Comparison of microbial communities in sequencing batch reactors (SBRs) exposed to trace erythromycin and erythromycin-H2O

Wastewater treatment plants (WWTPs) are major collection pools of antibiotics of which low concentrations may induce antibiotic resistance in their microbial communities and pose threat to human health. However, information is still limited on the microbial community alteration in WWTPs upon exposure to low-dose antibiotics due to absence of negative control systems without input of resistant bacteria and resistance genes. Here we report the impact of trace erythromycin (ERY) and dehydrated erythromycin (ERY-H₂O) on microbial community dynamics in three long-term (1 year) running sequencing batch reactors (SBRs), R1 (ERY-H₂O), R2 (ERY), and negative control R3. The PhyloChip microarray analysis showed that ERY-H₂O and ERY significantly altered their microbial communities based on bacterial richness (e.g., 825 operational taxonomic units (OTUs) in R1, 699 OTUs in R2, and 920 OTUs in R3) and population abundance (15 and 48 subfamilies with >80 % abundance decrease in R1 and R2, respectively). ERY-H₂O and ERY have broad but distinct antimicrobial spectrums. For example, bacteria of all the major phyla (i.e., Proteobacteria, Actinobacteria, Bacteroidetes, and Chloroflexi) present in SBRs were severely inhibited by ERY-H₂O and ERY, but bacteria of Acidobacteria, Chlorobi, Firmicutes, Nitrospira and OP10 phyla were only inhibited by ERY. Very limited bacterial groups showed antibiotic resistance to ERY-H₂O or ERY through forming biofilms (e.g., Zoogloea) or synthesizing resistant proteins (e.g., Thauera, Candidatus Accumulibacter, Candidatus Competibacter, and Dechloromonas) in the SBRs. Inhibition was observed to be the main effect of ERY-H₂O and ERY on microbial communities in the reactors. The results would broaden our knowledge of effects of low-dose antibiotics on microbial communities in WWTPs.     

Dimerization Interface of 3-Hydroxyacyl-CoA Dehydrogenase Tunes the Formation of Its Catalytic Intermediate

3-hydroxyacyl-CoA dehydrogenase (HAD, EC 1.1.1.35) is a homodimeric enzyme localized in the mitochondrial matrix, which catalyzes the third step in fatty acid β-oxidation. The crystal structures of human HAD and subsequent complexes with cofactor/substrate enabled better understanding of HAD catalytic mechanism. However, numerous human diseases were found related to mutations at HAD dimerization interface that is away from the catalytic pocket. The role of HAD dimerization in its catalytic activity needs to be elucidated. Here, we solved the crystal structure of Caenorhabditis elegans HAD (cHAD) that is highly conserved to human HAD. Even though the cHAD mutants (R204A, Y209A and R204A/Y209A) with attenuated interactions on the dimerization interface still maintain a dimerization form, their enzymatic activities significantly decrease compared to that of the wild type. Such reduced activities are in consistency with the reduced ratios of the catalytic intermediate formation. Further molecular dynamics simulations results reveal that the alteration of the dimerization interface will increase the fluctuation of a distal region (a.a. 60–80) that plays an important role in the substrate binding. The increased fluctuation decreases the stability of the catalytic intermediate formation, and therefore the enzymatic activity is attenuated. Our study reveals the molecular mechanism about the essential role of the HAD dimerization interface in its catalytic activity via allosteric effects.     

Repeated measures random forests (RMRF): Identifying factors associated with nocturnal hypoglycemia

Nocturnal hypoglycemia is a common phenomenon among patients with diabetes and can lead to a broad range of adverse events and complications. Identifying factors associated with hypoglycemia can improve glucose control and patient care. We propose a repeated measures random forest (RMRF) algorithm that can handle nonlinear relationships and interactions and the correlated responses from patients evaluated over several nights. Simulation results show that our proposed algorithm captures the informative variable more often than naïvely assuming independence. RMRF also outperforms standard random forest and extremely randomized trees algorithms. We demonstrate scenarios where RMRF attains greater prediction accuracy than generalized linear models. We apply the RMRF algorithm to analyze a diabetes study with 2524 nights from 127 patients with type 1 diabetes. We find that nocturnal hypoglycemia is associated with HbA1c, bedtime blood glucose (BG), insulin on board, time system activated, exercise intensity, and daytime hypoglycemia. The RMRF can accurately classify nights at high risk of nocturnal hypoglycemia.     

Polymorphic allele of human MRC1 confer protection against tuberculosis in a Chinese population

Mannose receptor is a member of the C-type lectin receptor family involved in pathogen molecular-pattern recognition, and plays a critical role in shaping host immune response. Single nucleotide polymorphisms (SNPs) in the MRC1 gene may affect expression levels and differences in the structure and function of proteins in different individuals, thereby affecting individual susceptibility to pulmonary tuberculosis. However, to date, MRC1 polymorphisms associated with susceptibility to pulmonary tuberculosis have not yet been reported. The present study aimed to investigate potential associations of SNPs in the MRC1 gene with pulmonary tuberculosis in a Chinese population. Six SNPs (G1186A, G1195A, T1212C, C1221G, C1303T and C1323T) in exon 7 of the MRC1 gene were genotyped using the PCR and DNA sequencing methods in the pulmonary tuberculosis patients and the healthy controls. Linkage disequilibrium analysis was performed between polymorphic sites. The study found that the allele frequency of G1186A (rs34039386) of the MRC1 gene in a Chinese population was higher in the pulmonary tuberculosis group than the healthy control group. There was a significant difference in frequency distribution between the two groups (P = 0.037; OR = 0.76; 95% CI, 0.58-0.98). Genotypic analysis also indicated that the AG genotypes in a Chinese population were significantly correlated with pulmonary tuberculosis (P < 0.01; OR = 0.57; 95% CI, 0.37-0.87). After adjustment for age and gender, G1186A sites were found to be dominant (P < 0.01; OR = 0.59; 95% CI, 0.40-0.87), over-dominant (P = 0.045; OR = 0.69; 95% CI, 0.47-0.99) and additive models (P = 0.041; OR = 0.76; 95% CI, 0.59-0.99) in association with pulmonary tuberculosis. But, no association was found between the other 5 SNPs (G1195A, T1212C, C1221G, C1303T and C1323T) and tuberculosis (P > 0.05). This study is the first to report that genetic variants in the MRC1 gene can be associated with pulmonary tuberculosis in a Chinese population, and may reduce the risk of infecting pulmonary tuberculosis. This also provides a new experimental basis to clarify the pathogenesis of pulmonary tuberculosis.     

Granzyme K cleaves the nucleosome assembly protein SET to induce single-stranded DNA nicks of target cells

Although granzymes (Gzms) A- and B-induced cell death pathways have been defined, little is known about how other orphan Gzms function in CTL-mediated cytotoxicity. GzmK and A are tryptases among all the Gzms of humans and they are closely linked on the same chromosome. In this study, we showed that GzmK can be efficiently delivered into target cells with a cationic lipid protein transfection reagent Pro-Ject. We found human GzmK triggers rapid cell death independently of caspase activation. The features of death are characterized by rapid externalization of phosphatidylserine, nuclear morphological changes and single-stranded DNA nicks. GzmK hydrolyzes the nucleosome assembly protein SET in its recombinant and native forms or in intact cells. Cleavage of SET by GzmK abrogates its nucleosome assembly activity. After GzmK loading, SET and DNase NM23H1 rapidly translocate into the nucleus and SET is cleaved, where the nuclease activity of NM23H1 is activated to nick chromosomal DNA.     

Potential effects of elevated carbon dioxide on leaf-feeding forest insects

The elevated concentration of atmospheric CO₂ may result in a decline of leaf nutritional quality (especially N) and an increase in some kinds of defensive secondary components (such as phenolics). The changes in the phytochemistry of trees, combined with the effect of elevated CO₂ per se, have a potential negative influence on insect herbivores. Here, we review the effect of elevated CO₂ on the performance of leaffeeding forest insects at individual-level and community-level. The elevated CO₂ per se have little influence on the metabolism of insects. Over half of the tree-insect experimental systems show that the performance of individual insect become poorer under high-CO₂ grown trees; but the others show that the insects have just little or no response to the treatments. The direction and magnitude of the changes in the performance of insects could be mediated by various factors. The effects of treatment are strongly species-dependent. The magnitude of changes in the phytochemistry, the sensitivity and adaptive capacity of insects to the poorer leaf quality, the differences in plant growth conditions and experimental methods, and the mediated effects of other environmental factors (such as soil nutrient availability, light, temperature, O₃) were all closely related to the final performance of insects. However, the larvae’s consumption usually increased under enriched CO₂ treatment, which was widely thought to be a compensatory response to poorer plant quality. The experiments on forest community-level found identically a reduction in herbivory, which was contrary to the results from small-scale experiments. The changes in insect population and the actual response of consumption by leaf-feeding forest insects under CO₂ enrichment remain unclear, and more field-based experiments need to be conducted. __________ Translated from Chinese Journal of Applied Ecology, 2006, 17(4): 720–726 [译自: 应用生态学报]     

Effects of domestic wastewater slow infiltration on the growth of poplar 'Zhonglin 2001' plantation

A slow infiltration experiment with different hydraulic loads (0, 3, 6, 9, 12, and 15 cm per week) of domestic wastewater was conducted in a 'Zhonglin 2001' poplar plantation to study the effects of the wastewater slow infiltration on the growth of the plantation. Comparing with the control (0 cm), the other five treatments increased the soil organic matter, total N, total P, total K, and Na+ contents in the plantation averagely by 1.940 g x kg(-1), 0.115 g x kg(-1), 0.029 g x kg(-1), 1.454 g x kg(-1) and 0.030 g x kg(-1), respectively. At lower hydraulic loads (3-12 cm per week), the poplar biomass growth and the N, P and Na+ contents in different poplar organs averagely increased by 17.583 t x hm(-2) x a(-1), 3.086 g x kg(-1), 0.645 g x kg(-1), and 0.121 g x kg(-1), with the maximum (36.252 t x hm(-2) x a(-1), 13.162 g x kg(-1), 5.137 g x kg(-1), and 0.361 g x kg(-1), respectively) at hydraulic loads 6-12 cm per week. The further increase of the hydraulic load decreased the poplar biomass growth and the N, P and Na+ contents in different poplar organs. The K content in different poplar organs decreased with increasing hydraulic load. Treating with domestic wastewater increased the leaf length, decreased the leaf asymmetry, and delayed leaf-falling. At high hydraulic load (15 cm per week), the higher soil Na+ and water contents would threat the poplar growth. The proper domestic wastewater hydraulic loads for the growth of poplar 'Zhonglin 2001' plantation would be 3-12 cm per week.     

Inhibitory role of TACE/ADAM17 cytotail in protein ectodomain shedding

AIM:To determine if the cytotail of the principal sheddase tumor necrosis factor-α converting enzyme (TACE;ADAM17) controls protein ectodomain shedding.METHODS:Site-directed mutagenesis was performed to derive TACE variants. The resulting TACE expression plasmids with amino acid substitutions in the extracel-lular,cysteine-rich disintegrin domain (CRD) and/or deleted cytotail,along with an expression vector for the enhanced green fluorescence protein were transfected into shedding-defective M1 mutants stably expressing transmembrane L-selectin or transforming growth factor (TGF)-α. The expression levels of the TACE substrates at the cell surface were determined by flow cytometry. RESULTS:Consistent with published data,a single point mutation (C600Y) in the CRD led to shedding defi-ciency. However,removal of the cytotail from the C600Y TACE variant partially restored ectodomain cleavage of TGF-α and L-selectin. Cytotail-deleted mutants with any other substituting amino acid residues in place of Cys600 displayed similar function compared with tail-less C600Y TACE.CONCLUSION:The cytotail plays an inhibitory role,which becomes evident when it is removed from an enzyme with another mutation that affects the enzyme function.