas in a fixed bed reactor was studied.Based on results of Brunauer-Emmett-Teller(BET),X-ray diffraction(XRD),scanning electron microscope(SEM),and X-ray photoelectron spectroscopy(XPS) studies,the modification mechanisms of the CeMnTi sorbents are discussed.Mn doping improved the specific surface area and dispersion of cerium oxides on the sorbent surface,while Ce doping increased the proportion of Mn^(4+)in manganese oxides by a synergetic effect between manganese oxides and cerium oxides.The effects of the active component,temperature,and coal gas components on the mercury removal performance of the sorbents were investigated.The results showed that the CeMnTi sorbents exhibited high mercury removal efficiency.Ce_(0.2)Mn_(0.1)Ti adsorbed 91.55% elemental mercury from coal gas at 160℃.H2 S and O2 significantly improved the ability of sorbents to remove mercury.Part of the H2_(S) formed stable sulfates or sulfites through a series of oxidation reaction chains on the sorbent surface.HCl also improved the mercury removal performance,but reduced the promotion effect of H2_(S) for mercury removal when coexisting with H2_(S).CO and H2 had a minor inhibitory effect on mercury adsorption.The recycling performance of the sorbents was investigated by thermal regeneration.The thermal decomposition of the used sorbents indicated that mercury compounds were present mainly in the form of HgO and HgS,and higher temperature was beneficial for regeneration.The formation of sulfates and sulfites in the presence of H2_(S) led to a decrease in mercury removal efficiency.