Identification and validation of an immune-related gene prognostic signature for clear cell renal carcinoma

Clear Cell Renal Carcinoma (ccRCC) accounts for nearly 80% of renal carcinoma cases, and immunotherapy plays an important role in ccRCC therapy. However, the responses to immunotherapy and overall survival for ccRCC patients are still hard to predict. Here, we constructed an immune-related predictive signature using 19 genes based on TCGA datasets. We also analyzed its relationships between disease prognosis, infiltrating immune cells, immune subtypes, mutation load, immune dysfunction, immune escape, etc. We found that our signature can distinguish immune characteristics and predict immunotherapeutic response for ccRCC patients with better prognostic prediction value than other immune scores. The expression levels of prognostic genes were determined by RT-qPCR assay. This signature may help to predict overall survival and guide the treatment for patients with ccRCC

Comparative transcriptome in large-scale human and cattle populations:Comparative transcriptome in humans and cattle

BACKGROUND: Cross-species comparison of transcriptomes is important for elucidating evolutionary molecular mechanisms underpinning phenotypic variation between and within species, yet to date it has been essentially limited to model organisms with relatively small sample sizes. RESULTS: Here, we systematically analyze and compare 10,830 and 4866 publicly available RNA-seq samples in humans and cattle, respectively, representing 20 common tissues. Focusing on 17,315 orthologous genes, we demonstrate that mean/median gene expression, inter-individual variation of expression, expression quantitative trait loci, and gene co-expression networks are generally conserved between humans and cattle. By examining large-scale genome-wide association studies for 46 human traits (average n = 327,973) and 45 cattle traits (average n = 24,635), we reveal that the heritability of complex traits in both species is significantly more enriched in transcriptionally conserved than diverged genes across tissues. CONCLUSIONS: In summary, our study provides a comprehensive comparison of transcriptomes between humans and cattle, which might help decipher the genetic and evolutionary basis of complex traits in both species. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02745-4

Biomimetic Z-scheme photocatalyst with a tandem solid-state electron flow catalyzing H_2 evolution

Similar to natural photosynthetic systems, artificial photosynthetic systems require synergistic cooperation between light harvesting, charge separation and redox catalysis. Herein, a three-dimensional (3D) hierarchical photocatalyst is designed with a novel Z-scheme two-photon excitation, defined by the complementary absorption of higher energy and lower energy photons by cadmium sulfide nanowires (CdS NWs) and cobalt–benzimidazole (Co-bIm) coordination polymers (CBPs), respectively. Without any noble-metal co-catalyst, the microscopically integrated CdS–CBP photocatalysts demonstrated dramatically enhanced photocatalytic activities of H_2 evolution, which were up to 10.6 folds higher than those of pristine CdS NWs. Structurally, the intimate interfacial contact between the 3D CdS NW scaffold and the discrete CBP microstructures benefits their strong electronic interaction and efficient charge separation. Upon simultaneous light excitation, a tandem solid-state electron flow from CdS to CBP and then from metal (Co) to ligand (bIm) precisely catalyzes the reduction of pre-activated H atoms on the bIm ligands for efficient H_2 evolution

Biomimetic Z-scheme photocatalyst with a tandem solid-state electron flow catalyzing H_2 evolution

Similar to natural photosynthetic systems, artificial photosynthetic systems require synergistic cooperation between light harvesting, charge separation and redox catalysis. Herein, a three-dimensional (3D) hierarchical photocatalyst is designed with a novel Z-scheme two-photon excitation, defined by the complementary absorption of higher energy and lower energy photons by cadmium sulfide nanowires (CdS NWs) and cobalt–benzimidazole (Co-bIm) coordination polymers (CBPs), respectively. Without any noble-metal co-catalyst, the microscopically integrated CdS–CBP photocatalysts demonstrated dramatically enhanced photocatalytic activities of H_2 evolution, which were up to 10.6 folds higher than those of pristine CdS NWs. Structurally, the intimate interfacial contact between the 3D CdS NW scaffold and the discrete CBP microstructures benefits their strong electronic interaction and efficient charge separation. Upon simultaneous light excitation, a tandem solid-state electron flow from CdS to CBP and then from metal (Co) to ligand (bIm) precisely catalyzes the reduction of pre-activated H atoms on the bIm ligands for efficient H_2 evolution

A multi-tissue atlas of regulatory variants in cattle:Cattle Genotype-Tissue Expression Atlas

Characterization of genetic regulatory variants acting on the livestock gene expression is essential for interpreting the molecular mechanisms underlying traits of economic value and for increasing the rate of genetic gain through artificial selection. Here we build a Cattle Genotype-Tissue Expression atlas (CattleGTEx) as part of the pilot phase of Farm animal GTEx (FarmGTEx) project for the research community based on publicly available 7,180 RNA-Seq samples. We describe the transcriptomic landscape of over 100 tissues/cell types and report hundreds of thousands of genetic associations with gene expression and alternative splicing for 23 distinct tissues. We evaluate the tissue-sharing patterns of these genetic regulatory effects, and functionally annotate them using multi-omics data. Finally, we link gene expression in different tissues to 43 economically important traits using both transcriptome-wide association and colocalization analyses to decipher the molecular regulatory mechanisms underpinning such agronomic traits in cattle

Isolation and Characterization of Cytotoxic, Aggregative Citrobacter freundii

Citrobacter freundii is an infrequent but established cause of diarrhea in humans. However, little is known of its genetic diversity and potential for virulence. We analyzed 26 isolates, including 12 from human diarrheal patients, 2 from human fecal samples of unknown diarrheal status, and 12 from animals, insects, and other sources. Pulsed field gel electrophoresis using XbaI allowed us to divide the 26 isolates into 20 pulse types, while multi-locus sequence typing using 7 housekeeping genes allowed us to divide the 26 isolates into 6 sequence types (STs) with the majority belonging to 4 STs. We analyzed adhesion and cytotoxicity to HEp-2 cells in these 26 strains. All were found to adhere to HEp-2 cells. One strain, CF74, which had been isolated from a goat, showed the strongest aggregative adhesion pattern. Lactate dehydrogenase (LDH) released from HEp-2 cells was evaluated as a measure of cytotoxicity, averaging 7.46%. Strain CF74 induced the highest level of LDH, 24.3%, and caused >50% cell rounding, detachment, and death. We named strain CF74 “cytotoxic and aggregative C. freundii.” Genome sequencing of CF74 revealed that it had acquired 7 genomic islands, including 2 fimbriae islands and a type VI secretion system island, all of which are potential virulence factors. Our results show that aggregative adherence and cytotoxicity play an important role in the pathogenesis of C. freundii