Primerjalna študija genetske raznovrstnosti talnih bakterij in gliv v različnih sukcesijah vegetacije na krasu v provinci Guizhou, Kitajska

To study the soil genetic diversity of bacteria and fungi in different vegetation successions (grassland, shrubbery, primary forest and secondary forest) from the karst area, the Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) technology was applied. The results showed that: (1) the diversity of bacterial communities and the fungal communities in karst area were higher than non karst area in each vegetation succession. Compared with the survey from bacterial (the Shannon index was 2.97 in primary forest, 2.91 in secondary forest, 3.18 in shrubbery, 3.14 in grassland and 2.68 in non karst), fungal diversity between karst areas (the Shannon index was 3.56 in primary forest, 3.78 in secondary forest, 3.73 in shrubbery and 3.70 in grassland) and non karst areas (the Shannon index was 3.08) was more evident, which may be related to the alterations of the composition of plant community and the source of carbon in soil with the vegetation succession of karst ecosystem; (2) The comparation of bacterial diversity index and the richness comprehensively evaluated as follows: shrubbery > grassland > primary forest > nsecondary forest. The diversity index and the richness of fungal communities was as follows: secondary forest > shrubbery > grassland > primary forest. The results suggest that the fungal communities have been greatly changed via vegetation successions, but the diversity index and the richness of the bacterial communities have not been seriously affected. The results provide scientific basis for understanding karst surface ecosystem, which contributes to the future aim of protecting the karst from desertification.Za proučevanje genetske pestrosti talnih bakterij in gliv v različnih sukcesijah vegetacije (travišče, grmičevje, primarni gozd in sekundarni gozd) na krasu je bila uporabljena tehnologija verižne reakcije s polimerazo-denaturirajoča gradientna gelska elektroforeza (PCR-DGGE). Rezultati raziskave so pokazali, da: (1) je bila v vsaki sukcesiji vegetacije pestrost bakterijskih in glivnih združb na kraškem območju višja kot na nekraškem. V primerjavi z bakterijsko raznovrstnostjo (Shannonov indeks je bil 2,97 v primarnem gozdu, 2,91 v sekundarnem gozdu, 3,18 v tleh grmičevja, 3,14 v tleh travišč in 2,68 v nekraškem območju) je bila raznovrstnost gliv med kraškimi območji (Shannonov indeks je bil v primarnem gozdu 3,56, 3,78 v sekundarnem gozdu, 3,73 v tleh grmičevja in 3,70 v tleh travišč) in nekraškimi (Shannonov indeks je bil 3,08) jasneje izražena. To je lahko povezano s spremembami v sestavi rastlinske združbe in vira ogljika v tleh glede na stanje sukcesije v vegetaciji kraškega ekosistema. (2) Primerjava kazalnikov bakterijske raznovrstnosti in abundance je bila celostno ovrednotena in sledi takole: grmičevje > travišče > primarni gozd > sekundarni gozd. Kazalnika raznovrstnosti in abundance glivnih združb kažeta sledeči trend: sekundarni gozd > grmičevje > travišče > primarni gozd. Rezultati izkazujejo, da so se glivne združbe precej spremenile zaradi sukcesije v vegetaciji, vendar pa na drugi strani ni bilo bistvenega vpliva na kazalnika bakterijske raznovrstnosti in abundance. Rezultati med drugim dajejo tudi znanstveno podlago za razumevanje delovanja kraškega površinskega ekosistema, kar ključno prispeva k cilju zaščite krasa pred dezertifikacijo (širjenjem puščav)

Development characteristics and main controlling factors of Carboniferous volcanic reservoirs in the Shixi area, Junggar Basin

The Carboniferous volcanic reservoirs in the Shixi area of the Junggar Basin are complex and diverse. Identifying the characteristics and main factors controlling high-quality volcanic reservoirs is the key to increasing oil and gas reserves and production in this area. Through core observations, thin section identification, physical property and pore structure analyses, combined with production data, the main controlling factors and development modes of high-quality reservoirs were analysed. The results show that the Carboniferous strata in the Shixi area mainly contain andesite and dacite of overflow facies, followed by volcanic breccia and tuff of explosive facies. Volcanic reservoirs in the study area are high-porosity–low-permeability and medium-porosity–low-permeability reservoirs. Volcanic breccia of explosive facies has the best physical properties, showing the characteristics of high porosity and medium permeability. The reservoir space is mainly composed of gas cavities, corrosion pores and fractures, among which the corrosion pores are the most important reservoir spaces of the Carboniferous volcanic rocks. Lithology and lithofacies, weathering and corrosion, and fractures are the main factors controlling the development of high-quality volcanic reservoirs. Volcanic rocks that had experienced weathering and denudation for a long time developed a large number of secondary corrosion pores due to the corrosion of soluble minerals or volcanic ash. Fractures further improved the physical properties, causing volcanic rocks to eventually develop into weathering crust reservoirs. The physical properties of the volcanic rocks far away from the weathering crust were improved through primary gas cavities and structural fractures, and these volcanic rocks eventually developed into the inner reservoir

The Integrated Genomic Landscape of Thymic Epithelial Tumors

Thymic epithelial tumors (TETs) are one of the rarest adult malignancies. Among TETs, thymoma is the most predominant, characterized by a unique association with autoimmune diseases, followed by thymic carcinoma, which is less common but more clinically aggressive. Using multi-platform omics analyses on 117 TETs, we define four subtypes of these tumors defined by genomic hallmarks and an association with survival and World Health Organization histological subtype. We further demonstrate a marked prevalence of a thymoma-specific mutated oncogene, GTF2I, and explore its biological effects on multi-platform analysis. We further observe enrichment of mutations in HRAS, NRAS, and TP53. Last, we identify a molecular link between thymoma and the autoimmune disease myasthenia gravis, characterized by tumoral overexpression of muscle autoantigens, and increased aneuploidy

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Integrated genomic characterization of pancreatic ductal adenocarcinoma

We performed integrated genomic, transcriptomic, and proteomic profiling of 150 pancreatic ductal adenocarcinoma (PDAC) specimens, including samples with characteristic low neoplastic cellularity. Deep whole-exome sequencing revealed recurrent somatic mutations in KRAS, TP53, CDKN2A, SMAD4, RNF43, ARID1A, TGFβR2, GNAS, RREB1, and PBRM1. KRAS wild-type tumors harbored alterations in other oncogenic drivers, including GNAS, BRAF, CTNNB1, and additional RAS pathway genes. A subset of tumors harbored multiple KRAS mutations, with some showing evidence of biallelic mutations. Protein profiling identified a favorable prognosis subset with low epithelial-mesenchymal transition and high MTOR pathway scores. Associations of non-coding RNAs with tumor-specific mRNA subtypes were also identified. Our integrated multi-platform analysis reveals a complex molecular landscape of PDAC and provides a roadmap for precision medicine

Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types

Protein ubiquitination is a dynamic and reversibleprocess of adding single ubiquitin molecules orvarious ubiquitin chains to target proteins. Here,using multidimensional omic data of 9,125 tumorsamples across 33 cancer types from The CancerGenome Atlas, we perform comprehensive molecu-lar characterization of 929 ubiquitin-related genesand 95 deubiquitinase genes. Among them, we sys-tematically identify top somatic driver candidates,including mutatedFBXW7with cancer-type-specificpatterns and amplifiedMDM2showing a mutuallyexclusive pattern withBRAFmutations. Ubiquitinpathway genes tend to be upregulated in cancermediated by diverse mechanisms. By integratingpan-cancer multiomic data, we identify a group oftumor samples that exhibit worse prognosis. Thesesamples are consistently associated with the upre-gulation of cell-cycle and DNA repair pathways, char-acterized by mutatedTP53,MYC/TERTamplifica-tion, andAPC/PTENdeletion. Our analysishighlights the importance of the ubiquitin pathwayin cancer development and lays a foundation fordeveloping relevant therapeutic strategies