Caseymckenzie4850

This study aimed to investigate the molecular mechanism under the pathophysiology of subarachnoid hemorrhage (SAH) and identify the potential biomarkers for predicting the risk of SAH. Differentially expressed mRNAs (DEGs), microRNAs, and lncRNAs were screened. Protein-protein interaction (PPI), drug-gene, and competing endogenous RNA (ceRNA) networks were constructed to determine candidate RNAs. The optimized RNAs signature was established using least absolute shrinkage and selection operator and recursive feature elimination algorithms. A total of 124 SAH-related DEGs were identified, and were enriched in inflammatory response, TNF signaling pathway, and others. PPI network revealed 118 hub genes such as TNF, MMP9, and TLR4. Drug-gene network revealed that chrysin targeted more genes, such as TNF and MMP9. JMJD1C-AS-hsa-miR-204-HDAC4/SIRT1 and LINC01144-hsa-miR-128-ADRB2/TGFBR3 regulatory axes were found from ceRNA network. From these networks, 125 candidate RNAs were obtained. Of which, an optimal 38 RNAs signatures (2 lncRNAs, 1 miRNA, and 35 genes) were identified to construct a Support Vector Machine classifier. The predictive value of 38 biomarkers had an AUC of 0.990. Similar predictive performance was found in external validation dataset (AUC of 0.845). Our findings provided the potential for 38 RNAs to serve as biomarkers for predicting the risk of SAH. However, their application values should be further validated in clinical.The freshwater gastropod Tarebia granifera (Lamarck, 1816) is found in Taiwan, Hainan, and Guangdong provinces in China, and is one of the main intermediate hosts of trematodes that infect humans. The taxonomic positions of some cerithioidean families are still unclear, and whole mitochondrial genome studies are scarce in the Thiaridae. In this study, we describe the complete mitogenome of Tarebia granifera (Lamarck, 1816). The mitogenome is 15,555 bp in length, with a total of 37 genes, including 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. It is consistent with the essential features of previously studied mitochondrial genomes of species belonging to the superfamily Cerithioidea. Our study demonstrates the usefulness of mitogenomic data for resolving phylogenetic relationships of families within Cerithioidea and may also contribute to the prevention and control of the parasitic diseases caused by trematodes, which use T. granifera as an intermediate host.Phalaenopsis stobartiana Reichenbach f. 1877 is mainly distributed in Yunnan province of China and has a high ornamental and breeding value. Here, we reported the chloroplast genome of P. stobartiana. The length of the chloroplast genome was 145,900 bp, encoding 120 genes. The average GC content was 36.8%. Phylogenetic analysis revealed that P. stobartiana and P. wilsonii are closely related. The chloroplast genome could be used for further phylogenetic research, and provide molecular data for future genetic protection and breeding programs.The complete mitochondrial genome of Congrogadus subducens is first presented in this study. The whole mitogenome is a closed circular molecule of 16,881 bp in size, including 13 protein-coding, 22 transfer RNA, 2 ribosomal RNA genes and a non-coding control region. The overall base composition of the mitochondrial DNA is 30.2% for A, 28.6% for T, 26.4% for C and 14.8% for G. The phylogenetic analysis conducted using 18 protein-coding genes showed that C. subducens was most closely related to the Pseudochromidae. This work will be useful for further research on species identification and evolutionary relationships within related species.The complete mitochondrial genome of the X-ray tetra (Pristella maxillaris, Ulrey, 1894) was determined by using next-generation sequencing technology, and its mitochondrial genome characteristics were analyzed. The sequence total length was 16,753 bp, and the A + T content was 57.44%. The position and composition of the 37 genes were consistent with those of other Characidae species in this family. There are 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region. Except for ND2 and COX1, which use ATT and GTG as start codons, respectively, all other protein-coding genes use ATG as the start codon. COX1 uses AGG as the stop codon; ATP6 and COX3 use incomplete TA as the stop codon; COX2 and ND4 use incomplete T as the stop codon; ATP8 uses TAG as the stop codon, and the other seven protein-coding genes use TAA as the stop codon. Based on the concatenated nucleotide sequences of 13 protein-coding genes from 18 Characidae species, phylogenetic analysis revealed that P. maxillaris belongs to the family Characidae and is most closely related to Hyphessobrycon amandae. Determining the mitogenomes of P. maxillaris improves our understanding of the phylogeny and evolution of Characidae.The complete chloroplast genome sequence of Pedicularis shansiensis Tsoong was determined and described. The circular chloroplast genome is 151,902 bp in length and contains a large single-copy region of 83,180 bp, a small single-copy region of 17,284 bp and two inverted repeat regions of 25,719 bp. CDK inhibitor The chloroplast genome contains 132 genes, including 86 protein-coding, 8 rRNA, and 38 tRNA genes. Phylogenetic analysis shows Pedicularis species cluster together and P. shansiensis forms a clade with P. dissect.The complete plastome of Spiraea trilobata, a shrub, is determined. The plastome is 155,981 bp in length and comprises a large single-copy region (84,417 bp), a small single-copy region (18,878 bp), and a pair of inverted repeats regions (26,343 bp). A total of 113 unique genes are annotated for the plastome of S. trilobata, containing 79 protein coding genes (PCGs), 30 tRNAs, and four rRNAs. The GC content of this plastome is 36.8%. Phylogenomic analysis based on 17 plastomes reveals that S. trilobata is sister to Spiraea blumei. Compared with S. blumei, S. trilobata lacks both trnM-CAU and ycf1. In addition, the GC content of both species is the same.Tetradium daniellii (Benn.) T. G. Hartley is an important medicinal, ornamental, and timber tree species and belongs to genus Tetradium in family of Rutaceae. It is widely distributed in warm temperate deciduous broad-leaved forest areas in northern China, Korean Peninsula and Japan. In this study, we sequenced its sample and determined complete chloroplast genome. The CP genome of T. daniellii has a circle structure with the length 158,446 bp, includes a small single copy region (17, 972 bp), a large single copy (86, 478 bp) and two inverted repeats (26,998 bp). There were 131 genes, which included 86 protein-coding genes, 8 rRNA and 37 tRNA, and overall GC content covered by 38.3%. The gene trnK-UUU, rps16, trnG-UCC, atpF, rpoC1, trnL-UAA, trnV-UAC, petB, petD, rpl16, rpl2, ndhB, trnI-GAU, trnA-UGC and ndhA contained an intron; gene clpP, ycf3 contained 2 introns. The phylogenetic result showed that T. daniellii had the closest relationship with Tetradium ruticarpum (NC_052830).Rhus punjabensis var. sinica belongs to the family Anacardiaceae in the order Sapindales. In this study, we first reported the complete chloroplast genome sequence of R. punjabensis var. sinica. The cp genome was sequenced on Illumina Hiseq 2000 platform. The sequence was found to be 159,617 bp in length with 37.9% GC contents, including a large single-copy region of 87,694 bp, a small single-copy region of 18,971 bp, and a pair of inverted repeats of 26,476 bp. The chloroplast genome of R. punjabensis var. sinica contains 133 genes, including 86 protein-coding genes, 8 rRNA genes, and 2 pseudogenes identified by CPGAVAS2 and BLAST search, and 37 tRNA genes annotated by tRNAscan-SE. Maximum-likelihood (ML) phylogenetic analysis showed that R. punjabensis var. sinica was sister to Rhus potaninii.Bolboschoenus planiculmis is a typical wetland sedge with both ecological and agricultural value. We report the first complete chloroplast genome sequence of this species. The total genome size is 186,539 bp, containing a large single-copy region (LSC) of 104,654 bp, a small single copy region (SSC) of 9,659 bp and two inverted repeats (IRs) of 36,113 bp by each. The GC content is 33.59%. The genome encodes 105 unique genes, including 71 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis shows this species has a strong sister relationship with Cyperus. Our work could be helpful in understanding the evolution of Cyperaceae.Nicotiana plumbaginifolia Vivianiis 1802 is an annual herb, native to Mexico and South America. It is one of the most widely distributed tobacco species. As a wild tobacco, N. plumbaginifolia has provided several economically important disease-resistance genes to cultivated tobacco. We assembled the complete chloroplast genome of N. plumbaginifolia. The chloroplast genome is 155,945 bp in length, which includes a large single copy region (86,621 bp), a small single copy region (18,528 bp) and two separated inverted repeat regions (25,398 bp). A total of 117 unique genes were annotated, consisting of 84 protein-coding genes, 29 tRNA genes and 4 rRNA genes. Based on chloroplast genomes of 17 Nicotiana species, phylogenetic analyses indicated that N. plumbaginifolia was closely related to N. suaveolens and N. amplexicaulis.The Ficus squamosa and Ficus heterostyla share an undescribed pollinating fig wasp Ceratosolen sp. in Xishuangbanna region, which constitutes the most excellent model to study the role of convergent evolution and hybridization in the species-specific fig-wasp mutualism. The plastomes were 160,350 bp for Ficus squamosa and 160,300 bp for F. heterostyla, both in length with the typical quadripartite structure. In the two genomes, the LSC region was 88,615 bp (F. squamosa) and 88,535 bp (F. heterostyla), the SSC region was 20,071 bp (F. squamosa) and 20,101 bp (F. heterostyla), and the IR regions of both figs were 25,832 bp. They contained 113 unique genes, including a set of 78 protein-coding genes, 30 transfer RNA (tRNA) genes, four ribosomal RNA (rRNA) genes, and one pseudogene (infA). Phylogenetic analysis based on the complete chloroplast (cp) genomes within the Ficus genus suggests that they are closely related sister species.Geum aleppicum is an important landscaping plant with high medicinal value. In this study, the complete chloroplast genome of G. aleppicum was assembled and analyzed. The assembled genome is 156,036 bp in length, which contains a large single-copy (LSC) region of 85,358 bp, a small single-copy (SSC) region of 18,410 bp, and two inverted repeat regions (IRa and IRb) of 26,134 bp. A total of 137 genes were predicted, including 89 protein-coding genes, 40 tRNA genes, and eight rRNA genes. The phylogenetic analysis indicated that G. aleppicum had the closest relationship with G. japonicum var. chinense, and all the species of Geum grouped together with highly bootstrap support.The complete mitochondrial genomes were sequenced in two individuals of charr Salvelinus alpinus erythrinus from Arctic Canada. The genome sequences were 16,652 bp in length; the genome organization and GC content (45.6%) are consistent with those of charr mitochondrial genomes published previously. The difference between the two genomes studied is low, 0.02%. Our results indicate the phylogenetic closeness of S. alpinus erythrinus and Salvelinus sp. 4 from Lake Nachikinskoe, Kamchatka and their origin from a common ancestor.