Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in regulating the nitrification process in lake ecosystems. However, the relative effects of climate, catchment land use and local conditions on the sediment ammonia-oxidizing communities in lakes remain unclear. In this study, the diversity and abundance of AOA and AOB communities were investigated in ten Yangtze lakes by polymerase chain reaction (PCR), clone library and quantitative PCR techniques. The results showed that the abundances of both AOA and AOB in bare sediments were considerably but not significantly higher than those in vegetated sediments. Interestingly, AOB communities were more sensitive to changes in local environmental factors and vegetation characteristics than were AOA communities. Amongst climate and land use variables, mean annual precipitation, percentage of agriculture and percentage of vegetation were the key determinants of AOB abundance and diversity. Additionally, total organic carbon and chlorophyll-a concentrations in lake water were significantly related to AOB abundance and diversity. The results of the ordination analysis indicated that 81.2 and 84.3% of the cumulative variance for the species composition of AOA and AOB communities could be explained by the climate, land use and local factors. The climate and local environments played important roles in shaping AOA communities, whereas catchment agriculture and water chlorophyll-a concentration were key influencing factors of AOB communities. Our findings suggest that the composition and structure of sediment ammonia-oxidizing communities in Yangtze lakes are strongly influenced by different spatial scale factors.
Objective
To explore the predictor of invalid conservative treatment of acute calculous cholecystitis (ACC) in pregnant women.
Methods
A total of 107 pregnant patients with ACC in a tertiary hospital from Jan. 2010 to Jun. 2017 were studied retrospectively.
Results
Univariate analysis revealed that body temperature >37.3 ℃ (χ2=4.721, P 37.3 ℃, AST were the independent risk factors predicting invalid conservative management.
Conclusion
Gallbladder dilation, body temperature >37.3 ℃, high level of TBiL and AST are the early predictors for the invalid conservative management for ACC in pregnant women.
Key words:
Cholecystitis, acute; Choleystolithiasis; Pregnancy; Risk factors
- The folder '1_all_cds_pep' contains the CDS and PEP sequences for the 95 samples from Alismatales and outgroups.- '2_MO_alignment_trees' contains the 1005 nuclear orthologs, alignment, concatenated ML tree, and ASTRAL tree.- '3_chloroplast_alignment_trees' contains chloroplast genes for 92 samples, alignment, concatenated ML tree, and ASTRAL tree.- '4_3492_extracted_clades' contains the 3492 clusters, which were used for whole genome duplication analyses. The 3492 clusters were mapped to ASTRAL species tree to count the number of duplicated genes at each node.- '5_phylogenetic_conflict' contains data related to phylogenetic conflict analyses.- '6_divergence_time' contains a data matrix for BEAST analyses and output - 'alismatales_40genes_1000M_generations_fix_hypothesis1.xml' is the input for BEAST - 'alismatales_40genes_1000M_generations_fix_hypothesis1.10percent.tre' is the summary tree generated with TreeAnnotator. It is also the tree in Supplementary Fig. S4- '7_whole_genome_duplication' contains the ks values used for Ks plot- '8_gene_evolution_ko_analyses' contains the sequence alignment and phylogenetic trees of gene families. It also included a matrix containing the KEGG information. - 'gene_orthologs' contains the alignments and individual gene trees: 'mafft_file_for_tree_build' - 20 alignment files for tree building 'ortholog_tree' files of the final gene families trees - 'KEGG_orthologs' contains the numbers of gene annotation with the specific KEGG ortholog: 'matrix_for_enrichment_test.tsv' - gene copy number matrix for all 4687 KOs and 95 species- 'taxon_list_nov52021' contains abbreviations of species names and full names Analyses for folders startwith 1, 2, 3, and 4 following methods at https://bitbucket.org/yanglab/phylogenomic_dataset_construction/src/master/ Instruction for analyses on phylogenetic conflict, corresponding to the folder '5_phylogenetic_conflict'5.1. Quartet Sampling analyses (in folder: /5_phylogenetic_conflict/5.1_fig_s2_alismatales_input_quartet_sampling)quartet_sampling.py --tree MO_1005_astral_speciestree --align ortholog_MO_1005_concatinated.fa.phy --reps 100 --threads 6 --lnlike 2quartet_sampling.py --tree MO_1005_astral_speciestree --align ortholog_MO_1005_concatinated.fa.phy --reps 100 --threads 6 --lnlike 2 5.2. PhyloNet (in folder: /5_phylogenetic_conflict/5.2_fig3_phylonet)The folder '5.2_fig3_phylonet' contains two kinds of files. The files endwith '.nex' are the input file, while the files endwith 'output' are the output.Excute command for each of input files.java -jar -Xmx140G /PATH_TO_PHYLONET/PhyloNet_3.8.2.jar .nex > _output 5.3. Consel (in folder: /5_phylogenetic_conflict/5.3_fig4a_all_consel_feb19/estimate_site_wise_log_likelihood_values)First, estimate the branch length (in folder: /5.3_fig4a_all_consel_feb19/estimate_site_wise_log_likelihood_values)for a in *aln-cln; do raxml -T 10 -f d -s $a -m GTRGAMMA -g alismatales_10species_topology1.tre -n $a"_output_topology1.cons" -p 123456 -N 10 -o atri291; done &for a in *aln-cln; do raxml -T 10 -f d -s $a -m GTRGAMMA -g alismatales_10species_topology2.tre -n $a"_output_topology2.cons" -p 123456 -N 10 -o atri291; done &for a in *aln-cln; do raxml -T 10 -f d -s $a -m GTRGAMMA -g alismatales_10species_topology3.tre -n $a"_output_topology3.cons" -p 123456 -N 10 -o atri291; done & The above commands generate 3 tree files endwith '.cons'. Combine the three files, and change the file name, '*_output_3topologies' Then, estimate site-wise log-likelihood valuesfor a in *alismatales.fa.aln-clndo raxml -T 16 -f G -z $a'_output_3topologies' -s $a -r $a’_output_3topologies’ -m GTRGAMMA -n $a"_sitelh"done Use the files 'RAxML_perSiteLLs*sitelh' generated from the last step for further analyses. Change the file names generated from last step, as the input of seqmt and makermt need to have the same same, only the extension latter need to vary. For example, change 'RAxML_perSiteLLs.cluster939_1.ortho.fa_alismatales.fa.aln-cln.sitelh' to 'cluster939_1.ortho.fa_alismatales.fa.aln-cln.sitelh'. Then excute for filename in $(ls *.sitelh); do seqmt --puzzle $filename; donefor filename in $(ls *.aln-cln); do makermt $filename; donefor filename in $(ls *.rmt); do consel $filename; donefor filename in $(ls *.pv); do catpv $filename > $filename.out; done Use shell scripts to extract the scores in the files endwith *out, and generate a file similar to 'Congruent_au_test.csv'Execute python au.py. This command will show the results 5.4. Counting RAxML likelihood scores (in folder: /5_phylogenetic_conflict/5.4_fig4b_likelihood_raxml_output)Extract the ML cores from the 'RAxML_info.RAxML_bestTree*' file, using command:for i in $(ls RAxML_info*);doecho $i >> ../all_ln_consel.txtgrep "Tree" $i >> ../all_ln_consel.txtdone Then, use more shell scripts to generate a file with a format similar to 'all_ln_consel.txt'. This process can be assisted by a script 'extract_raxml_infor_ln.py'Execute python ln_counts.py. The command will show the results 5.5. Trees used to count support for the three hypotheses of Alismatales (in folder: /5_phylogenetic_conflict/5.5_fig4c_798trees) 5.6. Output from the polytomy test (in folder: /5_phylogenetic_conflict/5.6_polytomy_test)
If you have any questions, please do not hesitate to contact me lychen83@qq.com Lingyun Chen
The construction of dominant algal species and bacterial strains in algal treatment technology was crucial for pollutant removal. In order to enhance the purification capability of microalgae toward heavy metals in water as well as biogas slurry and biogas, symbiotic systems were respectively constructed using Chlorella vulgaris and two different endogenous bacteria (microalgal endophytic bacteria S395-2 and plant endophytic bacteria BEB7). The results demonstrated that the endogenous bacteria (S395-2 and BEB7) effectively promote the growth, biomass yield, photosynthetic activity, and carbonic anhydrase activity of microalgae. Additionally, BEB7 exhibited superior promotion effects on microalgae compared to S395-2. Moreover, the BEB7-microalgae co-cultivation system not only efficiently removed heavy metals from water but also effectively purified the nutrients and CO
AIM:To study the influence and mechanisms of dexamethasone on mesenteric lymph node of rats with severe acute pancreatitis (SAP). METHODS:The SAP rats were assigned to model, treated or sham-operated groups.The mortality, pathological changes of mesenteric lymph nodes, expression levels of NF-kB, P-selectin, Bax, Bcl-2 and caspase-3 protein and changes in apoptotic indexes in lymph nodes were observed at 3, 6 and 12 h after operation.The blood levels of endotoxin, superoxide dismutase (SOD), malondialdehyde (MDA), and endothelin-1 (ET-1) in blood were determined.RESULTS: SOD content, expression of Bax protein and apoptotic index were significantly higher in the treated group than in the model group at different time points (P < 0.05 or P < 0.01).Other blood-detecting indexes and histopathological scores of mesenteric lymph nodes were lower in the treated than in the model group (P < 0.05, P < 0.01 or P < 0.01).NF-kB protein expression was negative in all groups.Comparing P-selectin and caspase-3 expression levels among all three groups, there was no marked difference between the model and treated group.CONCLUSION: Dexamethasone can protect mesenteric lymph nodes.The mechanism may be by reducing the content of inflammatory mediators in the blood and inducing lymphocyte apoptosis.
Abstract Cryptochromes (CRYs), which are responsible for sensing blue light in plants, play a critical role in regulating blue light signals and circadian rhythms. However, their functions extend beyond light detection, as they also aid plants in adapting to stress and potentially other regulatory mechanisms. Aquatic angiosperms, which independently evolved from various angiosperm lineages, have developed specific adaptations to unique light qualities and environmental stressors found in aquatic habitats compared to terrestrial ones. It was hypothesized that the sequences and regulatory networks of angiosperm CRY1/2 underwent adaptive evolution in different aquatic angiosperm lineages. To test this hypothesis, we compiled comprehensive datasets consisting of 55 green plant genomes (including 37 angiosperm genomes), 80 angiosperm transcriptomes, and 4 angiosperm expression networks. Through comparative analysis, we found that CRY1 originated from a common ancestor of seed plants, whereas CRY2 originated from a common ancestor of land plants. In angiosperms, the CRY1/2 sequences of aquatic lineages exhibited positive selection, and the conserved valine-proline motif of CRY2 showed a convergent loss in 2 aquatic species. Coexpressed genes associated with blue light receptors (CRY) showed adaptations to aquatic environments, specifically in relation to flooding and osmotic stress. These discoveries shed light on the adaptive evolution of CRY1/2, encompassing their origins, sequences, and regulatory networks. Furthermore, these results provide valuable insights for investigating the uncharacterized functions and regulatory pathways of CRY and offer potential targets for enhancing growth and adaptation in agricultural plants.
Immune function disorders are common during acute renal failure (ARF), but the mechanisms are unknown. As the spleen is the largest organ of the immune system, we aimed to observe if there are morphological changes in the spleen in rabbits with ARF. In addition, we tried to explore its mechanism from the perspective of oxygen free radicals, nitric oxide (NO), myeloperoxidase (MPO), and membrane pump activities. ARF animal models were established by either hypodermic injection of 1.3 mL/kg bw 1% HgCl₂ or intramuscular injection of 10 mL/kg bw 50% glycerin. Animals were divided into 12 h, 24 h, and 48 h treatment groups with six rabbits in each group. Compared with control animals, congestion was found in the spleen and splenic trabeculae were increased in the two ARF model groups at multiple time points. The malonaldehyde, NO, nitric oxide synthase, and MPO levels in the ARF models were increased compared with the control group at 24 h or 48 h, and the superoxide dismutase and adenosine triphosphatase activities were significantly lower than the levels in the control group at multiple time points. These indices of free radical damage were induced gradually with ARF development, and there were statistically significant differences at different time points. These data suggested that histological damage of spleen during ARF may lead to immune disorders, which might be related to free radical injury, NO excessive release, polymorphonuclear neutrophils (PMN) sequestration, and membrane pump dysfunction.
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