Comparative transcriptome analysis and simple sequence repeat marker development for two closely related Isodon species used as ‘Xihuangcao’ herbs

Purpose: To facilitate the molecular identification of original plants, resolve taxonomic problems and identify standards for ‘Xihuangcao’-based products on the market.Methods: A transcriptomic analysis of two closely related species, i.e., Isodon serra (Maxim.) (IS) and I. lophanthoides (Buch.-Ham. ex D. Don) Hara, was conducted by using the Illumina HiSeq 2500 platform, and expressed sequence tag-derived simple sequence repeat (EST-SSR) markers were developed based on these transcriptomes.Results: In total, 149,650 and 103,221 contigs were obtained, with N50 values of 1,400 and 1,516, from the IS and I. lophanthoides RNA-Seq datasets, respectively. These contigs were clustered into 107,777 and 68,220 unigenes, which were functionally annotated to identify the genes involved in therapeutic components. In total, 14,138 and 11,756 EST-SSR motifs were identified, and of these motifs, 7,453 and 6,428 were used to design primers for IS and I. lophanthoides, respectively. After PCR verification and fluorescence-based genotyping, 24 SSR markers with bright bands, high polymorphism, and single amplification were obtained and used to identify closely related Isodon species/varieties.Conclusion: These data could help herbal scientists identify high-quality herbal plants and provide a reference for genetic improvement and population genetic and phylogenetic studies investigating ‘Xihuangcao’ herbs.Keywords: Xihuangcao, Transcriptome, EST-SSR, Molecular marker

Intelligent Omni-Surfaces Aided Wireless Communications: Does the Reciprocity Hold?

Intelligent omni-surfaces (IOS) have attracted great attention recently due to its potential to achieve full-dimensional communications by simultaneously reflecting and refracting signals toward both sides of the surface. However, it still remains an open question whether the reciprocity holds between the uplink and downlink channels in the IOS-aided wireless communications. In this work, we first present a physics-compliant IOS related channel model, based on which the channel reciprocity is investigated. We then demonstrate the angle-dependent electromagnetic response of the IOS element in terms of both incident and departure angles. This serves as the key feature of IOS that drives our analytical results on beam non-reciprocity. Finally, simulation and experimental results are provided to verify our theoretical analyses.Comment: 5 pages, 6 figure

Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim

<p>Abstract</p> <p>Background</p> <p><it>Epimedium sagittatum </it>(Sieb. Et Zucc.) Maxim, a traditional Chinese medicinal plant species, has been used extensively as genuine medicinal materials. Certain <it>Epimedium </it>species are endangered due to commercial overexploition, while sustainable application studies, conservation genetics, systematics, and marker-assisted selection (MAS) of <it>Epimedium </it>is less-studied due to the lack of molecular markers. Here, we report a set of expressed sequence tags (ESTs) and simple sequence repeats (SSRs) identified in these ESTs for <it>E. sagittatum</it>.</p> <p>Results</p> <p>cDNAs of <it>E. sagittatum </it>are sequenced using 454 GS-FLX pyrosequencing technology. The raw reads are cleaned and assembled into a total of 76,459 consensus sequences comprising of 17,231 contigs and 59,228 singlets. About 38.5% (29,466) of the consensus sequences significantly match to the non-redundant protein database (E-value < 1e-10), 22,295 of which are further annotated using Gene Ontology (GO) terms. A total of 2,810 EST-SSRs is identified from the <it>Epimedium </it>EST dataset. Trinucleotide SSR is the dominant repeat type (55.2%) followed by dinucleotide (30.4%), tetranuleotide (7.3%), hexanucleotide (4.9%), and pentanucleotide (2.2%) SSR. The dominant repeat motif is AAG/CTT (23.6%) followed by AG/CT (19.3%), ACC/GGT (11.1%), AT/AT (7.5%), and AAC/GTT (5.9%). Thirty-two SSR-ESTs are randomly selected and primer pairs are synthesized for testing the transferability across 52 <it>Epimedium </it>species. Eighteen primer pairs (85.7%) could be successfully transferred to <it>Epimedium </it>species and sixteen of those show high genetic diversity with 0.35 of observed heterozygosity (<it>Ho</it>) and 0.65 of expected heterozygosity (<it>He</it>) and high number of alleles per locus (11.9).</p> <p>Conclusion</p> <p>A large EST dataset with a total of 76,459 consensus sequences is generated, aiming to provide sequence information for deciphering secondary metabolism, especially for flavonoid pathway in <it>Epimedium</it>. A total of 2,810 EST-SSRs is identified from EST dataset and ~1580 EST-SSR markers are transferable. <it>E. sagittatum </it>EST-SSR transferability to the major <it>Epimedium </it>germplasm is up to 85.7%. Therefore, this EST dataset and EST-SSRs will be a powerful resource for further studies such as taxonomy, molecular breeding, genetics, genomics, and secondary metabolism in <it>Epimedium </it>species.</p

A multicenter study of fetal chromosomal abnormalities in Chinese women of advanced maternal age

AbstractObjectiveThis study aimed to determine the rates of different fetal chromosomal abnormalities among women of advanced maternal age in China and to discuss the possible misdiagnosis risks of newer molecular techniques, for selection of appropriate prenatal screening and diagnostic technologies.Materials and MethodsSecond trimester amniocentesis and fetal karyotype results of 46,258 women were retrospectively reviewed. All women were ≥ 35 years old with singleton pregnancies. The rates of clinically significant chromosomal abnormalities (CSCAs), incidence of chromosomal abnormalities, and correlations with age were determined.ResultsFrom 2001 to 2010, the proportion of women of advanced maternal age undergoing prenatal diagnosis increased from 20% to 46%. The mean age was 37.4 years (range, 35–46 years). A total of 708 cases of CSCAs, with a rate of 1.53% were found. Trisomy 21 was the most common single chromosome abnormality and accounted for 55.9% of all CSCAs with an incidence of 0.86%. Trisomy 13, trisomy 18, and trisomy 21, the most common chromosome autosomal aneuploidies, accounted for 73.6% of all CSCAs, with a rate of 1.13%. As a group, the most common chromosomal aneuploidies (13/18/21/X/Y) accounted for 93.9% of all abnormalities, with a rate of 1.44%. The incidence of trisomy 21, trisomy 13/18/21 as a group, and 13/18/21/X/Y as a group was significantly greater in women aged 39 years and older (p < 0.001), but was not different between women aged 35 years, 36 years, 37 years, and 38 years.ConclusionThese findings may assist in genetic counseling of advanced maternal age pregnant women, and provide a basis for the selection of prenatal screening and diagnostic technologies

RIS-based IMT-2030 Testbed for MmWave Multi-stream Ultra-massive MIMO Communications

As one enabling technique of the future sixth generation (6G) network, ultra-massive multiple-input-multiple-output (MIMO) can support high-speed data transmissions and cell coverage extension. However, it is hard to realize the ultra-massive MIMO via traditional phased arrays due to unacceptable power consumption. To address this issue, reconfigurable intelligent surface-based (RIS-based) antennas are an energy-efficient enabler of the ultra-massive MIMO, since they are free of energy-hungry phase shifters. In this article, we report the performances of the RIS-enabled ultra-massive MIMO via a project called Verification of MmWave Multi-stream Transmissions Enabled by RIS-based Ultra-massive MIMO for 6G (V4M), which was proposed to promote the evolution towards IMT-2030. In the V4M project, we manufacture RIS-based antennas with 1024 one-bit elements working at 26 GHz, based on which an mmWave dual-stream ultra-massive MIMO prototype is implemented for the first time. To approach practical settings, the Tx and Rx of the prototype are implemented by one commercial new radio base station and one off-the-shelf user equipment, respectively. The measured data rate of the dual-stream prototype approaches the theoretical peak rate. Our contributions to the V4M project are also discussed by presenting technological challenges and corresponding solutions.Comment: 8 pages, 5 figures, to be published in IEEE Wireless Communication

Identification of an unfolded protein response-related signature for predicting the prognosis of pancreatic ductal adenocarcinoma

BackgroundPancreatic ductal adenocarcinoma (PDAC) is a highly aggressive lethal malignancy. An effective prognosis prediction model is urgently needed for treatment optimization.MethodsThe differentially expressed unfolded protein response (UPR)‒related genes between pancreatic tumor and normal tissue were analyzed using the TCGA-PDAC dataset, and these genes that overlapped with UPR‒related prognostic genes from the E-MTAB-6134 dataset were further analyzed. Univariate, LASSO and multivariate Cox regression analyses were applied to establish a prognostic gene signature, which was evaluated by Kaplan‒Meier curve and receiver operating characteristic (ROC) analyses. E‒MTAB‒6134 was set as the training dataset, while TCGA-PDAC, GSE21501 and ICGC-PACA-AU were used for external validation. Subsequently, a nomogram integrating risk scores and clinical parameters was established, and gene set enrichment analysis (GSEA), tumor immunity analysis and drug sensitivity analysis were conducted.ResultsA UPR-related signature comprising twelve genes was constructed and divided PDAC patients into high- and low-risk groups based on the median risk score. The UPR-related signature accurately predicted the prognosis and acted as an independent prognostic factor of PDAC patients, and the AUCs of the UPR-related signature in predicting PDAC prognosis at 1, 2 and 3 years were all more than 0.7 in the training and validation datasets. The UPR-related signature showed excellent performance in outcome prediction even in different clinicopathological subgroups, including the female (p&lt;0.0001), male (p&lt;0.0001), grade 1/2 (p&lt;0.0001), grade 3 (p=0.028), N0 (p=0.043), N1 (p&lt;0.001), and R0 (p&lt;0.0001) groups. Furthermore, multiple immune-related pathways were enriched in the low-risk group, and risk scores in the low-risk group were also associated with significantly higher levels of tumor-infiltrating lymphocytes (TILs). In addition, DepMap drug sensitivity analysis and our validation experiment showed that PDAC cell lines with high UPR-related risk scores or UPR activation are more sensitive to floxuridine, which is used as an antineoplastic agent.ConclusionHerein, we identified a novel UPR-related prognostic signature that showed high value in predicting survival in patients with PDAC. Targeting these UPR-related genes might be an alternative for PDAC therapy. Further experimental studies are required to reveal how these genes mediate ER stress and PDAC progression